Starting phenix.real_space_refine on Mon Dec 30 06:20:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ell_31184/12_2024/7ell_31184.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ell_31184/12_2024/7ell_31184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ell_31184/12_2024/7ell_31184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ell_31184/12_2024/7ell_31184.map" model { file = "/net/cci-nas-00/data/ceres_data/7ell_31184/12_2024/7ell_31184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ell_31184/12_2024/7ell_31184.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 242 5.16 5 C 38469 2.51 5 N 10040 2.21 5 O 11833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 410 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 60584 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 282 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "a" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4662 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 42, 'TRANS': 567} Chain breaks: 1 Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "b" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "c" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "d" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "E" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "e" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "F" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "f" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "G" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "g" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "H" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "h" Number of atoms: 4761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 623, 4756 Classifications: {'peptide': 623} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 577} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 623, 4756 Classifications: {'peptide': 623} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 577} Chain breaks: 1 bond proxies already assigned to first conformer: 4849 Chain: "I" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 222 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 3, 'TRANS': 28} Chain: "i" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "J" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "j" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "K" Number of atoms: 10115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1283, 10115 Classifications: {'peptide': 1283} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 73, 'TRANS': 1206} Chain breaks: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA h 62 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA h 62 " occ=0.50 Time building chain proxies: 27.95, per 1000 atoms: 0.46 Number of scatterers: 60584 At special positions: 0 Unit cell: (292.11, 166.92, 247.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 242 16.00 O 11833 8.00 N 10040 7.00 C 38469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.62 Conformation dependent library (CDL) restraints added in 7.0 seconds 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15022 Finding SS restraints... Secondary structure from input PDB file: 292 helices and 109 sheets defined 40.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.10 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'a' and resid 104 through 119 removed outlier: 3.509A pdb=" N ALA a 117 " --> pdb=" O LYS a 113 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU a 118 " --> pdb=" O ALA a 114 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU a 119 " --> pdb=" O GLU a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 128 Processing helix chain 'a' and resid 136 through 141 removed outlier: 3.855A pdb=" N LEU a 140 " --> pdb=" O LYS a 136 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU a 141 " --> pdb=" O TYR a 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 136 through 141' Processing helix chain 'a' and resid 151 through 156 Processing helix chain 'a' and resid 167 through 185 removed outlier: 3.784A pdb=" N LEU a 185 " --> pdb=" O ALA a 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 187 through 198 Processing helix chain 'a' and resid 211 through 223 removed outlier: 3.730A pdb=" N ASP a 221 " --> pdb=" O LYS a 217 " (cutoff:3.500A) Processing helix chain 'a' and resid 227 through 231 Processing helix chain 'a' and resid 232 through 244 removed outlier: 3.685A pdb=" N ARG a 243 " --> pdb=" O ALA a 239 " (cutoff:3.500A) Processing helix chain 'a' and resid 263 through 269 removed outlier: 3.979A pdb=" N ALA a 269 " --> pdb=" O VAL a 265 " (cutoff:3.500A) Processing helix chain 'a' and resid 278 through 296 removed outlier: 3.889A pdb=" N LYS a 282 " --> pdb=" O PRO a 278 " (cutoff:3.500A) Processing helix chain 'a' and resid 297 through 302 Processing helix chain 'a' and resid 309 through 313 Processing helix chain 'a' and resid 324 through 326 No H-bonds generated for 'chain 'a' and resid 324 through 326' Processing helix chain 'a' and resid 409 through 413 removed outlier: 3.817A pdb=" N TRP a 413 " --> pdb=" O PHE a 410 " (cutoff:3.500A) Processing helix chain 'a' and resid 416 through 420 removed outlier: 3.696A pdb=" N GLY a 420 " --> pdb=" O SER a 417 " (cutoff:3.500A) Processing helix chain 'a' and resid 453 through 458 removed outlier: 4.129A pdb=" N LEU a 457 " --> pdb=" O GLU a 453 " (cutoff:3.500A) Processing helix chain 'a' and resid 479 through 483 Processing helix chain 'a' and resid 523 through 529 Processing helix chain 'a' and resid 534 through 554 removed outlier: 3.605A pdb=" N CYS a 538 " --> pdb=" O ASP a 534 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 577 removed outlier: 3.704A pdb=" N LEU a 577 " --> pdb=" O ALA a 573 " (cutoff:3.500A) Processing helix chain 'a' and resid 588 through 606 removed outlier: 3.511A pdb=" N LEU a 592 " --> pdb=" O PRO a 588 " (cutoff:3.500A) Processing helix chain 'a' and resid 607 through 611 Processing helix chain 'a' and resid 620 through 637 removed outlier: 3.932A pdb=" N LYS a 632 " --> pdb=" O ALA a 628 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR a 633 " --> pdb=" O GLN a 629 " (cutoff:3.500A) Processing helix chain 'a' and resid 643 through 671 Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.920A pdb=" N SER B 27 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'b' and resid 59 through 61 No H-bonds generated for 'chain 'b' and resid 59 through 61' Processing helix chain 'b' and resid 71 through 75 Processing helix chain 'b' and resid 104 through 120 removed outlier: 3.964A pdb=" N THR b 109 " --> pdb=" O GLU b 105 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN b 110 " --> pdb=" O HIS b 106 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS b 113 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU b 115 " --> pdb=" O PHE b 111 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA b 117 " --> pdb=" O LYS b 113 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU b 118 " --> pdb=" O ALA b 114 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU b 119 " --> pdb=" O GLU b 115 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE b 120 " --> pdb=" O MET b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 129 removed outlier: 3.643A pdb=" N LYS b 127 " --> pdb=" O GLU b 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 136 through 140 Processing helix chain 'b' and resid 151 through 157 removed outlier: 3.802A pdb=" N ASN b 157 " --> pdb=" O ARG b 153 " (cutoff:3.500A) Processing helix chain 'b' and resid 167 through 185 removed outlier: 3.926A pdb=" N ALA b 181 " --> pdb=" O SER b 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS b 183 " --> pdb=" O GLN b 179 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA b 184 " --> pdb=" O ALA b 180 " (cutoff:3.500A) Processing helix chain 'b' and resid 185 through 198 removed outlier: 3.731A pdb=" N ILE b 190 " --> pdb=" O GLU b 186 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR b 197 " --> pdb=" O ARG b 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 211 through 223 removed outlier: 3.549A pdb=" N VAL b 215 " --> pdb=" O PRO b 211 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS b 217 " --> pdb=" O GLN b 213 " (cutoff:3.500A) Processing helix chain 'b' and resid 227 through 231 Processing helix chain 'b' and resid 232 through 243 removed outlier: 3.638A pdb=" N ARG b 243 " --> pdb=" O ALA b 239 " (cutoff:3.500A) Processing helix chain 'b' and resid 267 through 271 removed outlier: 3.558A pdb=" N ALA b 271 " --> pdb=" O SER b 268 " (cutoff:3.500A) Processing helix chain 'b' and resid 278 through 297 removed outlier: 4.080A pdb=" N LYS b 282 " --> pdb=" O PRO b 278 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER b 283 " --> pdb=" O LEU b 279 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS b 284 " --> pdb=" O GLU b 280 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA b 289 " --> pdb=" O LEU b 285 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET b 290 " --> pdb=" O THR b 286 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU b 292 " --> pdb=" O GLN b 288 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR b 294 " --> pdb=" O MET b 290 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 303 removed outlier: 3.501A pdb=" N SER b 303 " --> pdb=" O ILE b 300 " (cutoff:3.500A) Processing helix chain 'b' and resid 309 through 313 Processing helix chain 'b' and resid 409 through 413 Processing helix chain 'b' and resid 415 through 419 removed outlier: 3.654A pdb=" N ILE b 419 " --> pdb=" O ALA b 416 " (cutoff:3.500A) Processing helix chain 'b' and resid 453 through 458 removed outlier: 4.218A pdb=" N LEU b 457 " --> pdb=" O GLU b 453 " (cutoff:3.500A) Processing helix chain 'b' and resid 523 through 530 removed outlier: 3.561A pdb=" N ASN b 528 " --> pdb=" O PRO b 524 " (cutoff:3.500A) Processing helix chain 'b' and resid 534 through 554 removed outlier: 3.933A pdb=" N LYS b 545 " --> pdb=" O ASP b 541 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE b 546 " --> pdb=" O ARG b 542 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS b 551 " --> pdb=" O ALA b 547 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP b 553 " --> pdb=" O ALA b 549 " (cutoff:3.500A) Processing helix chain 'b' and resid 565 through 578 removed outlier: 3.833A pdb=" N GLN b 571 " --> pdb=" O PRO b 567 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU b 577 " --> pdb=" O ALA b 573 " (cutoff:3.500A) Processing helix chain 'b' and resid 588 through 606 removed outlier: 3.507A pdb=" N ASP b 606 " --> pdb=" O ALA b 602 " (cutoff:3.500A) Processing helix chain 'b' and resid 607 through 612 removed outlier: 3.881A pdb=" N THR b 612 " --> pdb=" O THR b 609 " (cutoff:3.500A) Processing helix chain 'b' and resid 620 through 638 removed outlier: 4.020A pdb=" N TRP b 624 " --> pdb=" O ASP b 620 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN b 629 " --> pdb=" O ILE b 625 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL b 631 " --> pdb=" O LEU b 627 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS b 632 " --> pdb=" O ALA b 628 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR b 633 " --> pdb=" O GLN b 629 " (cutoff:3.500A) Processing helix chain 'b' and resid 643 through 672 removed outlier: 3.691A pdb=" N VAL b 668 " --> pdb=" O PHE b 664 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER b 669 " --> pdb=" O LEU b 665 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA b 670 " --> pdb=" O ASP b 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'c' and resid 71 through 75 Processing helix chain 'c' and resid 104 through 120 removed outlier: 3.913A pdb=" N LYS c 113 " --> pdb=" O THR c 109 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU c 115 " --> pdb=" O PHE c 111 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET c 116 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA c 117 " --> pdb=" O LYS c 113 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU c 118 " --> pdb=" O ALA c 114 " (cutoff:3.500A) Processing helix chain 'c' and resid 121 through 128 removed outlier: 3.534A pdb=" N LEU c 125 " --> pdb=" O ASN c 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 136 through 140 Processing helix chain 'c' and resid 151 through 156 Processing helix chain 'c' and resid 167 through 185 removed outlier: 3.709A pdb=" N ALA c 181 " --> pdb=" O SER c 177 " (cutoff:3.500A) Processing helix chain 'c' and resid 185 through 197 removed outlier: 3.709A pdb=" N ILE c 190 " --> pdb=" O GLU c 186 " (cutoff:3.500A) Processing helix chain 'c' and resid 211 through 223 removed outlier: 3.768A pdb=" N ASP c 221 " --> pdb=" O LYS c 217 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN c 222 " --> pdb=" O LEU c 218 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 232 removed outlier: 3.683A pdb=" N ARG c 231 " --> pdb=" O SER c 227 " (cutoff:3.500A) Processing helix chain 'c' and resid 232 through 244 removed outlier: 3.825A pdb=" N LEU c 240 " --> pdb=" O ALA c 236 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA c 241 " --> pdb=" O ALA c 237 " (cutoff:3.500A) Processing helix chain 'c' and resid 263 through 270 removed outlier: 3.638A pdb=" N SER c 268 " --> pdb=" O ALA c 264 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA c 269 " --> pdb=" O VAL c 265 " (cutoff:3.500A) Processing helix chain 'c' and resid 278 through 283 removed outlier: 3.521A pdb=" N LYS c 282 " --> pdb=" O PRO c 278 " (cutoff:3.500A) Processing helix chain 'c' and resid 283 through 297 removed outlier: 3.714A pdb=" N GLU c 287 " --> pdb=" O SER c 283 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA c 289 " --> pdb=" O LEU c 285 " (cutoff:3.500A) Processing helix chain 'c' and resid 297 through 302 removed outlier: 3.563A pdb=" N ILE c 301 " --> pdb=" O GLU c 297 " (cutoff:3.500A) Processing helix chain 'c' and resid 309 through 313 Processing helix chain 'c' and resid 453 through 458 Processing helix chain 'c' and resid 515 through 519 Processing helix chain 'c' and resid 523 through 529 removed outlier: 3.523A pdb=" N ASN c 528 " --> pdb=" O PRO c 524 " (cutoff:3.500A) Processing helix chain 'c' and resid 534 through 554 removed outlier: 3.730A pdb=" N ARG c 542 " --> pdb=" O CYS c 538 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE c 546 " --> pdb=" O ARG c 542 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA c 547 " --> pdb=" O ALA c 543 " (cutoff:3.500A) Processing helix chain 'c' and resid 565 through 578 removed outlier: 4.227A pdb=" N ALA c 573 " --> pdb=" O GLN c 569 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE c 574 " --> pdb=" O GLY c 570 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER c 575 " --> pdb=" O GLN c 571 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU c 578 " --> pdb=" O ILE c 574 " (cutoff:3.500A) Processing helix chain 'c' and resid 588 through 606 removed outlier: 3.953A pdb=" N LYS c 594 " --> pdb=" O GLY c 590 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA c 596 " --> pdb=" O LEU c 592 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN c 601 " --> pdb=" O SER c 597 " (cutoff:3.500A) Processing helix chain 'c' and resid 607 through 610 Processing helix chain 'c' and resid 620 through 637 removed outlier: 4.331A pdb=" N LYS c 632 " --> pdb=" O ALA c 628 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR c 633 " --> pdb=" O GLN c 629 " (cutoff:3.500A) Processing helix chain 'c' and resid 643 through 672 removed outlier: 4.328A pdb=" N VAL c 648 " --> pdb=" O VAL c 644 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER c 649 " --> pdb=" O LYS c 645 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER c 656 " --> pdb=" O SER c 652 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS c 667 " --> pdb=" O GLY c 663 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS c 671 " --> pdb=" O LYS c 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 42 Processing helix chain 'd' and resid 104 through 120 removed outlier: 3.740A pdb=" N LYS d 113 " --> pdb=" O THR d 109 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU d 115 " --> pdb=" O PHE d 111 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET d 116 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU d 118 " --> pdb=" O ALA d 114 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE d 120 " --> pdb=" O MET d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 126 Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 136 through 141 removed outlier: 4.007A pdb=" N LEU d 140 " --> pdb=" O LYS d 136 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU d 141 " --> pdb=" O TYR d 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 136 through 141' Processing helix chain 'd' and resid 151 through 156 Processing helix chain 'd' and resid 167 through 185 removed outlier: 4.081A pdb=" N ALA d 184 " --> pdb=" O ALA d 180 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU d 185 " --> pdb=" O ALA d 181 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 198 removed outlier: 3.602A pdb=" N ASP d 191 " --> pdb=" O LYS d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 211 through 223 Processing helix chain 'd' and resid 227 through 232 removed outlier: 3.502A pdb=" N ARG d 231 " --> pdb=" O SER d 227 " (cutoff:3.500A) Processing helix chain 'd' and resid 232 through 244 removed outlier: 3.621A pdb=" N ARG d 243 " --> pdb=" O ALA d 239 " (cutoff:3.500A) Processing helix chain 'd' and resid 263 through 271 removed outlier: 4.011A pdb=" N ALA d 269 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU d 270 " --> pdb=" O ALA d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 278 through 297 removed outlier: 3.510A pdb=" N LYS d 282 " --> pdb=" O PRO d 278 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR d 286 " --> pdb=" O LYS d 282 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU d 287 " --> pdb=" O SER d 283 " (cutoff:3.500A) Processing helix chain 'd' and resid 297 through 302 removed outlier: 3.605A pdb=" N ILE d 301 " --> pdb=" O GLU d 297 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA d 302 " --> pdb=" O PRO d 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 297 through 302' Processing helix chain 'd' and resid 309 through 313 Processing helix chain 'd' and resid 409 through 413 Processing helix chain 'd' and resid 415 through 420 Processing helix chain 'd' and resid 523 through 530 Processing helix chain 'd' and resid 534 through 554 removed outlier: 3.746A pdb=" N ILE d 546 " --> pdb=" O ARG d 542 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA d 549 " --> pdb=" O LYS d 545 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS d 551 " --> pdb=" O ALA d 547 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE d 552 " --> pdb=" O GLU d 548 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP d 553 " --> pdb=" O ALA d 549 " (cutoff:3.500A) Processing helix chain 'd' and resid 565 through 577 removed outlier: 3.517A pdb=" N GLN d 569 " --> pdb=" O SER d 565 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN d 571 " --> pdb=" O PRO d 567 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE d 574 " --> pdb=" O GLY d 570 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU d 577 " --> pdb=" O ALA d 573 " (cutoff:3.500A) Processing helix chain 'd' and resid 588 through 606 removed outlier: 3.528A pdb=" N LYS d 594 " --> pdb=" O GLY d 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY d 605 " --> pdb=" O GLN d 601 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP d 606 " --> pdb=" O ALA d 602 " (cutoff:3.500A) Processing helix chain 'd' and resid 607 through 612 Processing helix chain 'd' and resid 620 through 637 removed outlier: 3.949A pdb=" N TRP d 624 " --> pdb=" O ASP d 620 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS d 632 " --> pdb=" O ALA d 628 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR d 633 " --> pdb=" O GLN d 629 " (cutoff:3.500A) Processing helix chain 'd' and resid 643 through 672 removed outlier: 3.703A pdb=" N ALA d 647 " --> pdb=" O GLY d 643 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL d 648 " --> pdb=" O VAL d 644 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA d 670 " --> pdb=" O ASP d 666 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS d 671 " --> pdb=" O LYS d 667 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE d 672 " --> pdb=" O VAL d 668 " (cutoff:3.500A) Processing helix chain 'e' and resid 71 through 75 Processing helix chain 'e' and resid 104 through 120 removed outlier: 3.515A pdb=" N ILE e 108 " --> pdb=" O THR e 104 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR e 109 " --> pdb=" O GLU e 105 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA e 117 " --> pdb=" O LYS e 113 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU e 118 " --> pdb=" O ALA e 114 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU e 119 " --> pdb=" O GLU e 115 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE e 120 " --> pdb=" O MET e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 121 through 129 removed outlier: 4.049A pdb=" N LYS e 127 " --> pdb=" O GLU e 123 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET e 128 " --> pdb=" O PHE e 124 " (cutoff:3.500A) Processing helix chain 'e' and resid 136 through 141 Processing helix chain 'e' and resid 151 through 157 removed outlier: 4.052A pdb=" N ASN e 157 " --> pdb=" O ARG e 153 " (cutoff:3.500A) Processing helix chain 'e' and resid 167 through 199 removed outlier: 4.261A pdb=" N ALA e 184 " --> pdb=" O ALA e 180 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU e 185 " --> pdb=" O ALA e 181 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU e 186 " --> pdb=" O LEU e 182 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYS e 187 " --> pdb=" O LYS e 183 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP e 188 " --> pdb=" O ALA e 184 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE e 190 " --> pdb=" O GLU e 186 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU e 199 " --> pdb=" O ALA e 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 211 through 223 removed outlier: 3.891A pdb=" N LYS e 217 " --> pdb=" O GLN e 213 " (cutoff:3.500A) Processing helix chain 'e' and resid 232 through 243 Processing helix chain 'e' and resid 263 through 271 removed outlier: 3.882A pdb=" N SER e 268 " --> pdb=" O ALA e 264 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA e 269 " --> pdb=" O VAL e 265 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU e 270 " --> pdb=" O ALA e 266 " (cutoff:3.500A) Processing helix chain 'e' and resid 278 through 297 removed outlier: 3.525A pdb=" N GLN e 288 " --> pdb=" O LYS e 284 " (cutoff:3.500A) Processing helix chain 'e' and resid 298 through 302 Processing helix chain 'e' and resid 309 through 313 removed outlier: 3.515A pdb=" N ALA e 313 " --> pdb=" O ALA e 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 309 through 313' Processing helix chain 'e' and resid 409 through 413 Processing helix chain 'e' and resid 415 through 419 removed outlier: 3.731A pdb=" N ILE e 419 " --> pdb=" O ALA e 416 " (cutoff:3.500A) Processing helix chain 'e' and resid 453 through 458 removed outlier: 4.072A pdb=" N LEU e 457 " --> pdb=" O GLU e 453 " (cutoff:3.500A) Processing helix chain 'e' and resid 514 through 519 Processing helix chain 'e' and resid 523 through 529 removed outlier: 4.164A pdb=" N ASN e 528 " --> pdb=" O PRO e 524 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR e 529 " --> pdb=" O GLU e 525 " (cutoff:3.500A) Processing helix chain 'e' and resid 534 through 554 removed outlier: 3.577A pdb=" N ARG e 542 " --> pdb=" O CYS e 538 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS e 545 " --> pdb=" O ASP e 541 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE e 546 " --> pdb=" O ARG e 542 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE e 552 " --> pdb=" O GLU e 548 " (cutoff:3.500A) Processing helix chain 'e' and resid 566 through 578 removed outlier: 4.108A pdb=" N GLN e 571 " --> pdb=" O PRO e 567 " (cutoff:3.500A) Processing helix chain 'e' and resid 588 through 606 removed outlier: 3.545A pdb=" N LEU e 592 " --> pdb=" O PRO e 588 " (cutoff:3.500A) Processing helix chain 'e' and resid 607 through 610 removed outlier: 4.175A pdb=" N ILE e 610 " --> pdb=" O PRO e 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 607 through 610' Processing helix chain 'e' and resid 620 through 637 removed outlier: 3.594A pdb=" N GLN e 629 " --> pdb=" O ILE e 625 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS e 632 " --> pdb=" O ALA e 628 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR e 633 " --> pdb=" O GLN e 629 " (cutoff:3.500A) Processing helix chain 'e' and resid 643 through 672 removed outlier: 3.624A pdb=" N LEU e 651 " --> pdb=" O ALA e 647 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER e 652 " --> pdb=" O VAL e 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'f' and resid 81 through 85 removed outlier: 4.497A pdb=" N ALA f 85 " --> pdb=" O SER f 82 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 120 removed outlier: 3.795A pdb=" N ALA f 117 " --> pdb=" O LYS f 113 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU f 118 " --> pdb=" O ALA f 114 " (cutoff:3.500A) Processing helix chain 'f' and resid 121 through 128 Processing helix chain 'f' and resid 136 through 141 Processing helix chain 'f' and resid 151 through 156 Processing helix chain 'f' and resid 167 through 185 removed outlier: 3.653A pdb=" N VAL f 175 " --> pdb=" O GLN f 171 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA f 181 " --> pdb=" O SER f 177 " (cutoff:3.500A) Processing helix chain 'f' and resid 187 through 199 removed outlier: 3.667A pdb=" N ALA f 195 " --> pdb=" O ASP f 191 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU f 199 " --> pdb=" O ALA f 195 " (cutoff:3.500A) Processing helix chain 'f' and resid 211 through 221 removed outlier: 3.842A pdb=" N ASP f 221 " --> pdb=" O LYS f 217 " (cutoff:3.500A) Processing helix chain 'f' and resid 227 through 232 removed outlier: 3.858A pdb=" N ARG f 231 " --> pdb=" O SER f 227 " (cutoff:3.500A) Processing helix chain 'f' and resid 232 through 243 removed outlier: 3.942A pdb=" N ARG f 243 " --> pdb=" O ALA f 239 " (cutoff:3.500A) Processing helix chain 'f' and resid 263 through 271 removed outlier: 3.668A pdb=" N LEU f 270 " --> pdb=" O ALA f 266 " (cutoff:3.500A) Processing helix chain 'f' and resid 281 through 297 removed outlier: 3.567A pdb=" N LEU f 285 " --> pdb=" O GLU f 281 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU f 287 " --> pdb=" O SER f 283 " (cutoff:3.500A) Processing helix chain 'f' and resid 297 through 302 removed outlier: 3.745A pdb=" N ILE f 301 " --> pdb=" O GLU f 297 " (cutoff:3.500A) Processing helix chain 'f' and resid 309 through 313 Processing helix chain 'f' and resid 322 through 326 Processing helix chain 'f' and resid 409 through 413 Processing helix chain 'f' and resid 453 through 458 removed outlier: 3.680A pdb=" N LEU f 457 " --> pdb=" O GLU f 453 " (cutoff:3.500A) Processing helix chain 'f' and resid 514 through 519 removed outlier: 3.538A pdb=" N ILE f 519 " --> pdb=" O ALA f 516 " (cutoff:3.500A) Processing helix chain 'f' and resid 525 through 530 Processing helix chain 'f' and resid 534 through 554 removed outlier: 4.578A pdb=" N LYS f 545 " --> pdb=" O ASP f 541 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE f 546 " --> pdb=" O ARG f 542 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS f 551 " --> pdb=" O ALA f 547 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE f 552 " --> pdb=" O GLU f 548 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP f 553 " --> pdb=" O ALA f 549 " (cutoff:3.500A) Processing helix chain 'f' and resid 565 through 578 removed outlier: 3.842A pdb=" N GLN f 569 " --> pdb=" O SER f 565 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN f 571 " --> pdb=" O PRO f 567 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA f 573 " --> pdb=" O GLN f 569 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE f 574 " --> pdb=" O GLY f 570 " (cutoff:3.500A) Processing helix chain 'f' and resid 588 through 606 removed outlier: 3.527A pdb=" N LYS f 594 " --> pdb=" O GLY f 590 " (cutoff:3.500A) Processing helix chain 'f' and resid 607 through 610 removed outlier: 4.057A pdb=" N ILE f 610 " --> pdb=" O PRO f 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 607 through 610' Processing helix chain 'f' and resid 620 through 637 removed outlier: 4.391A pdb=" N LYS f 632 " --> pdb=" O ALA f 628 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR f 633 " --> pdb=" O GLN f 629 " (cutoff:3.500A) Processing helix chain 'f' and resid 643 through 672 removed outlier: 3.572A pdb=" N VAL f 648 " --> pdb=" O VAL f 644 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER f 656 " --> pdb=" O SER f 652 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL f 668 " --> pdb=" O PHE f 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 27 Processing helix chain 'G' and resid 38 through 42 removed outlier: 3.584A pdb=" N ASN G 42 " --> pdb=" O GLY G 39 " (cutoff:3.500A) Processing helix chain 'g' and resid 104 through 120 removed outlier: 3.737A pdb=" N ASN g 110 " --> pdb=" O HIS g 106 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS g 113 " --> pdb=" O THR g 109 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU g 115 " --> pdb=" O PHE g 111 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET g 116 " --> pdb=" O THR g 112 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA g 117 " --> pdb=" O LYS g 113 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU g 118 " --> pdb=" O ALA g 114 " (cutoff:3.500A) Processing helix chain 'g' and resid 121 through 126 Processing helix chain 'g' and resid 127 through 129 No H-bonds generated for 'chain 'g' and resid 127 through 129' Processing helix chain 'g' and resid 136 through 141 Processing helix chain 'g' and resid 151 through 156 Processing helix chain 'g' and resid 167 through 185 removed outlier: 3.786A pdb=" N ALA g 181 " --> pdb=" O SER g 177 " (cutoff:3.500A) Processing helix chain 'g' and resid 185 through 198 removed outlier: 3.523A pdb=" N ILE g 190 " --> pdb=" O GLU g 186 " (cutoff:3.500A) Processing helix chain 'g' and resid 211 through 223 removed outlier: 3.570A pdb=" N LYS g 217 " --> pdb=" O GLN g 213 " (cutoff:3.500A) Processing helix chain 'g' and resid 227 through 232 Processing helix chain 'g' and resid 232 through 242 removed outlier: 3.520A pdb=" N ALA g 236 " --> pdb=" O TYR g 232 " (cutoff:3.500A) Processing helix chain 'g' and resid 263 through 271 removed outlier: 3.686A pdb=" N ALA g 269 " --> pdb=" O VAL g 265 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU g 270 " --> pdb=" O ALA g 266 " (cutoff:3.500A) Processing helix chain 'g' and resid 278 through 297 removed outlier: 3.700A pdb=" N LYS g 282 " --> pdb=" O PRO g 278 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU g 287 " --> pdb=" O SER g 283 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL g 293 " --> pdb=" O ALA g 289 " (cutoff:3.500A) Processing helix chain 'g' and resid 297 through 302 removed outlier: 3.575A pdb=" N ILE g 301 " --> pdb=" O GLU g 297 " (cutoff:3.500A) Processing helix chain 'g' and resid 309 through 313 Processing helix chain 'g' and resid 409 through 413 Processing helix chain 'g' and resid 416 through 420 removed outlier: 3.728A pdb=" N GLY g 420 " --> pdb=" O SER g 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 453 through 458 removed outlier: 4.048A pdb=" N LEU g 457 " --> pdb=" O GLU g 453 " (cutoff:3.500A) Processing helix chain 'g' and resid 523 through 529 removed outlier: 3.584A pdb=" N THR g 529 " --> pdb=" O GLU g 525 " (cutoff:3.500A) Processing helix chain 'g' and resid 534 through 554 removed outlier: 3.576A pdb=" N CYS g 538 " --> pdb=" O ASP g 534 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP g 541 " --> pdb=" O ARG g 537 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE g 546 " --> pdb=" O ARG g 542 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA g 547 " --> pdb=" O ALA g 543 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU g 548 " --> pdb=" O SER g 544 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP g 553 " --> pdb=" O ALA g 549 " (cutoff:3.500A) Processing helix chain 'g' and resid 565 through 578 removed outlier: 4.064A pdb=" N ILE g 574 " --> pdb=" O GLY g 570 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU g 577 " --> pdb=" O ALA g 573 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU g 578 " --> pdb=" O ILE g 574 " (cutoff:3.500A) Processing helix chain 'g' and resid 588 through 606 removed outlier: 3.767A pdb=" N LEU g 592 " --> pdb=" O PRO g 588 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER g 593 " --> pdb=" O LYS g 589 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS g 594 " --> pdb=" O GLY g 590 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE g 604 " --> pdb=" O MET g 600 " (cutoff:3.500A) Processing helix chain 'g' and resid 607 through 611 removed outlier: 3.528A pdb=" N ILE g 611 " --> pdb=" O SER g 608 " (cutoff:3.500A) Processing helix chain 'g' and resid 620 through 637 removed outlier: 3.542A pdb=" N TRP g 624 " --> pdb=" O ASP g 620 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS g 632 " --> pdb=" O ALA g 628 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR g 633 " --> pdb=" O GLN g 629 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR g 637 " --> pdb=" O THR g 633 " (cutoff:3.500A) Processing helix chain 'g' and resid 643 through 672 removed outlier: 3.531A pdb=" N GLU g 655 " --> pdb=" O LEU g 651 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER g 656 " --> pdb=" O SER g 652 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE g 657 " --> pdb=" O SER g 653 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA g 670 " --> pdb=" O ASP g 666 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 42 Processing helix chain 'h' and resid 67 through 71 Processing helix chain 'h' and resid 104 through 120 removed outlier: 3.535A pdb=" N ASN h 110 " --> pdb=" O HIS h 106 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR h 112 " --> pdb=" O ILE h 108 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS h 113 " --> pdb=" O THR h 109 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA h 117 " --> pdb=" O LYS h 113 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU h 118 " --> pdb=" O ALA h 114 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU h 119 " --> pdb=" O GLU h 115 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE h 120 " --> pdb=" O MET h 116 " (cutoff:3.500A) Processing helix chain 'h' and resid 121 through 129 Processing helix chain 'h' and resid 136 through 141 removed outlier: 4.100A pdb=" N LEU h 140 " --> pdb=" O LYS h 136 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU h 141 " --> pdb=" O TYR h 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 136 through 141' Processing helix chain 'h' and resid 151 through 156 Processing helix chain 'h' and resid 167 through 199 removed outlier: 3.610A pdb=" N ALA h 181 " --> pdb=" O SER h 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA h 184 " --> pdb=" O ALA h 180 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU h 186 " --> pdb=" O LEU h 182 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS h 187 " --> pdb=" O LYS h 183 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TRP h 188 " --> pdb=" O ALA h 184 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE h 190 " --> pdb=" O GLU h 186 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU h 192 " --> pdb=" O TRP h 188 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU h 199 " --> pdb=" O ALA h 195 " (cutoff:3.500A) Processing helix chain 'h' and resid 211 through 223 removed outlier: 3.950A pdb=" N LYS h 217 " --> pdb=" O GLN h 213 " (cutoff:3.500A) Processing helix chain 'h' and resid 227 through 231 Processing helix chain 'h' and resid 232 through 244 removed outlier: 3.656A pdb=" N ALA h 241 " --> pdb=" O ALA h 237 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS h 242 " --> pdb=" O VAL h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 265 through 271 removed outlier: 4.031A pdb=" N ALA h 269 " --> pdb=" O VAL h 265 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU h 270 " --> pdb=" O ALA h 266 " (cutoff:3.500A) Processing helix chain 'h' and resid 278 through 296 removed outlier: 3.531A pdb=" N THR h 294 " --> pdb=" O MET h 290 " (cutoff:3.500A) Processing helix chain 'h' and resid 299 through 303 Processing helix chain 'h' and resid 309 through 313 Processing helix chain 'h' and resid 409 through 413 Processing helix chain 'h' and resid 415 through 420 removed outlier: 3.771A pdb=" N ILE h 419 " --> pdb=" O ALA h 416 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY h 420 " --> pdb=" O SER h 417 " (cutoff:3.500A) Processing helix chain 'h' and resid 514 through 519 removed outlier: 3.556A pdb=" N LEU h 518 " --> pdb=" O PRO h 515 " (cutoff:3.500A) Processing helix chain 'h' and resid 523 through 529 removed outlier: 4.559A pdb=" N ASN h 528 " --> pdb=" O PRO h 524 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR h 529 " --> pdb=" O GLU h 525 " (cutoff:3.500A) Processing helix chain 'h' and resid 534 through 554 removed outlier: 3.933A pdb=" N LYS h 545 " --> pdb=" O ASP h 541 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE h 546 " --> pdb=" O ARG h 542 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP h 553 " --> pdb=" O ALA h 549 " (cutoff:3.500A) Processing helix chain 'h' and resid 565 through 578 removed outlier: 4.070A pdb=" N GLN h 571 " --> pdb=" O PRO h 567 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU h 577 " --> pdb=" O ALA h 573 " (cutoff:3.500A) Processing helix chain 'h' and resid 588 through 606 removed outlier: 3.569A pdb=" N LYS h 594 " --> pdb=" O GLY h 590 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP h 606 " --> pdb=" O ALA h 602 " (cutoff:3.500A) Processing helix chain 'h' and resid 607 through 612 Processing helix chain 'h' and resid 620 through 637 removed outlier: 3.562A pdb=" N TRP h 624 " --> pdb=" O ASP h 620 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS h 632 " --> pdb=" O ALA h 628 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR h 633 " --> pdb=" O GLN h 629 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR h 637 " --> pdb=" O THR h 633 " (cutoff:3.500A) Processing helix chain 'h' and resid 643 through 672 removed outlier: 4.004A pdb=" N VAL h 648 " --> pdb=" O VAL h 644 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER h 649 " --> pdb=" O LYS h 645 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE h 657 " --> pdb=" O SER h 653 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS h 667 " --> pdb=" O GLY h 663 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL h 668 " --> pdb=" O PHE h 664 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER h 669 " --> pdb=" O LEU h 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 27 Processing helix chain 'I' and resid 37 through 42 removed outlier: 3.595A pdb=" N ASN I 42 " --> pdb=" O PRO I 38 " (cutoff:3.500A) Processing helix chain 'i' and resid 81 through 85 removed outlier: 3.970A pdb=" N ALA i 85 " --> pdb=" O SER i 82 " (cutoff:3.500A) Processing helix chain 'i' and resid 104 through 120 removed outlier: 3.764A pdb=" N LYS i 113 " --> pdb=" O THR i 109 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU i 115 " --> pdb=" O PHE i 111 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET i 116 " --> pdb=" O THR i 112 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA i 117 " --> pdb=" O LYS i 113 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU i 118 " --> pdb=" O ALA i 114 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU i 119 " --> pdb=" O GLU i 115 " (cutoff:3.500A) Processing helix chain 'i' and resid 121 through 128 removed outlier: 3.596A pdb=" N LYS i 127 " --> pdb=" O GLU i 123 " (cutoff:3.500A) Processing helix chain 'i' and resid 136 through 141 removed outlier: 3.671A pdb=" N LEU i 140 " --> pdb=" O LYS i 136 " (cutoff:3.500A) Processing helix chain 'i' and resid 151 through 156 Processing helix chain 'i' and resid 167 through 185 removed outlier: 3.602A pdb=" N ASP i 176 " --> pdb=" O THR i 172 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER i 177 " --> pdb=" O MET i 173 " (cutoff:3.500A) Processing helix chain 'i' and resid 185 through 198 Processing helix chain 'i' and resid 211 through 221 removed outlier: 3.703A pdb=" N ASP i 221 " --> pdb=" O LYS i 217 " (cutoff:3.500A) Processing helix chain 'i' and resid 227 through 232 removed outlier: 3.656A pdb=" N ARG i 231 " --> pdb=" O SER i 227 " (cutoff:3.500A) Processing helix chain 'i' and resid 232 through 242 removed outlier: 3.535A pdb=" N VAL i 238 " --> pdb=" O LYS i 234 " (cutoff:3.500A) Processing helix chain 'i' and resid 263 through 270 removed outlier: 3.510A pdb=" N SER i 268 " --> pdb=" O ALA i 264 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA i 269 " --> pdb=" O VAL i 265 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU i 270 " --> pdb=" O ALA i 266 " (cutoff:3.500A) Processing helix chain 'i' and resid 278 through 296 removed outlier: 3.842A pdb=" N LYS i 282 " --> pdb=" O PRO i 278 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR i 286 " --> pdb=" O LYS i 282 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA i 295 " --> pdb=" O ASP i 291 " (cutoff:3.500A) Processing helix chain 'i' and resid 297 through 302 removed outlier: 3.773A pdb=" N ILE i 301 " --> pdb=" O GLU i 297 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 313 Processing helix chain 'i' and resid 322 through 326 Processing helix chain 'i' and resid 409 through 413 Processing helix chain 'i' and resid 453 through 458 removed outlier: 3.945A pdb=" N LEU i 457 " --> pdb=" O GLU i 453 " (cutoff:3.500A) Processing helix chain 'i' and resid 514 through 519 Processing helix chain 'i' and resid 523 through 529 removed outlier: 3.846A pdb=" N THR i 529 " --> pdb=" O GLU i 525 " (cutoff:3.500A) Processing helix chain 'i' and resid 534 through 554 removed outlier: 3.814A pdb=" N ASP i 541 " --> pdb=" O ARG i 537 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG i 542 " --> pdb=" O CYS i 538 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE i 546 " --> pdb=" O ARG i 542 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA i 547 " --> pdb=" O ALA i 543 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU i 548 " --> pdb=" O SER i 544 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA i 549 " --> pdb=" O LYS i 545 " (cutoff:3.500A) Processing helix chain 'i' and resid 565 through 578 removed outlier: 3.767A pdb=" N GLN i 569 " --> pdb=" O SER i 565 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER i 575 " --> pdb=" O GLN i 571 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU i 578 " --> pdb=" O ILE i 574 " (cutoff:3.500A) Processing helix chain 'i' and resid 588 through 606 removed outlier: 3.896A pdb=" N LYS i 594 " --> pdb=" O GLY i 590 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA i 596 " --> pdb=" O LEU i 592 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA i 602 " --> pdb=" O ARG i 598 " (cutoff:3.500A) Processing helix chain 'i' and resid 607 through 611 removed outlier: 3.570A pdb=" N ILE i 611 " --> pdb=" O SER i 608 " (cutoff:3.500A) Processing helix chain 'i' and resid 620 through 638 removed outlier: 3.896A pdb=" N GLY i 630 " --> pdb=" O ALA i 626 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS i 632 " --> pdb=" O ALA i 628 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU i 635 " --> pdb=" O VAL i 631 " (cutoff:3.500A) Processing helix chain 'i' and resid 643 through 671 removed outlier: 3.781A pdb=" N LEU i 651 " --> pdb=" O ALA i 647 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER i 652 " --> pdb=" O VAL i 648 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE i 657 " --> pdb=" O SER i 653 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA i 670 " --> pdb=" O ASP i 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 27 Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'j' and resid 71 through 75 Processing helix chain 'j' and resid 104 through 120 removed outlier: 3.507A pdb=" N THR j 109 " --> pdb=" O GLU j 105 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU j 115 " --> pdb=" O PHE j 111 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET j 116 " --> pdb=" O THR j 112 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA j 117 " --> pdb=" O LYS j 113 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU j 118 " --> pdb=" O ALA j 114 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE j 120 " --> pdb=" O MET j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 121 through 129 removed outlier: 4.773A pdb=" N LYS j 127 " --> pdb=" O GLU j 123 " (cutoff:3.500A) Processing helix chain 'j' and resid 136 through 141 removed outlier: 3.984A pdb=" N LEU j 140 " --> pdb=" O LYS j 136 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU j 141 " --> pdb=" O TYR j 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 136 through 141' Processing helix chain 'j' and resid 151 through 156 Processing helix chain 'j' and resid 167 through 185 removed outlier: 3.576A pdb=" N VAL j 175 " --> pdb=" O GLN j 171 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA j 181 " --> pdb=" O SER j 177 " (cutoff:3.500A) Processing helix chain 'j' and resid 185 through 199 removed outlier: 3.516A pdb=" N THR j 197 " --> pdb=" O ARG j 193 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU j 199 " --> pdb=" O ALA j 195 " (cutoff:3.500A) Processing helix chain 'j' and resid 211 through 223 removed outlier: 3.534A pdb=" N VAL j 215 " --> pdb=" O PRO j 211 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS j 217 " --> pdb=" O GLN j 213 " (cutoff:3.500A) Processing helix chain 'j' and resid 227 through 232 removed outlier: 4.179A pdb=" N ARG j 231 " --> pdb=" O SER j 227 " (cutoff:3.500A) Processing helix chain 'j' and resid 232 through 243 removed outlier: 3.887A pdb=" N ARG j 243 " --> pdb=" O ALA j 239 " (cutoff:3.500A) Processing helix chain 'j' and resid 263 through 271 removed outlier: 3.663A pdb=" N ALA j 269 " --> pdb=" O VAL j 265 " (cutoff:3.500A) Processing helix chain 'j' and resid 278 through 297 removed outlier: 4.001A pdb=" N THR j 286 " --> pdb=" O LYS j 282 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN j 288 " --> pdb=" O LYS j 284 " (cutoff:3.500A) Processing helix chain 'j' and resid 298 through 301 Processing helix chain 'j' and resid 309 through 313 Processing helix chain 'j' and resid 409 through 413 Processing helix chain 'j' and resid 415 through 419 removed outlier: 3.716A pdb=" N GLN j 418 " --> pdb=" O ALA j 415 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE j 419 " --> pdb=" O ALA j 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 415 through 419' Processing helix chain 'j' and resid 453 through 458 removed outlier: 4.398A pdb=" N LEU j 457 " --> pdb=" O GLU j 453 " (cutoff:3.500A) Processing helix chain 'j' and resid 479 through 483 Processing helix chain 'j' and resid 523 through 529 removed outlier: 3.729A pdb=" N ASN j 528 " --> pdb=" O PRO j 524 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR j 529 " --> pdb=" O GLU j 525 " (cutoff:3.500A) Processing helix chain 'j' and resid 534 through 554 removed outlier: 3.661A pdb=" N ASP j 541 " --> pdb=" O ARG j 537 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG j 542 " --> pdb=" O CYS j 538 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE j 546 " --> pdb=" O ARG j 542 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA j 547 " --> pdb=" O ALA j 543 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS j 551 " --> pdb=" O ALA j 547 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE j 552 " --> pdb=" O GLU j 548 " (cutoff:3.500A) Processing helix chain 'j' and resid 565 through 577 removed outlier: 3.769A pdb=" N GLN j 571 " --> pdb=" O PRO j 567 " (cutoff:3.500A) Processing helix chain 'j' and resid 588 through 606 removed outlier: 3.567A pdb=" N LEU j 592 " --> pdb=" O PRO j 588 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER j 593 " --> pdb=" O LYS j 589 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN j 601 " --> pdb=" O SER j 597 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP j 606 " --> pdb=" O ALA j 602 " (cutoff:3.500A) Processing helix chain 'j' and resid 607 through 610 Processing helix chain 'j' and resid 620 through 637 removed outlier: 4.056A pdb=" N LYS j 632 " --> pdb=" O ALA j 628 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR j 633 " --> pdb=" O GLN j 629 " (cutoff:3.500A) Processing helix chain 'j' and resid 643 through 672 removed outlier: 3.513A pdb=" N VAL j 648 " --> pdb=" O VAL j 644 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS j 650 " --> pdb=" O THR j 646 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU j 651 " --> pdb=" O ALA j 647 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER j 652 " --> pdb=" O VAL j 648 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS j 667 " --> pdb=" O GLY j 663 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 34 Processing helix chain 'K' and resid 69 through 74 removed outlier: 3.847A pdb=" N TYR K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 101 removed outlier: 3.734A pdb=" N ARG K 91 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU K 93 " --> pdb=" O LYS K 89 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG K 99 " --> pdb=" O TYR K 95 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE K 100 " --> pdb=" O GLU K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 125 removed outlier: 3.825A pdb=" N ALA K 116 " --> pdb=" O ASN K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 136 Processing helix chain 'K' and resid 144 through 148 Processing helix chain 'K' and resid 203 through 212 removed outlier: 3.856A pdb=" N LEU K 207 " --> pdb=" O THR K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 269 removed outlier: 3.745A pdb=" N VAL K 268 " --> pdb=" O PHE K 264 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG K 269 " --> pdb=" O SER K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 292 Processing helix chain 'K' and resid 296 through 310 removed outlier: 3.723A pdb=" N ARG K 300 " --> pdb=" O SER K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 323 through 335 Processing helix chain 'K' and resid 360 through 365 Processing helix chain 'K' and resid 406 through 418 removed outlier: 3.636A pdb=" N ASP K 411 " --> pdb=" O MET K 407 " (cutoff:3.500A) Processing helix chain 'K' and resid 449 through 453 removed outlier: 3.720A pdb=" N GLU K 452 " --> pdb=" O LEU K 449 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU K 453 " --> pdb=" O SER K 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 449 through 453' Processing helix chain 'K' and resid 458 through 461 removed outlier: 4.482A pdb=" N PHE K 461 " --> pdb=" O ASP K 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 458 through 461' Processing helix chain 'K' and resid 462 through 475 removed outlier: 3.653A pdb=" N GLN K 466 " --> pdb=" O ASP K 462 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA K 475 " --> pdb=" O LEU K 471 " (cutoff:3.500A) Processing helix chain 'K' and resid 480 through 494 Processing helix chain 'K' and resid 529 through 536 Processing helix chain 'K' and resid 588 through 605 Processing helix chain 'K' and resid 620 through 631 removed outlier: 3.601A pdb=" N TRP K 624 " --> pdb=" O THR K 620 " (cutoff:3.500A) Processing helix chain 'K' and resid 632 through 635 removed outlier: 3.672A pdb=" N ILE K 635 " --> pdb=" O LEU K 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 632 through 635' Processing helix chain 'K' and resid 667 through 689 removed outlier: 4.431A pdb=" N TYR K 681 " --> pdb=" O HIS K 677 " (cutoff:3.500A) Processing helix chain 'K' and resid 723 through 735 removed outlier: 3.703A pdb=" N SER K 728 " --> pdb=" O ARG K 724 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU K 730 " --> pdb=" O GLY K 726 " (cutoff:3.500A) Processing helix chain 'K' and resid 759 through 767 removed outlier: 3.622A pdb=" N LYS K 766 " --> pdb=" O SER K 762 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER K 767 " --> pdb=" O ALA K 763 " (cutoff:3.500A) Processing helix chain 'K' and resid 777 through 782 removed outlier: 3.579A pdb=" N GLU K 781 " --> pdb=" O PRO K 777 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL K 782 " --> pdb=" O ARG K 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 777 through 782' Processing helix chain 'K' and resid 802 through 818 removed outlier: 3.545A pdb=" N CYS K 806 " --> pdb=" O SER K 802 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU K 814 " --> pdb=" O MET K 810 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL K 815 " --> pdb=" O TYR K 811 " (cutoff:3.500A) Processing helix chain 'K' and resid 834 through 839 Processing helix chain 'K' and resid 891 through 899 Processing helix chain 'K' and resid 902 through 916 removed outlier: 4.065A pdb=" N LYS K 916 " --> pdb=" O LYS K 912 " (cutoff:3.500A) Processing helix chain 'K' and resid 962 through 974 removed outlier: 3.582A pdb=" N LYS K 968 " --> pdb=" O ASP K 964 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE K 969 " --> pdb=" O ALA K 965 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA K 973 " --> pdb=" O ILE K 969 " (cutoff:3.500A) Processing helix chain 'K' and resid 988 through 990 No H-bonds generated for 'chain 'K' and resid 988 through 990' Processing helix chain 'K' and resid 991 through 996 removed outlier: 3.947A pdb=" N LEU K 996 " --> pdb=" O ARG K 992 " (cutoff:3.500A) Processing helix chain 'K' and resid 1003 through 1014 Processing helix chain 'K' and resid 1189 through 1194 removed outlier: 3.593A pdb=" N LEU K1194 " --> pdb=" O ASP K1191 " (cutoff:3.500A) Processing helix chain 'K' and resid 1216 through 1220 removed outlier: 3.746A pdb=" N ILE K1220 " --> pdb=" O LEU K1217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'a' and resid 63 through 65 Processing sheet with id=AA3, first strand: chain 'a' and resid 101 through 102 Processing sheet with id=AA4, first strand: chain 'a' and resid 307 through 308 Processing sheet with id=AA5, first strand: chain 'a' and resid 319 through 322 Processing sheet with id=AA6, first strand: chain 'a' and resid 334 through 336 removed outlier: 3.626A pdb=" N ARG a 335 " --> pdb=" O VAL a 367 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ARG a 366 " --> pdb=" O ALA a 470 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ALA a 470 " --> pdb=" O ARG a 366 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS a 398 " --> pdb=" O ILE a 473 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL a 399 " --> pdb=" O TYR a 427 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR a 427 " --> pdb=" O VAL a 399 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE a 401 " --> pdb=" O VAL a 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 344 through 350 Processing sheet with id=AA8, first strand: chain 'a' and resid 432 through 434 Processing sheet with id=AA9, first strand: chain 'a' and resid 503 through 505 removed outlier: 4.454A pdb=" N VAL a 503 " --> pdb=" O VAL a 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AB2, first strand: chain 'b' and resid 63 through 65 removed outlier: 3.775A pdb=" N TYR b 147 " --> pdb=" O TRP b 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 101 through 102 Processing sheet with id=AB4, first strand: chain 'b' and resid 307 through 308 Processing sheet with id=AB5, first strand: chain 'b' and resid 319 through 322 Processing sheet with id=AB6, first strand: chain 'b' and resid 334 through 336 removed outlier: 7.108A pdb=" N ARG b 366 " --> pdb=" O ALA b 470 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ALA b 470 " --> pdb=" O ARG b 366 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS b 398 " --> pdb=" O ILE b 473 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL b 399 " --> pdb=" O TYR b 427 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR b 427 " --> pdb=" O VAL b 399 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE b 401 " --> pdb=" O VAL b 425 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 345 through 350 removed outlier: 3.690A pdb=" N PHE b 345 " --> pdb=" O LEU b 361 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU b 359 " --> pdb=" O ILE b 347 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 432 through 434 Processing sheet with id=AB9, first strand: chain 'b' and resid 504 through 505 Processing sheet with id=AC1, first strand: chain 'c' and resid 63 through 65 Processing sheet with id=AC2, first strand: chain 'c' and resid 101 through 102 Processing sheet with id=AC3, first strand: chain 'c' and resid 307 through 308 Processing sheet with id=AC4, first strand: chain 'c' and resid 319 through 321 removed outlier: 3.691A pdb=" N LEU c 492 " --> pdb=" O ASP c 381 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 334 through 336 removed outlier: 7.788A pdb=" N ARG c 366 " --> pdb=" O ALA c 470 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ALA c 470 " --> pdb=" O ARG c 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL c 368 " --> pdb=" O LEU c 468 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR c 471 " --> pdb=" O GLY c 400 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS c 398 " --> pdb=" O ILE c 473 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN c 426 " --> pdb=" O PHE c 401 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL c 403 " --> pdb=" O VAL c 424 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL c 424 " --> pdb=" O VAL c 403 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLN c 405 " --> pdb=" O ALA c 422 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA c 422 " --> pdb=" O GLN c 405 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 345 through 348 removed outlier: 3.586A pdb=" N PHE c 345 " --> pdb=" O LEU c 361 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 432 through 434 Processing sheet with id=AC8, first strand: chain 'c' and resid 503 through 505 removed outlier: 4.685A pdb=" N VAL c 503 " --> pdb=" O VAL c 510 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AD1, first strand: chain 'd' and resid 63 through 65 Processing sheet with id=AD2, first strand: chain 'd' and resid 101 through 102 Processing sheet with id=AD3, first strand: chain 'd' and resid 307 through 308 Processing sheet with id=AD4, first strand: chain 'd' and resid 319 through 321 Processing sheet with id=AD5, first strand: chain 'd' and resid 334 through 336 removed outlier: 7.203A pdb=" N ARG d 366 " --> pdb=" O ALA d 470 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA d 470 " --> pdb=" O ARG d 366 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR d 471 " --> pdb=" O GLY d 400 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS d 398 " --> pdb=" O ILE d 473 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN d 426 " --> pdb=" O PHE d 401 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL d 403 " --> pdb=" O VAL d 424 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL d 424 " --> pdb=" O VAL d 403 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN d 405 " --> pdb=" O ALA d 422 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA d 422 " --> pdb=" O GLN d 405 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 344 through 350 removed outlier: 3.515A pdb=" N ILE d 347 " --> pdb=" O LEU d 359 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU d 359 " --> pdb=" O ILE d 347 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 432 through 434 Processing sheet with id=AD8, first strand: chain 'd' and resid 503 through 505 removed outlier: 4.459A pdb=" N VAL d 503 " --> pdb=" O VAL d 510 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AE1, first strand: chain 'e' and resid 64 through 65 removed outlier: 3.568A pdb=" N TYR e 147 " --> pdb=" O TRP e 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'e' and resid 101 through 102 Processing sheet with id=AE3, first strand: chain 'e' and resid 307 through 308 Processing sheet with id=AE4, first strand: chain 'e' and resid 319 through 322 Processing sheet with id=AE5, first strand: chain 'e' and resid 334 through 336 removed outlier: 7.365A pdb=" N ARG e 366 " --> pdb=" O ALA e 470 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ALA e 470 " --> pdb=" O ARG e 366 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU e 468 " --> pdb=" O VAL e 368 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER e 406 " --> pdb=" O ASN e 465 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR e 471 " --> pdb=" O GLY e 400 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY e 400 " --> pdb=" O THR e 471 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL e 399 " --> pdb=" O TYR e 427 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR e 427 " --> pdb=" O VAL e 399 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE e 401 " --> pdb=" O VAL e 425 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR e 423 " --> pdb=" O VAL e 403 " (cutoff:3.500A) removed outlier: 13.347A pdb=" N ALA e 422 " --> pdb=" O GLN e 346 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N GLN e 348 " --> pdb=" O ALA e 422 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N VAL e 424 " --> pdb=" O GLN e 348 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR e 350 " --> pdb=" O VAL e 424 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ASN e 426 " --> pdb=" O THR e 350 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE e 345 " --> pdb=" O LEU e 361 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'e' and resid 432 through 434 Processing sheet with id=AE7, first strand: chain 'e' and resid 503 through 504 removed outlier: 4.056A pdb=" N VAL e 503 " --> pdb=" O VAL e 510 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AE9, first strand: chain 'f' and resid 63 through 65 removed outlier: 3.552A pdb=" N TYR f 147 " --> pdb=" O TRP f 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'f' and resid 101 through 102 removed outlier: 3.508A pdb=" N THR f 142 " --> pdb=" O VAL f 165 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'f' and resid 307 through 308 Processing sheet with id=AF3, first strand: chain 'f' and resid 319 through 321 Processing sheet with id=AF4, first strand: chain 'f' and resid 334 through 336 removed outlier: 7.205A pdb=" N ARG f 366 " --> pdb=" O ALA f 470 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ALA f 470 " --> pdb=" O ARG f 366 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR f 471 " --> pdb=" O GLY f 400 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY f 400 " --> pdb=" O THR f 471 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS f 398 " --> pdb=" O ILE f 473 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL f 399 " --> pdb=" O TYR f 427 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR f 427 " --> pdb=" O VAL f 399 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE f 401 " --> pdb=" O VAL f 425 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'f' and resid 345 through 350 Processing sheet with id=AF6, first strand: chain 'f' and resid 432 through 434 Processing sheet with id=AF7, first strand: chain 'f' and resid 503 through 505 removed outlier: 4.497A pdb=" N VAL f 503 " --> pdb=" O VAL f 510 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AF9, first strand: chain 'g' and resid 63 through 65 removed outlier: 3.768A pdb=" N TYR g 147 " --> pdb=" O TRP g 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 101 through 102 removed outlier: 3.653A pdb=" N ILE g 166 " --> pdb=" O VAL g 101 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 307 through 308 Processing sheet with id=AG3, first strand: chain 'g' and resid 319 through 322 Processing sheet with id=AG4, first strand: chain 'g' and resid 334 through 336 Processing sheet with id=AG5, first strand: chain 'g' and resid 345 through 350 Processing sheet with id=AG6, first strand: chain 'g' and resid 421 through 429 removed outlier: 6.858A pdb=" N PHE g 401 " --> pdb=" O VAL g 425 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR g 427 " --> pdb=" O VAL g 399 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL g 399 " --> pdb=" O TYR g 427 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS g 398 " --> pdb=" O ILE g 473 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR g 471 " --> pdb=" O GLY g 400 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'g' and resid 432 through 433 Processing sheet with id=AG8, first strand: chain 'g' and resid 503 through 505 removed outlier: 4.297A pdb=" N VAL g 503 " --> pdb=" O VAL g 510 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA g 508 " --> pdb=" O VAL g 505 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 19 through 20 Processing sheet with id=AH1, first strand: chain 'h' and resid 63 through 65 removed outlier: 4.105A pdb=" N TYR h 147 " --> pdb=" O TRP h 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'h' and resid 101 through 102 Processing sheet with id=AH3, first strand: chain 'h' and resid 307 through 308 Processing sheet with id=AH4, first strand: chain 'h' and resid 319 through 321 Processing sheet with id=AH5, first strand: chain 'h' and resid 334 through 336 Processing sheet with id=AH6, first strand: chain 'h' and resid 345 through 349 removed outlier: 3.607A pdb=" N PHE h 345 " --> pdb=" O LEU h 361 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'h' and resid 421 through 428 removed outlier: 3.577A pdb=" N THR h 423 " --> pdb=" O VAL h 403 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE h 401 " --> pdb=" O VAL h 425 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR h 427 " --> pdb=" O VAL h 399 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL h 399 " --> pdb=" O TYR h 427 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'h' and resid 432 through 434 Processing sheet with id=AH9, first strand: chain 'h' and resid 503 through 505 removed outlier: 4.300A pdb=" N VAL h 503 " --> pdb=" O VAL h 510 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'i' and resid 63 through 65 removed outlier: 3.754A pdb=" N TYR i 147 " --> pdb=" O TRP i 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'i' and resid 101 through 102 Processing sheet with id=AI3, first strand: chain 'i' and resid 307 through 308 Processing sheet with id=AI4, first strand: chain 'i' and resid 319 through 321 removed outlier: 3.538A pdb=" N LEU i 492 " --> pdb=" O ASP i 381 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'i' and resid 334 through 336 removed outlier: 7.559A pdb=" N ARG i 366 " --> pdb=" O ALA i 470 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ALA i 470 " --> pdb=" O ARG i 366 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR i 467 " --> pdb=" O PHE i 404 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL i 399 " --> pdb=" O TYR i 427 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR i 427 " --> pdb=" O VAL i 399 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE i 401 " --> pdb=" O VAL i 425 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'i' and resid 344 through 347 Processing sheet with id=AI7, first strand: chain 'i' and resid 432 through 434 Processing sheet with id=AI8, first strand: chain 'i' and resid 503 through 505 removed outlier: 4.429A pdb=" N VAL i 503 " --> pdb=" O VAL i 510 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AJ1, first strand: chain 'j' and resid 46 through 48 removed outlier: 4.020A pdb=" N TYR j 147 " --> pdb=" O TRP j 48 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'j' and resid 101 through 102 Processing sheet with id=AJ3, first strand: chain 'j' and resid 307 through 308 Processing sheet with id=AJ4, first strand: chain 'j' and resid 319 through 321 Processing sheet with id=AJ5, first strand: chain 'j' and resid 334 through 336 removed outlier: 7.628A pdb=" N ARG j 366 " --> pdb=" O ALA j 470 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ALA j 470 " --> pdb=" O ARG j 366 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU j 468 " --> pdb=" O VAL j 368 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS j 398 " --> pdb=" O ILE j 473 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL j 399 " --> pdb=" O TYR j 427 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR j 427 " --> pdb=" O VAL j 399 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE j 401 " --> pdb=" O VAL j 425 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N THR j 350 " --> pdb=" O VAL j 424 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ASN j 426 " --> pdb=" O THR j 350 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'j' and resid 345 through 346 Processing sheet with id=AJ7, first strand: chain 'j' and resid 432 through 434 Processing sheet with id=AJ8, first strand: chain 'j' and resid 503 through 505 removed outlier: 4.003A pdb=" N VAL j 503 " --> pdb=" O VAL j 510 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'K' and resid 18 through 19 removed outlier: 6.578A pdb=" N ILE K 18 " --> pdb=" O VAL K 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ9 Processing sheet with id=AK1, first strand: chain 'K' and resid 43 through 47 removed outlier: 3.623A pdb=" N ALA K 56 " --> pdb=" O LEU K 46 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'K' and resid 157 through 159 removed outlier: 6.362A pdb=" N VAL K 220 " --> pdb=" O ARG K 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS K 284 " --> pdb=" O VAL K 222 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'K' and resid 240 through 241 Processing sheet with id=AK4, first strand: chain 'K' and resid 351 through 353 removed outlier: 6.239A pdb=" N VAL K 351 " --> pdb=" O VAL K 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK4 Processing sheet with id=AK5, first strand: chain 'K' and resid 389 through 390 Processing sheet with id=AK6, first strand: chain 'K' and resid 394 through 396 removed outlier: 4.392A pdb=" N LYS K 739 " --> pdb=" O TRP K 396 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY K 705 " --> pdb=" O ARG K 758 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'K' and resid 399 through 405 removed outlier: 4.681A pdb=" N GLN K 399 " --> pdb=" O ASP K 776 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU K 774 " --> pdb=" O THR K 401 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP K 403 " --> pdb=" O LEU K 772 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU K 772 " --> pdb=" O ASP K 403 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'K' and resid 430 through 431 Processing sheet with id=AK9, first strand: chain 'K' and resid 435 through 440 removed outlier: 3.800A pdb=" N LEU K 435 " --> pdb=" O PHE K 644 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER K 637 " --> pdb=" O PHE K 656 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN K 572 " --> pdb=" O SER K 611 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N VAL K 613 " --> pdb=" O GLN K 572 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL K 574 " --> pdb=" O VAL K 613 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LYS K 615 " --> pdb=" O VAL K 574 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N SER K 576 " --> pdb=" O LYS K 615 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'K' and resid 497 through 498 Processing sheet with id=AL2, first strand: chain 'K' and resid 865 through 869 removed outlier: 6.235A pdb=" N VAL K 846 " --> pdb=" O THR K 866 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LEU K 868 " --> pdb=" O VAL K 846 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N CYS K 848 " --> pdb=" O LEU K 868 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL K 886 " --> pdb=" O LEU K 923 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLN K 925 " --> pdb=" O VAL K 886 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'K' and resid 941 through 943 removed outlier: 3.720A pdb=" N ARG K 948 " --> pdb=" O ASP K 943 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'K' and resid 1029 through 1030 removed outlier: 4.112A pdb=" N GLU K1029 " --> pdb=" O VAL K1043 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL K1043 " --> pdb=" O GLU K1029 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'K' and resid 1063 through 1064 removed outlier: 3.626A pdb=" N PHE K1063 " --> pdb=" O CYS K1055 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'K' and resid 1063 through 1064 removed outlier: 3.626A pdb=" N PHE K1063 " --> pdb=" O CYS K1055 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'K' and resid 1127 through 1129 removed outlier: 3.685A pdb=" N THR K1127 " --> pdb=" O THR K1146 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'K' and resid 1162 through 1165 Processing sheet with id=AL9, first strand: chain 'K' and resid 1228 through 1230 Processing sheet with id=AM1, first strand: chain 'K' and resid 1239 through 1241 removed outlier: 6.978A pdb=" N VAL K1240 " --> pdb=" O ILE K1247 " (cutoff:3.500A) 2321 hydrogen bonds defined for protein. 6168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 29.10 Time building geometry restraints manager: 13.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 19736 1.34 - 1.46: 10180 1.46 - 1.58: 31511 1.58 - 1.69: 1 1.69 - 1.81: 439 Bond restraints: 61867 Sorted by residual: bond pdb=" N PRO c 344 " pdb=" CD PRO c 344 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.08e+01 bond pdb=" N LEU f 359 " pdb=" CA LEU f 359 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.21e-02 6.83e+03 1.03e+01 bond pdb=" N PRO i 344 " pdb=" CD PRO i 344 " ideal model delta sigma weight residual 1.473 1.515 -0.042 1.40e-02 5.10e+03 9.18e+00 bond pdb=" N PRO f 344 " pdb=" CD PRO f 344 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.19e+00 bond pdb=" N ILE d 328 " pdb=" CA ILE d 328 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.00e+00 ... (remaining 61862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 84099 4.29 - 8.57: 339 8.57 - 12.86: 19 12.86 - 17.15: 2 17.15 - 21.43: 2 Bond angle restraints: 84461 Sorted by residual: angle pdb=" CA PRO c 344 " pdb=" N PRO c 344 " pdb=" CD PRO c 344 " ideal model delta sigma weight residual 112.00 99.93 12.07 1.40e+00 5.10e-01 7.44e+01 angle pdb=" CA PRO i 344 " pdb=" N PRO i 344 " pdb=" CD PRO i 344 " ideal model delta sigma weight residual 112.00 100.00 12.00 1.40e+00 5.10e-01 7.35e+01 angle pdb=" CA PRO g 344 " pdb=" N PRO g 344 " pdb=" CD PRO g 344 " ideal model delta sigma weight residual 112.00 100.02 11.98 1.40e+00 5.10e-01 7.32e+01 angle pdb=" CA PRO j 344 " pdb=" N PRO j 344 " pdb=" CD PRO j 344 " ideal model delta sigma weight residual 112.00 100.17 11.83 1.40e+00 5.10e-01 7.14e+01 angle pdb=" C ILE b 337 " pdb=" N PRO b 338 " pdb=" CA PRO b 338 " ideal model delta sigma weight residual 119.84 130.38 -10.54 1.25e+00 6.40e-01 7.11e+01 ... (remaining 84456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 34040 17.95 - 35.90: 2986 35.90 - 53.85: 521 53.85 - 71.80: 134 71.80 - 89.75: 84 Dihedral angle restraints: 37765 sinusoidal: 14616 harmonic: 23149 Sorted by residual: dihedral pdb=" CA ALA c 374 " pdb=" C ALA c 374 " pdb=" N PRO c 375 " pdb=" CA PRO c 375 " ideal model delta harmonic sigma weight residual -180.00 -143.56 -36.44 0 5.00e+00 4.00e-02 5.31e+01 dihedral pdb=" CA ALA f 374 " pdb=" C ALA f 374 " pdb=" N PRO f 375 " pdb=" CA PRO f 375 " ideal model delta harmonic sigma weight residual 180.00 -146.07 -33.93 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA ALA i 374 " pdb=" C ALA i 374 " pdb=" N PRO i 375 " pdb=" CA PRO i 375 " ideal model delta harmonic sigma weight residual -180.00 -148.30 -31.70 0 5.00e+00 4.00e-02 4.02e+01 ... (remaining 37762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 8789 0.083 - 0.166: 1088 0.166 - 0.248: 37 0.248 - 0.331: 9 0.331 - 0.414: 1 Chirality restraints: 9924 Sorted by residual: chirality pdb=" CG LEU j 359 " pdb=" CB LEU j 359 " pdb=" CD1 LEU j 359 " pdb=" CD2 LEU j 359 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" CA TRP K 5 " pdb=" N TRP K 5 " pdb=" C TRP K 5 " pdb=" CB TRP K 5 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE d 76 " pdb=" CA ILE d 76 " pdb=" CG1 ILE d 76 " pdb=" CG2 ILE d 76 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 9921 not shown) Planarity restraints: 10909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR f 343 " 0.145 5.00e-02 4.00e+02 2.06e-01 6.78e+01 pdb=" N PRO f 344 " -0.354 5.00e-02 4.00e+02 pdb=" CA PRO f 344 " 0.126 5.00e-02 4.00e+02 pdb=" CD PRO f 344 " 0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR i 343 " -0.144 5.00e-02 4.00e+02 2.03e-01 6.62e+01 pdb=" N PRO i 344 " 0.350 5.00e-02 4.00e+02 pdb=" CA PRO i 344 " -0.124 5.00e-02 4.00e+02 pdb=" CD PRO i 344 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR c 343 " 0.139 5.00e-02 4.00e+02 1.98e-01 6.27e+01 pdb=" N PRO c 344 " -0.341 5.00e-02 4.00e+02 pdb=" CA PRO c 344 " 0.115 5.00e-02 4.00e+02 pdb=" CD PRO c 344 " 0.087 5.00e-02 4.00e+02 ... (remaining 10906 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 7 2.05 - 2.77: 12462 2.77 - 3.48: 90424 3.48 - 4.19: 142893 4.19 - 4.90: 246776 Nonbonded interactions: 492562 Sorted by model distance: nonbonded pdb=" O VAL g 323 " pdb=" CD1 LEU g 326 " model vdw 1.342 3.460 nonbonded pdb=" OD2 ASP a 225 " pdb=" NE2 HIS K 625 " model vdw 1.411 3.120 nonbonded pdb=" CG2 THR d 325 " pdb=" OG1 THR f 445 " model vdw 1.808 3.460 nonbonded pdb=" OE1 GLU g 330 " pdb=" OE1 GLU g 525 " model vdw 1.810 3.040 nonbonded pdb=" O GLU a 525 " pdb=" OD1 ASN a 528 " model vdw 1.826 3.040 ... (remaining 492557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 11 through 42) selection = (chain 'C' and resid 11 through 42) selection = (chain 'D' and resid 11 through 42) selection = (chain 'E' and resid 11 through 42) selection = (chain 'F' and resid 11 through 42) selection = (chain 'G' and resid 11 through 42) selection = (chain 'H' and resid 11 through 42) selection = chain 'I' selection = (chain 'J' and resid 11 through 42) } ncs_group { reference = (chain 'a' and (resid 43 through 61 or resid 63 through 675)) selection = (chain 'b' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'c' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'd' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'e' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'f' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'g' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'h' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'i' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'j' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 1.800 Check model and map are aligned: 0.340 Set scattering table: 0.410 Process input model: 116.180 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 61867 Z= 0.406 Angle : 0.862 21.432 84461 Z= 0.473 Chirality : 0.052 0.414 9924 Planarity : 0.008 0.206 10909 Dihedral : 14.827 89.751 22743 Min Nonbonded Distance : 1.342 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.92 % Favored : 90.85 % Rotamer: Outliers : 0.62 % Allowed : 0.74 % Favored : 98.63 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.91 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.09), residues: 7872 helix: -1.08 (0.10), residues: 2492 sheet: -1.69 (0.15), residues: 1040 loop : -1.52 (0.09), residues: 4340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP K 624 HIS 0.009 0.002 HIS f 106 PHE 0.027 0.002 PHE g 603 TYR 0.031 0.002 TYR d 143 ARG 0.011 0.001 ARG K 738 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1504 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 1462 time to evaluate : 5.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 VAL cc_start: 0.6869 (OUTLIER) cc_final: 0.6391 (p) REVERT: A 21 LYS cc_start: 0.9474 (mmmt) cc_final: 0.9205 (ttmm) REVERT: A 23 SER cc_start: 0.9111 (t) cc_final: 0.8376 (p) REVERT: A 35 SER cc_start: 0.9498 (m) cc_final: 0.8898 (t) REVERT: a 183 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8760 (tptp) REVERT: a 186 GLU cc_start: 0.8474 (pt0) cc_final: 0.8077 (pt0) REVERT: a 291 ASP cc_start: 0.8877 (t0) cc_final: 0.8201 (t0) REVERT: a 336 MET cc_start: 0.8862 (ttt) cc_final: 0.8379 (tmm) REVERT: a 404 PHE cc_start: 0.8974 (m-80) cc_final: 0.8746 (m-80) REVERT: a 502 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8223 (mm-30) REVERT: B 40 MET cc_start: 0.8353 (ttp) cc_final: 0.7722 (tmm) REVERT: b 221 ASP cc_start: 0.8969 (t70) cc_final: 0.8684 (t70) REVERT: b 518 LEU cc_start: 0.9204 (mt) cc_final: 0.8804 (mt) REVERT: b 541 ASP cc_start: 0.9022 (m-30) cc_final: 0.8721 (m-30) REVERT: b 619 SER cc_start: 0.9305 (t) cc_final: 0.9034 (p) REVERT: C 12 ASN cc_start: 0.8987 (t0) cc_final: 0.8352 (t0) REVERT: C 21 LYS cc_start: 0.9337 (ttpp) cc_final: 0.8954 (ttmm) REVERT: C 23 SER cc_start: 0.8494 (t) cc_final: 0.8232 (t) REVERT: c 66 MET cc_start: 0.8129 (ttm) cc_final: 0.7664 (ttp) REVERT: c 126 ASP cc_start: 0.8696 (m-30) cc_final: 0.7878 (t70) REVERT: c 250 MET cc_start: 0.8640 (tmm) cc_final: 0.8387 (tmm) REVERT: c 251 ASP cc_start: 0.9258 (t70) cc_final: 0.9007 (t0) REVERT: c 258 MET cc_start: 0.8167 (ptp) cc_final: 0.7911 (ptp) REVERT: c 341 MET cc_start: 0.7120 (mpp) cc_final: 0.6301 (mpp) REVERT: D 12 ASN cc_start: 0.9514 (t0) cc_final: 0.9100 (t0) REVERT: d 157 ASN cc_start: 0.8995 (t0) cc_final: 0.8783 (t0) REVERT: d 189 GLU cc_start: 0.7874 (tt0) cc_final: 0.7659 (tt0) REVERT: d 223 LEU cc_start: 0.9598 (mt) cc_final: 0.9374 (mp) REVERT: d 226 ASP cc_start: 0.8779 (p0) cc_final: 0.8417 (p0) REVERT: d 248 GLN cc_start: 0.9119 (mt0) cc_final: 0.8817 (mt0) REVERT: d 251 ASP cc_start: 0.8889 (t70) cc_final: 0.8682 (t0) REVERT: d 258 MET cc_start: 0.8504 (tpp) cc_final: 0.8297 (ttm) REVERT: d 284 LYS cc_start: 0.9640 (tptt) cc_final: 0.9414 (tptm) REVERT: d 291 ASP cc_start: 0.8779 (m-30) cc_final: 0.8515 (m-30) REVERT: E 12 ASN cc_start: 0.9205 (t0) cc_final: 0.8986 (t0) REVERT: E 13 VAL cc_start: 0.9526 (t) cc_final: 0.9287 (p) REVERT: e 66 MET cc_start: 0.7460 (mtt) cc_final: 0.7176 (mtt) REVERT: e 97 ASP cc_start: 0.8907 (p0) cc_final: 0.8493 (p0) REVERT: e 139 ASP cc_start: 0.8565 (m-30) cc_final: 0.8277 (m-30) REVERT: e 212 MET cc_start: 0.9127 (tpp) cc_final: 0.8612 (tpp) REVERT: e 251 ASP cc_start: 0.8971 (t70) cc_final: 0.8585 (t70) REVERT: e 253 SER cc_start: 0.9388 (m) cc_final: 0.8953 (t) REVERT: e 287 GLU cc_start: 0.8740 (pt0) cc_final: 0.8249 (pt0) REVERT: e 336 MET cc_start: 0.9204 (tmm) cc_final: 0.8763 (tpt) REVERT: e 341 MET cc_start: 0.8141 (pmm) cc_final: 0.7870 (pmm) REVERT: F 35 SER cc_start: 0.9141 (t) cc_final: 0.8825 (p) REVERT: f 187 LYS cc_start: 0.8893 (tptp) cc_final: 0.7953 (tptp) REVERT: f 251 ASP cc_start: 0.9084 (t70) cc_final: 0.8146 (t0) REVERT: f 254 GLU cc_start: 0.8795 (mp0) cc_final: 0.8151 (mp0) REVERT: G 16 ASP cc_start: 0.8903 (p0) cc_final: 0.8699 (p0) REVERT: g 49 ILE cc_start: 0.9584 (tp) cc_final: 0.9379 (tp) REVERT: g 64 ARG cc_start: 0.8427 (ptm-80) cc_final: 0.7820 (mmt180) REVERT: g 260 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8301 (tp30) REVERT: g 284 LYS cc_start: 0.9632 (tptt) cc_final: 0.9429 (tppt) REVERT: g 329 ASP cc_start: 0.9134 (OUTLIER) cc_final: 0.8813 (p0) REVERT: g 341 MET cc_start: 0.7525 (ptt) cc_final: 0.6826 (ptt) REVERT: g 598 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7725 (mtm-85) REVERT: g 645 LYS cc_start: 0.9565 (mtpt) cc_final: 0.9361 (mtmt) REVERT: H 25 GLU cc_start: 0.8662 (mp0) cc_final: 0.8402 (pm20) REVERT: H 35 SER cc_start: 0.9290 (t) cc_final: 0.8980 (t) REVERT: h 116 MET cc_start: 0.9025 (mtt) cc_final: 0.8763 (mtm) REVERT: h 199 LEU cc_start: 0.9105 (pp) cc_final: 0.8875 (pp) REVERT: h 251 ASP cc_start: 0.8686 (t0) cc_final: 0.8373 (t0) REVERT: h 404 PHE cc_start: 0.9196 (m-10) cc_final: 0.8831 (m-10) REVERT: h 483 MET cc_start: 0.9294 (tpt) cc_final: 0.9054 (tpp) REVERT: h 518 LEU cc_start: 0.9446 (mp) cc_final: 0.8989 (mt) REVERT: I 12 ASN cc_start: 0.9324 (t0) cc_final: 0.9047 (t0) REVERT: i 98 GLU cc_start: 0.7748 (pm20) cc_final: 0.7440 (pm20) REVERT: i 126 ASP cc_start: 0.7068 (t0) cc_final: 0.6639 (m-30) REVERT: i 161 LYS cc_start: 0.9670 (mmmt) cc_final: 0.9429 (mmmm) REVERT: i 183 LYS cc_start: 0.9644 (tptp) cc_final: 0.9192 (tptm) REVERT: i 212 MET cc_start: 0.8829 (tpp) cc_final: 0.8532 (tpp) REVERT: i 251 ASP cc_start: 0.8930 (t0) cc_final: 0.8667 (t0) REVERT: i 326 LEU cc_start: 0.9645 (mm) cc_final: 0.9405 (mp) REVERT: i 361 LEU cc_start: 0.9188 (mp) cc_final: 0.8966 (mp) REVERT: i 483 MET cc_start: 0.9118 (tmm) cc_final: 0.8861 (tmm) REVERT: i 512 GLU cc_start: 0.8711 (pp20) cc_final: 0.8403 (pp20) REVERT: i 559 ASP cc_start: 0.8628 (m-30) cc_final: 0.8283 (t0) REVERT: J 12 ASN cc_start: 0.9217 (t0) cc_final: 0.8922 (p0) REVERT: j 183 LYS cc_start: 0.5812 (mmtm) cc_final: 0.5280 (tppt) REVERT: j 223 LEU cc_start: 0.9575 (mt) cc_final: 0.9280 (mt) REVERT: j 250 MET cc_start: 0.8905 (ttp) cc_final: 0.8642 (tmm) REVERT: j 253 SER cc_start: 0.9332 (m) cc_final: 0.8783 (t) REVERT: j 254 GLU cc_start: 0.8230 (pm20) cc_final: 0.7935 (pm20) REVERT: j 336 MET cc_start: 0.9062 (tmm) cc_final: 0.8573 (tmm) REVERT: j 337 ILE cc_start: 0.9446 (mt) cc_final: 0.9062 (tp) REVERT: j 553 ASP cc_start: 0.8807 (t70) cc_final: 0.8536 (t0) REVERT: j 636 ARG cc_start: 0.5542 (ttp-170) cc_final: 0.4442 (tmt-80) REVERT: j 655 GLU cc_start: 0.9050 (pt0) cc_final: 0.8783 (mt-10) REVERT: K 33 ASP cc_start: 0.8913 (m-30) cc_final: 0.8620 (m-30) REVERT: K 69 ASP cc_start: 0.8549 (t70) cc_final: 0.7810 (t0) REVERT: K 95 TYR cc_start: 0.4896 (t80) cc_final: 0.3937 (t80) REVERT: K 96 GLU cc_start: 0.9386 (tp30) cc_final: 0.9105 (tp30) REVERT: K 130 TYR cc_start: 0.4794 (p90) cc_final: 0.4043 (p90) REVERT: K 142 MET cc_start: 0.8726 (mmm) cc_final: 0.8439 (tpt) REVERT: K 182 ASP cc_start: 0.8453 (m-30) cc_final: 0.8247 (m-30) REVERT: K 242 VAL cc_start: 0.9458 (m) cc_final: 0.8945 (p) REVERT: K 253 ASP cc_start: 0.9181 (m-30) cc_final: 0.8930 (m-30) REVERT: K 367 TYR cc_start: 0.8752 (t80) cc_final: 0.8446 (t80) REVERT: K 384 LEU cc_start: 0.9236 (mt) cc_final: 0.8859 (mp) REVERT: K 409 GLU cc_start: 0.8380 (tp30) cc_final: 0.8166 (tp30) REVERT: K 462 ASP cc_start: 0.9007 (m-30) cc_final: 0.8533 (m-30) REVERT: K 537 LYS cc_start: 0.9405 (mmtm) cc_final: 0.9050 (mmtt) REVERT: K 615 LYS cc_start: 0.9283 (tttm) cc_final: 0.8867 (ttpp) REVERT: K 704 THR cc_start: 0.7519 (OUTLIER) cc_final: 0.7163 (m) REVERT: K 736 ASN cc_start: 0.8548 (t0) cc_final: 0.8251 (m-40) REVERT: K 824 VAL cc_start: 0.9479 (m) cc_final: 0.8503 (p) REVERT: K 856 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8568 (mp10) REVERT: K 901 MET cc_start: 0.7212 (mtp) cc_final: 0.7000 (ttm) REVERT: K 941 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8953 (pm20) REVERT: K 954 PHE cc_start: 0.8968 (m-80) cc_final: 0.8449 (m-10) REVERT: K 1048 ASN cc_start: 0.8423 (t0) cc_final: 0.8063 (p0) REVERT: K 1095 ASP cc_start: 0.9067 (m-30) cc_final: 0.8845 (m-30) outliers start: 42 outliers final: 15 residues processed: 1486 average time/residue: 0.5801 time to fit residues: 1455.7815 Evaluate side-chains 946 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 928 time to evaluate : 5.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain a residue 327 ARG Chi-restraints excluded: chain a residue 339 LYS Chi-restraints excluded: chain b residue 359 LEU Chi-restraints excluded: chain c residue 327 ARG Chi-restraints excluded: chain d residue 326 LEU Chi-restraints excluded: chain d residue 327 ARG Chi-restraints excluded: chain d residue 359 LEU Chi-restraints excluded: chain e residue 359 LEU Chi-restraints excluded: chain f residue 359 LEU Chi-restraints excluded: chain g residue 326 LEU Chi-restraints excluded: chain g residue 328 ILE Chi-restraints excluded: chain g residue 329 ASP Chi-restraints excluded: chain g residue 359 LEU Chi-restraints excluded: chain h residue 343 THR Chi-restraints excluded: chain h residue 359 LEU Chi-restraints excluded: chain K residue 704 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 663 optimal weight: 8.9990 chunk 595 optimal weight: 9.9990 chunk 330 optimal weight: 0.0770 chunk 203 optimal weight: 4.9990 chunk 401 optimal weight: 0.9990 chunk 318 optimal weight: 6.9990 chunk 616 optimal weight: 0.0670 chunk 238 optimal weight: 7.9990 chunk 374 optimal weight: 5.9990 chunk 458 optimal weight: 10.0000 chunk 713 optimal weight: 9.9990 overall best weight: 2.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 121 ASN a 160 GLN a 179 GLN ** a 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 613 GLN b 288 GLN c 110 ASN ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 288 GLN ** c 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 564 ASN D 42 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 154 GLN ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 288 GLN e 358 HIS e 429 GLN e 564 ASN e 623 ASN f 571 GLN ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 110 ASN h 213 GLN h 288 GLN h 569 GLN h 623 ASN i 179 GLN ** i 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 576 GLN i 658 GLN j 110 ASN j 405 GLN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 321 GLN ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1245 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 61867 Z= 0.233 Angle : 0.728 16.923 84461 Z= 0.376 Chirality : 0.049 0.238 9924 Planarity : 0.007 0.169 10909 Dihedral : 5.971 58.522 8567 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 1.66 % Allowed : 10.76 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.09), residues: 7872 helix: 0.12 (0.10), residues: 2598 sheet: -1.37 (0.14), residues: 1198 loop : -1.22 (0.10), residues: 4076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP K 624 HIS 0.006 0.001 HIS K 625 PHE 0.020 0.002 PHE h 410 TYR 0.025 0.001 TYR d 95 ARG 0.014 0.001 ARG h 598 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1110 time to evaluate : 5.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.9343 (m) cc_final: 0.8915 (t) REVERT: A 37 SER cc_start: 0.9409 (t) cc_final: 0.9057 (p) REVERT: a 250 MET cc_start: 0.8958 (tpp) cc_final: 0.8685 (tpp) REVERT: a 336 MET cc_start: 0.8928 (ttt) cc_final: 0.8612 (tmm) REVERT: a 341 MET cc_start: 0.7967 (ptm) cc_final: 0.7308 (mmm) REVERT: a 461 ASP cc_start: 0.9050 (m-30) cc_final: 0.8832 (p0) REVERT: b 179 GLN cc_start: 0.9097 (tt0) cc_final: 0.8850 (tt0) REVERT: b 212 MET cc_start: 0.9086 (mmm) cc_final: 0.8847 (mmm) REVERT: b 221 ASP cc_start: 0.9064 (t70) cc_final: 0.8833 (t70) REVERT: b 275 SER cc_start: 0.9331 (OUTLIER) cc_final: 0.8429 (t) REVERT: b 541 ASP cc_start: 0.8829 (m-30) cc_final: 0.8522 (m-30) REVERT: b 548 GLU cc_start: 0.8648 (tp30) cc_final: 0.8437 (tp30) REVERT: b 559 ASP cc_start: 0.9079 (m-30) cc_final: 0.8795 (p0) REVERT: b 560 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8530 (mm-30) REVERT: C 12 ASN cc_start: 0.9040 (t0) cc_final: 0.8417 (t0) REVERT: C 25 GLU cc_start: 0.9070 (mp0) cc_final: 0.8792 (mp0) REVERT: C 40 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7639 (ttt) REVERT: c 116 MET cc_start: 0.9314 (mpp) cc_final: 0.8767 (mpp) REVERT: c 250 MET cc_start: 0.8532 (tmm) cc_final: 0.8202 (tmm) REVERT: c 251 ASP cc_start: 0.9201 (t70) cc_final: 0.8904 (t0) REVERT: c 294 THR cc_start: 0.9363 (m) cc_final: 0.9128 (p) REVERT: c 464 MET cc_start: 0.9241 (mmm) cc_final: 0.8882 (mmm) REVERT: c 611 ILE cc_start: 0.9338 (mm) cc_final: 0.9061 (mm) REVERT: D 12 ASN cc_start: 0.9512 (t0) cc_final: 0.9078 (t0) REVERT: D 25 GLU cc_start: 0.8982 (mp0) cc_final: 0.8749 (mp0) REVERT: D 26 THR cc_start: 0.8660 (p) cc_final: 0.8326 (t) REVERT: d 154 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.9160 (pp30) REVERT: d 157 ASN cc_start: 0.8978 (t0) cc_final: 0.8669 (t0) REVERT: d 176 ASP cc_start: 0.8998 (m-30) cc_final: 0.8781 (m-30) REVERT: d 221 ASP cc_start: 0.8995 (t0) cc_final: 0.8713 (t0) REVERT: d 226 ASP cc_start: 0.8795 (p0) cc_final: 0.8463 (p0) REVERT: d 250 MET cc_start: 0.9109 (tpt) cc_final: 0.8669 (tpp) REVERT: d 258 MET cc_start: 0.8476 (tpp) cc_final: 0.7859 (ttm) REVERT: d 260 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8490 (mm-30) REVERT: d 287 GLU cc_start: 0.9026 (tt0) cc_final: 0.8777 (tt0) REVERT: d 291 ASP cc_start: 0.8626 (m-30) cc_final: 0.8384 (m-30) REVERT: d 341 MET cc_start: 0.6603 (ptp) cc_final: 0.3319 (ptp) REVERT: d 376 MET cc_start: 0.8622 (tpp) cc_final: 0.8059 (tpt) REVERT: E 12 ASN cc_start: 0.9377 (t0) cc_final: 0.8885 (t0) REVERT: e 66 MET cc_start: 0.7435 (mtt) cc_final: 0.7120 (mtt) REVERT: e 98 GLU cc_start: 0.8675 (pm20) cc_final: 0.8422 (pm20) REVERT: e 223 LEU cc_start: 0.9710 (mt) cc_final: 0.9404 (mp) REVERT: e 336 MET cc_start: 0.9277 (tmm) cc_final: 0.8677 (tpp) REVERT: F 35 SER cc_start: 0.8940 (t) cc_final: 0.8517 (p) REVERT: f 73 GLU cc_start: 0.8783 (mp0) cc_final: 0.8487 (mp0) REVERT: f 123 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8076 (mm-30) REVERT: f 251 ASP cc_start: 0.8918 (t70) cc_final: 0.8340 (t0) REVERT: f 254 GLU cc_start: 0.8826 (mp0) cc_final: 0.8405 (mp0) REVERT: f 287 GLU cc_start: 0.8923 (tp30) cc_final: 0.8560 (tp30) REVERT: f 495 MET cc_start: 0.8218 (mmm) cc_final: 0.7455 (mmp) REVERT: f 548 GLU cc_start: 0.9176 (tp30) cc_final: 0.8927 (tp30) REVERT: f 639 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8657 (p) REVERT: g 64 ARG cc_start: 0.8583 (ptm-80) cc_final: 0.7772 (mmt180) REVERT: g 115 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: g 260 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8347 (tp30) REVERT: g 290 MET cc_start: 0.9190 (mtm) cc_final: 0.8968 (mtp) REVERT: g 330 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6946 (mt-10) REVERT: g 376 MET cc_start: 0.8856 (tpp) cc_final: 0.8621 (tpp) REVERT: g 529 THR cc_start: 0.5034 (p) cc_final: 0.4358 (p) REVERT: H 21 LYS cc_start: 0.9336 (ttmm) cc_final: 0.9019 (mtpt) REVERT: H 25 GLU cc_start: 0.8803 (mp0) cc_final: 0.8518 (pm20) REVERT: h 221 ASP cc_start: 0.9126 (m-30) cc_final: 0.8903 (t0) REVERT: h 251 ASP cc_start: 0.8409 (t0) cc_final: 0.8202 (t0) REVERT: h 404 PHE cc_start: 0.9232 (m-10) cc_final: 0.8916 (m-10) REVERT: I 12 ASN cc_start: 0.9369 (t0) cc_final: 0.8963 (t0) REVERT: i 98 GLU cc_start: 0.7887 (pm20) cc_final: 0.7590 (pm20) REVERT: i 126 ASP cc_start: 0.6986 (t0) cc_final: 0.6545 (m-30) REVERT: i 161 LYS cc_start: 0.9620 (mmmt) cc_final: 0.9393 (mmmm) REVERT: i 212 MET cc_start: 0.8456 (tpp) cc_final: 0.8229 (tpp) REVERT: i 223 LEU cc_start: 0.9704 (mm) cc_final: 0.9463 (mt) REVERT: i 251 ASP cc_start: 0.9071 (t0) cc_final: 0.8539 (t0) REVERT: i 254 GLU cc_start: 0.9097 (mp0) cc_final: 0.8743 (mp0) REVERT: i 376 MET cc_start: 0.8885 (tpp) cc_final: 0.8501 (mmm) REVERT: i 483 MET cc_start: 0.9099 (tmm) cc_final: 0.8741 (tmm) REVERT: i 512 GLU cc_start: 0.8671 (pp20) cc_final: 0.8462 (pp20) REVERT: i 559 ASP cc_start: 0.8574 (m-30) cc_final: 0.8164 (t0) REVERT: i 572 LEU cc_start: 0.9576 (mt) cc_final: 0.9373 (mt) REVERT: J 12 ASN cc_start: 0.9269 (t0) cc_final: 0.8743 (p0) REVERT: j 106 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.7827 (t-90) REVERT: j 183 LYS cc_start: 0.5903 (mmtm) cc_final: 0.5107 (tppt) REVERT: j 212 MET cc_start: 0.8587 (tpp) cc_final: 0.8296 (tpp) REVERT: j 223 LEU cc_start: 0.9493 (mt) cc_final: 0.9173 (mt) REVERT: j 250 MET cc_start: 0.8882 (ttp) cc_final: 0.8651 (tmm) REVERT: j 253 SER cc_start: 0.9373 (m) cc_final: 0.8831 (t) REVERT: j 539 MET cc_start: 0.9286 (tpp) cc_final: 0.8864 (tpt) REVERT: j 572 LEU cc_start: 0.9794 (mt) cc_final: 0.9587 (mt) REVERT: j 632 LYS cc_start: 0.9299 (mtmm) cc_final: 0.8764 (tptt) REVERT: j 636 ARG cc_start: 0.5299 (ttp-170) cc_final: 0.4710 (tmt-80) REVERT: K 33 ASP cc_start: 0.9004 (m-30) cc_final: 0.8657 (m-30) REVERT: K 69 ASP cc_start: 0.8640 (t70) cc_final: 0.8319 (t0) REVERT: K 95 TYR cc_start: 0.4801 (t80) cc_final: 0.3822 (t80) REVERT: K 96 GLU cc_start: 0.9392 (tp30) cc_final: 0.9050 (tp30) REVERT: K 142 MET cc_start: 0.8949 (mmm) cc_final: 0.8613 (tpt) REVERT: K 182 ASP cc_start: 0.8710 (m-30) cc_final: 0.7995 (m-30) REVERT: K 253 ASP cc_start: 0.9282 (m-30) cc_final: 0.8965 (m-30) REVERT: K 325 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8722 (ptp-110) REVERT: K 409 GLU cc_start: 0.8375 (tp30) cc_final: 0.7991 (tp30) REVERT: K 413 MET cc_start: 0.9124 (mmm) cc_final: 0.8763 (mmm) REVERT: K 462 ASP cc_start: 0.9024 (m-30) cc_final: 0.8677 (m-30) REVERT: K 594 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9375 (mp) REVERT: K 615 LYS cc_start: 0.9034 (tttm) cc_final: 0.8680 (ttpp) REVERT: K 814 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8438 (tm-30) REVERT: K 856 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8458 (mp10) REVERT: K 901 MET cc_start: 0.7776 (mtp) cc_final: 0.7530 (ttm) REVERT: K 954 PHE cc_start: 0.8686 (m-80) cc_final: 0.8211 (m-10) REVERT: K 1048 ASN cc_start: 0.8457 (t0) cc_final: 0.8024 (p0) REVERT: K 1095 ASP cc_start: 0.9034 (m-30) cc_final: 0.8761 (m-30) outliers start: 112 outliers final: 51 residues processed: 1165 average time/residue: 0.5729 time to fit residues: 1161.4702 Evaluate side-chains 968 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 909 time to evaluate : 5.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain a residue 231 ARG Chi-restraints excluded: chain a residue 339 LYS Chi-restraints excluded: chain a residue 552 ILE Chi-restraints excluded: chain a residue 640 LEU Chi-restraints excluded: chain a residue 651 LEU Chi-restraints excluded: chain b residue 275 SER Chi-restraints excluded: chain b residue 359 LEU Chi-restraints excluded: chain b residue 550 ILE Chi-restraints excluded: chain b residue 665 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain c residue 90 SER Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain c residue 262 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain d residue 154 GLN Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain d residue 359 LEU Chi-restraints excluded: chain d residue 403 VAL Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain e residue 176 ASP Chi-restraints excluded: chain e residue 359 LEU Chi-restraints excluded: chain e residue 403 VAL Chi-restraints excluded: chain e residue 610 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain f residue 253 SER Chi-restraints excluded: chain f residue 301 ILE Chi-restraints excluded: chain f residue 359 LEU Chi-restraints excluded: chain f residue 553 ASP Chi-restraints excluded: chain f residue 639 SER Chi-restraints excluded: chain g residue 115 GLU Chi-restraints excluded: chain g residue 328 ILE Chi-restraints excluded: chain g residue 359 LEU Chi-restraints excluded: chain g residue 509 VAL Chi-restraints excluded: chain g residue 541 ASP Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain h residue 279 LEU Chi-restraints excluded: chain h residue 359 LEU Chi-restraints excluded: chain h residue 527 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain j residue 106 HIS Chi-restraints excluded: chain j residue 574 ILE Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 325 ARG Chi-restraints excluded: chain K residue 478 ILE Chi-restraints excluded: chain K residue 583 ASP Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain K residue 706 ILE Chi-restraints excluded: chain K residue 984 LEU Chi-restraints excluded: chain K residue 1018 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 396 optimal weight: 10.0000 chunk 221 optimal weight: 20.0000 chunk 594 optimal weight: 9.9990 chunk 486 optimal weight: 0.0870 chunk 196 optimal weight: 8.9990 chunk 715 optimal weight: 9.9990 chunk 772 optimal weight: 20.0000 chunk 636 optimal weight: 0.9990 chunk 709 optimal weight: 20.0000 chunk 243 optimal weight: 3.9990 chunk 573 optimal weight: 30.0000 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN ** a 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 288 GLN ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 202 ASN ** c 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 342 ASN ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 196 GLN g 196 GLN g 288 GLN ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 659 ASN ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 346 GLN ** i 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 458 ASN ** j 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 405 GLN K 49 GLN K 58 GLN K 267 ASN ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 61867 Z= 0.248 Angle : 0.660 13.208 84461 Z= 0.337 Chirality : 0.047 0.275 9924 Planarity : 0.006 0.151 10909 Dihedral : 5.294 54.725 8544 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 2.03 % Allowed : 13.67 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.09), residues: 7872 helix: 0.67 (0.10), residues: 2573 sheet: -1.37 (0.14), residues: 1276 loop : -1.06 (0.10), residues: 4023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 624 HIS 0.007 0.001 HIS h 106 PHE 0.024 0.001 PHE K 188 TYR 0.028 0.001 TYR e 137 ARG 0.008 0.001 ARG K 757 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 954 time to evaluate : 5.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.9422 (m) cc_final: 0.8829 (t) REVERT: A 37 SER cc_start: 0.9467 (t) cc_final: 0.9233 (p) REVERT: a 189 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7955 (tm-30) REVERT: a 212 MET cc_start: 0.8780 (tpt) cc_final: 0.8483 (tpp) REVERT: a 231 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8780 (mtt90) REVERT: a 250 MET cc_start: 0.8891 (tpp) cc_final: 0.8589 (tpp) REVERT: a 341 MET cc_start: 0.7811 (ptm) cc_final: 0.7578 (mmm) REVERT: a 461 ASP cc_start: 0.9194 (m-30) cc_final: 0.8970 (t0) REVERT: a 548 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8622 (pm20) REVERT: B 27 SER cc_start: 0.9277 (m) cc_final: 0.9038 (t) REVERT: b 80 ASP cc_start: 0.4681 (p0) cc_final: 0.4018 (p0) REVERT: b 207 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: b 464 MET cc_start: 0.9278 (tpp) cc_final: 0.9014 (tpp) REVERT: b 492 LEU cc_start: 0.9091 (tp) cc_final: 0.8819 (tp) REVERT: b 541 ASP cc_start: 0.8822 (m-30) cc_final: 0.8581 (m-30) REVERT: b 560 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8990 (mm-30) REVERT: C 12 ASN cc_start: 0.9135 (t0) cc_final: 0.8514 (t0) REVERT: C 25 GLU cc_start: 0.9142 (mp0) cc_final: 0.8914 (mp0) REVERT: C 33 SER cc_start: 0.9423 (p) cc_final: 0.9086 (t) REVERT: C 40 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7686 (ttt) REVERT: c 93 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8307 (m) REVERT: c 250 MET cc_start: 0.8593 (tmm) cc_final: 0.8186 (tmm) REVERT: c 294 THR cc_start: 0.9387 (m) cc_final: 0.9123 (p) REVERT: c 376 MET cc_start: 0.9450 (mmm) cc_final: 0.8515 (tmm) REVERT: c 611 ILE cc_start: 0.9326 (mm) cc_final: 0.9073 (mm) REVERT: D 12 ASN cc_start: 0.9509 (t0) cc_final: 0.9046 (t0) REVERT: D 25 GLU cc_start: 0.9034 (mp0) cc_final: 0.8785 (mp0) REVERT: D 26 THR cc_start: 0.8740 (p) cc_final: 0.8270 (t) REVERT: d 154 GLN cc_start: 0.9434 (OUTLIER) cc_final: 0.9210 (pp30) REVERT: d 176 ASP cc_start: 0.9092 (m-30) cc_final: 0.8881 (m-30) REVERT: d 226 ASP cc_start: 0.8782 (p0) cc_final: 0.8432 (p0) REVERT: d 250 MET cc_start: 0.9114 (tpt) cc_final: 0.8760 (tpp) REVERT: d 370 LEU cc_start: 0.9562 (tp) cc_final: 0.9358 (tp) REVERT: d 376 MET cc_start: 0.8585 (tpp) cc_final: 0.8286 (tpt) REVERT: E 12 ASN cc_start: 0.9262 (t0) cc_final: 0.8856 (t0) REVERT: E 40 MET cc_start: 0.8125 (ppp) cc_final: 0.7852 (ppp) REVERT: e 66 MET cc_start: 0.7878 (mtt) cc_final: 0.7560 (mtt) REVERT: e 97 ASP cc_start: 0.8907 (p0) cc_final: 0.8528 (p0) REVERT: e 98 GLU cc_start: 0.8655 (pm20) cc_final: 0.8338 (pm20) REVERT: e 223 LEU cc_start: 0.9700 (mt) cc_final: 0.9393 (mp) REVERT: e 336 MET cc_start: 0.9301 (tmm) cc_final: 0.9024 (tpp) REVERT: e 629 GLN cc_start: 0.8925 (mp10) cc_final: 0.8720 (mp10) REVERT: F 35 SER cc_start: 0.8995 (t) cc_final: 0.8684 (p) REVERT: f 123 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8176 (mm-30) REVERT: f 251 ASP cc_start: 0.8985 (t70) cc_final: 0.8361 (t0) REVERT: f 254 GLU cc_start: 0.8783 (mp0) cc_final: 0.8249 (mp0) REVERT: f 632 LYS cc_start: 0.9409 (mtpp) cc_final: 0.9152 (mtpp) REVERT: f 669 SER cc_start: 0.9410 (m) cc_final: 0.9080 (p) REVERT: G 42 ASN cc_start: 0.8873 (t0) cc_final: 0.8476 (t0) REVERT: g 64 ARG cc_start: 0.8781 (ptm-80) cc_final: 0.7676 (mmt180) REVERT: g 260 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8420 (tp30) REVERT: g 287 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8819 (mt-10) REVERT: g 502 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8724 (mp0) REVERT: g 548 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8883 (mm-30) REVERT: H 21 LYS cc_start: 0.9363 (ttmm) cc_final: 0.9129 (mttt) REVERT: H 25 GLU cc_start: 0.9001 (mp0) cc_final: 0.8588 (pm20) REVERT: I 12 ASN cc_start: 0.9439 (t0) cc_final: 0.9186 (t0) REVERT: i 98 GLU cc_start: 0.8066 (pm20) cc_final: 0.7746 (pm20) REVERT: i 126 ASP cc_start: 0.6947 (t0) cc_final: 0.6471 (m-30) REVERT: i 161 LYS cc_start: 0.9649 (mmmt) cc_final: 0.9383 (mmmm) REVERT: i 251 ASP cc_start: 0.9150 (t0) cc_final: 0.8488 (t0) REVERT: i 254 GLU cc_start: 0.9059 (mp0) cc_final: 0.8554 (mp0) REVERT: i 458 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.7957 (p0) REVERT: i 502 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8064 (mt-10) REVERT: i 512 GLU cc_start: 0.8683 (pp20) cc_final: 0.8473 (pp20) REVERT: i 559 ASP cc_start: 0.8633 (m-30) cc_final: 0.8268 (t0) REVERT: J 12 ASN cc_start: 0.9291 (t0) cc_final: 0.9035 (t0) REVERT: j 54 GLU cc_start: 0.8547 (pp20) cc_final: 0.8217 (tm-30) REVERT: j 106 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.7365 (t-90) REVERT: j 183 LYS cc_start: 0.5803 (mmtm) cc_final: 0.5526 (tppt) REVERT: j 250 MET cc_start: 0.8974 (ttp) cc_final: 0.8622 (tmm) REVERT: j 341 MET cc_start: 0.7101 (ppp) cc_final: 0.6709 (ppp) REVERT: j 376 MET cc_start: 0.8970 (tpp) cc_final: 0.8419 (tpp) REVERT: j 539 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8814 (tpp) REVERT: j 632 LYS cc_start: 0.9385 (mtmm) cc_final: 0.8887 (tptt) REVERT: j 636 ARG cc_start: 0.5181 (ttp-170) cc_final: 0.4947 (tmm160) REVERT: K 33 ASP cc_start: 0.9156 (m-30) cc_final: 0.8709 (m-30) REVERT: K 44 LYS cc_start: 0.9279 (tppt) cc_final: 0.9062 (tptp) REVERT: K 69 ASP cc_start: 0.8596 (t70) cc_final: 0.8271 (t0) REVERT: K 95 TYR cc_start: 0.5032 (t80) cc_final: 0.4761 (t80) REVERT: K 96 GLU cc_start: 0.9372 (tp30) cc_final: 0.9057 (tp30) REVERT: K 142 MET cc_start: 0.9072 (mmm) cc_final: 0.8772 (tpp) REVERT: K 182 ASP cc_start: 0.8924 (m-30) cc_final: 0.8033 (p0) REVERT: K 253 ASP cc_start: 0.9362 (m-30) cc_final: 0.9095 (m-30) REVERT: K 325 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8938 (ptp-110) REVERT: K 409 GLU cc_start: 0.8519 (tp30) cc_final: 0.7941 (tp30) REVERT: K 413 MET cc_start: 0.9093 (mmm) cc_final: 0.8520 (mmm) REVERT: K 464 ASP cc_start: 0.9432 (p0) cc_final: 0.9199 (p0) REVERT: K 537 LYS cc_start: 0.9442 (mmtm) cc_final: 0.9235 (mptt) REVERT: K 838 GLU cc_start: 0.8931 (tt0) cc_final: 0.8449 (pt0) REVERT: K 856 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8389 (mp10) REVERT: K 901 MET cc_start: 0.8098 (mtp) cc_final: 0.7635 (ttm) REVERT: K 963 MET cc_start: 0.8271 (mpp) cc_final: 0.7911 (mpp) REVERT: K 1048 ASN cc_start: 0.8504 (t0) cc_final: 0.8022 (p0) REVERT: K 1072 MET cc_start: 0.8855 (mmm) cc_final: 0.8547 (mmm) REVERT: K 1095 ASP cc_start: 0.9012 (m-30) cc_final: 0.8802 (m-30) outliers start: 137 outliers final: 75 residues processed: 1038 average time/residue: 0.5556 time to fit residues: 1005.0327 Evaluate side-chains 942 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 856 time to evaluate : 5.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain a residue 231 ARG Chi-restraints excluded: chain a residue 339 LYS Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 548 GLU Chi-restraints excluded: chain a residue 651 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain b residue 105 GLU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 207 GLU Chi-restraints excluded: chain b residue 275 SER Chi-restraints excluded: chain b residue 359 LEU Chi-restraints excluded: chain b residue 527 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain c residue 90 SER Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain c residue 262 VAL Chi-restraints excluded: chain c residue 368 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain d residue 80 ASP Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 154 GLN Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain d residue 223 LEU Chi-restraints excluded: chain d residue 268 SER Chi-restraints excluded: chain d residue 359 LEU Chi-restraints excluded: chain d residue 403 VAL Chi-restraints excluded: chain d residue 546 ILE Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain e residue 359 LEU Chi-restraints excluded: chain e residue 403 VAL Chi-restraints excluded: chain e residue 610 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain f residue 138 SER Chi-restraints excluded: chain f residue 234 LYS Chi-restraints excluded: chain f residue 253 SER Chi-restraints excluded: chain f residue 301 ILE Chi-restraints excluded: chain f residue 359 LEU Chi-restraints excluded: chain f residue 446 THR Chi-restraints excluded: chain f residue 610 ILE Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 192 LEU Chi-restraints excluded: chain g residue 287 GLU Chi-restraints excluded: chain g residue 328 ILE Chi-restraints excluded: chain g residue 359 LEU Chi-restraints excluded: chain g residue 509 VAL Chi-restraints excluded: chain g residue 541 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain h residue 292 LEU Chi-restraints excluded: chain h residue 359 LEU Chi-restraints excluded: chain h residue 527 LEU Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain i residue 327 ARG Chi-restraints excluded: chain i residue 458 ASN Chi-restraints excluded: chain i residue 459 LYS Chi-restraints excluded: chain i residue 471 THR Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain j residue 106 HIS Chi-restraints excluded: chain j residue 187 LYS Chi-restraints excluded: chain j residue 359 LEU Chi-restraints excluded: chain j residue 539 MET Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 325 ARG Chi-restraints excluded: chain K residue 682 GLU Chi-restraints excluded: chain K residue 706 ILE Chi-restraints excluded: chain K residue 708 THR Chi-restraints excluded: chain K residue 824 VAL Chi-restraints excluded: chain K residue 860 CYS Chi-restraints excluded: chain K residue 1018 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 706 optimal weight: 4.9990 chunk 537 optimal weight: 0.5980 chunk 371 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 341 optimal weight: 9.9990 chunk 480 optimal weight: 5.9990 chunk 717 optimal weight: 30.0000 chunk 759 optimal weight: 20.0000 chunk 374 optimal weight: 10.0000 chunk 680 optimal weight: 10.0000 chunk 204 optimal weight: 0.9980 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 613 GLN b 179 GLN b 358 HIS ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 154 GLN d 202 ASN ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 121 ASN ** i 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 458 ASN j 196 GLN ** j 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 61867 Z= 0.231 Angle : 0.635 11.819 84461 Z= 0.324 Chirality : 0.046 0.188 9924 Planarity : 0.006 0.136 10909 Dihedral : 5.120 59.971 8544 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.39 % Rotamer: Outliers : 2.09 % Allowed : 15.35 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.10), residues: 7872 helix: 0.87 (0.10), residues: 2591 sheet: -1.42 (0.13), residues: 1316 loop : -0.89 (0.10), residues: 3965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 624 HIS 0.007 0.001 HIS a 106 PHE 0.025 0.001 PHE K 188 TYR 0.021 0.001 TYR d 95 ARG 0.007 0.000 ARG K 757 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 914 time to evaluate : 5.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.9320 (m) cc_final: 0.8804 (t) REVERT: a 189 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8212 (tm-30) REVERT: a 212 MET cc_start: 0.8822 (tpt) cc_final: 0.8326 (tpp) REVERT: a 231 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8800 (mtt90) REVERT: a 250 MET cc_start: 0.8906 (tpp) cc_final: 0.8627 (tpp) REVERT: a 336 MET cc_start: 0.9078 (tmm) cc_final: 0.8480 (tpp) REVERT: a 461 ASP cc_start: 0.9240 (m-30) cc_final: 0.9017 (t0) REVERT: a 548 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8635 (pm20) REVERT: b 115 GLU cc_start: 0.8602 (tt0) cc_final: 0.8170 (tm-30) REVERT: b 299 GLU cc_start: 0.9070 (mp0) cc_final: 0.8695 (mp0) REVERT: b 376 MET cc_start: 0.9287 (mmm) cc_final: 0.8203 (tmm) REVERT: b 464 MET cc_start: 0.9238 (tpp) cc_final: 0.8936 (tpp) REVERT: b 541 ASP cc_start: 0.8864 (m-30) cc_final: 0.8651 (m-30) REVERT: b 548 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8426 (tm-30) REVERT: b 560 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8961 (mm-30) REVERT: C 12 ASN cc_start: 0.9136 (t0) cc_final: 0.8506 (t0) REVERT: C 25 GLU cc_start: 0.9163 (mp0) cc_final: 0.8911 (mp0) REVERT: C 33 SER cc_start: 0.9412 (p) cc_final: 0.9085 (t) REVERT: C 40 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7567 (ttt) REVERT: c 73 GLU cc_start: 0.7901 (tp30) cc_final: 0.7691 (tp30) REVERT: c 250 MET cc_start: 0.8674 (tmm) cc_final: 0.8218 (tmm) REVERT: c 294 THR cc_start: 0.9407 (m) cc_final: 0.9122 (p) REVERT: c 299 GLU cc_start: 0.9152 (mp0) cc_final: 0.8700 (pm20) REVERT: c 376 MET cc_start: 0.9254 (mmm) cc_final: 0.8562 (mmm) REVERT: c 495 MET cc_start: 0.9138 (tpp) cc_final: 0.8468 (tpp) REVERT: D 12 ASN cc_start: 0.9493 (t0) cc_final: 0.9058 (t0) REVERT: D 25 GLU cc_start: 0.9030 (mp0) cc_final: 0.8827 (mp0) REVERT: D 26 THR cc_start: 0.8802 (p) cc_final: 0.8307 (t) REVERT: d 226 ASP cc_start: 0.8798 (p0) cc_final: 0.8417 (p0) REVERT: d 250 MET cc_start: 0.9101 (tpt) cc_final: 0.8757 (tpp) REVERT: E 12 ASN cc_start: 0.9226 (t0) cc_final: 0.8729 (t0) REVERT: e 66 MET cc_start: 0.7859 (mtt) cc_final: 0.7627 (mtt) REVERT: e 98 GLU cc_start: 0.8565 (pm20) cc_final: 0.8331 (pm20) REVERT: e 223 LEU cc_start: 0.9709 (mt) cc_final: 0.9383 (mp) REVERT: e 336 MET cc_start: 0.9293 (tmm) cc_final: 0.8955 (tpp) REVERT: F 35 SER cc_start: 0.8905 (t) cc_final: 0.8552 (p) REVERT: f 123 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8133 (mm-30) REVERT: f 251 ASP cc_start: 0.9017 (t70) cc_final: 0.8147 (t0) REVERT: f 254 GLU cc_start: 0.8786 (mp0) cc_final: 0.8229 (mp0) REVERT: f 632 LYS cc_start: 0.9398 (mtpp) cc_final: 0.9155 (mtpp) REVERT: f 669 SER cc_start: 0.9374 (m) cc_final: 0.9067 (p) REVERT: G 12 ASN cc_start: 0.9179 (t0) cc_final: 0.8738 (t0) REVERT: G 42 ASN cc_start: 0.8873 (t0) cc_final: 0.8388 (t0) REVERT: g 64 ARG cc_start: 0.8832 (ptm-80) cc_final: 0.7607 (mmt180) REVERT: g 260 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8370 (tp30) REVERT: g 502 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8782 (mp0) REVERT: H 25 GLU cc_start: 0.9092 (mp0) cc_final: 0.8686 (pm20) REVERT: I 12 ASN cc_start: 0.9485 (t0) cc_final: 0.9134 (t0) REVERT: I 21 LYS cc_start: 0.9100 (mttp) cc_final: 0.8875 (mtpt) REVERT: i 95 TYR cc_start: 0.7538 (m-80) cc_final: 0.7291 (m-80) REVERT: i 98 GLU cc_start: 0.8067 (pm20) cc_final: 0.7768 (pm20) REVERT: i 126 ASP cc_start: 0.7045 (t0) cc_final: 0.6532 (m-30) REVERT: i 161 LYS cc_start: 0.9654 (mmmt) cc_final: 0.9393 (mmmm) REVERT: i 179 GLN cc_start: 0.8960 (tt0) cc_final: 0.8598 (tt0) REVERT: i 250 MET cc_start: 0.8859 (tmm) cc_final: 0.8628 (tmm) REVERT: i 251 ASP cc_start: 0.9142 (t0) cc_final: 0.8449 (t0) REVERT: i 254 GLU cc_start: 0.9080 (mp0) cc_final: 0.8676 (mp0) REVERT: i 287 GLU cc_start: 0.9148 (tt0) cc_final: 0.8830 (tm-30) REVERT: i 458 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7794 (p0) REVERT: i 512 GLU cc_start: 0.8683 (pp20) cc_final: 0.8432 (pp20) REVERT: i 559 ASP cc_start: 0.8617 (m-30) cc_final: 0.8266 (t0) REVERT: J 12 ASN cc_start: 0.9304 (t0) cc_final: 0.8940 (t0) REVERT: j 54 GLU cc_start: 0.8542 (pp20) cc_final: 0.8314 (tm-30) REVERT: j 183 LYS cc_start: 0.5735 (mmtm) cc_final: 0.5484 (tppt) REVERT: j 250 MET cc_start: 0.8984 (ttp) cc_final: 0.8611 (tmm) REVERT: j 341 MET cc_start: 0.7393 (ppp) cc_final: 0.7164 (ppp) REVERT: j 539 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8730 (tpp) REVERT: j 632 LYS cc_start: 0.9411 (mtmm) cc_final: 0.9117 (tmtt) REVERT: j 636 ARG cc_start: 0.5171 (ttp-170) cc_final: 0.4924 (tmm160) REVERT: K 33 ASP cc_start: 0.9183 (m-30) cc_final: 0.8659 (m-30) REVERT: K 69 ASP cc_start: 0.8536 (t70) cc_final: 0.8237 (t0) REVERT: K 95 TYR cc_start: 0.4941 (t80) cc_final: 0.4620 (t80) REVERT: K 142 MET cc_start: 0.9123 (mmm) cc_final: 0.8850 (tpp) REVERT: K 182 ASP cc_start: 0.8963 (m-30) cc_final: 0.8087 (p0) REVERT: K 253 ASP cc_start: 0.9374 (m-30) cc_final: 0.9130 (m-30) REVERT: K 325 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8888 (ptp-110) REVERT: K 409 GLU cc_start: 0.8599 (tp30) cc_final: 0.7966 (tp30) REVERT: K 413 MET cc_start: 0.9067 (mmm) cc_final: 0.8467 (mmm) REVERT: K 464 ASP cc_start: 0.9304 (p0) cc_final: 0.8923 (p0) REVERT: K 537 LYS cc_start: 0.9449 (mmtm) cc_final: 0.9238 (mptt) REVERT: K 838 GLU cc_start: 0.8869 (tt0) cc_final: 0.8522 (pt0) REVERT: K 843 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.9166 (p) REVERT: K 856 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8426 (mp10) REVERT: K 901 MET cc_start: 0.8208 (mtp) cc_final: 0.7664 (ttm) REVERT: K 963 MET cc_start: 0.8308 (mpp) cc_final: 0.7927 (mpp) REVERT: K 1048 ASN cc_start: 0.8558 (t0) cc_final: 0.8015 (p0) REVERT: K 1072 MET cc_start: 0.8931 (mmm) cc_final: 0.8553 (mmm) REVERT: K 1235 MET cc_start: 0.9246 (mmt) cc_final: 0.9036 (mmm) outliers start: 141 outliers final: 72 residues processed: 1005 average time/residue: 0.6015 time to fit residues: 1063.0601 Evaluate side-chains 921 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 842 time to evaluate : 5.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain a residue 231 ARG Chi-restraints excluded: chain a residue 339 LYS Chi-restraints excluded: chain a residue 424 VAL Chi-restraints excluded: chain a residue 548 GLU Chi-restraints excluded: chain a residue 613 GLN Chi-restraints excluded: chain b residue 105 GLU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 275 SER Chi-restraints excluded: chain b residue 359 LEU Chi-restraints excluded: chain b residue 527 LEU Chi-restraints excluded: chain b residue 665 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain c residue 90 SER Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain c residue 262 VAL Chi-restraints excluded: chain c residue 368 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain d residue 80 ASP Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain d residue 223 LEU Chi-restraints excluded: chain d residue 240 LEU Chi-restraints excluded: chain d residue 268 SER Chi-restraints excluded: chain d residue 359 LEU Chi-restraints excluded: chain d residue 403 VAL Chi-restraints excluded: chain d residue 546 ILE Chi-restraints excluded: chain d residue 669 SER Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain e residue 359 LEU Chi-restraints excluded: chain e residue 403 VAL Chi-restraints excluded: chain e residue 572 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain f residue 138 SER Chi-restraints excluded: chain f residue 234 LYS Chi-restraints excluded: chain f residue 359 LEU Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 328 ILE Chi-restraints excluded: chain g residue 359 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain h residue 292 LEU Chi-restraints excluded: chain h residue 359 LEU Chi-restraints excluded: chain i residue 327 ARG Chi-restraints excluded: chain i residue 458 ASN Chi-restraints excluded: chain i residue 459 LYS Chi-restraints excluded: chain i residue 554 ASP Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain j residue 359 LEU Chi-restraints excluded: chain j residue 539 MET Chi-restraints excluded: chain j residue 600 MET Chi-restraints excluded: chain j residue 665 LEU Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 249 ILE Chi-restraints excluded: chain K residue 325 ARG Chi-restraints excluded: chain K residue 603 MET Chi-restraints excluded: chain K residue 682 GLU Chi-restraints excluded: chain K residue 706 ILE Chi-restraints excluded: chain K residue 708 THR Chi-restraints excluded: chain K residue 824 VAL Chi-restraints excluded: chain K residue 843 THR Chi-restraints excluded: chain K residue 860 CYS Chi-restraints excluded: chain K residue 1018 ILE Chi-restraints excluded: chain K residue 1185 VAL Chi-restraints excluded: chain K residue 1263 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 632 optimal weight: 4.9990 chunk 431 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 565 optimal weight: 10.0000 chunk 313 optimal weight: 20.0000 chunk 648 optimal weight: 7.9990 chunk 525 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 387 optimal weight: 9.9990 chunk 681 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 110 ASN ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 196 GLN ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 248 GLN ** g 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 222 GLN ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 GLN ** h 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 196 GLN ** j 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 61867 Z= 0.295 Angle : 0.641 11.689 84461 Z= 0.329 Chirality : 0.046 0.183 9924 Planarity : 0.005 0.060 10909 Dihedral : 5.083 59.915 8544 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.32 % Rotamer: Outliers : 2.64 % Allowed : 16.30 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.10), residues: 7872 helix: 1.02 (0.10), residues: 2595 sheet: -1.33 (0.13), residues: 1347 loop : -0.81 (0.10), residues: 3930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 624 HIS 0.012 0.001 HIS f 106 PHE 0.030 0.001 PHE K 188 TYR 0.021 0.001 TYR e 137 ARG 0.009 0.000 ARG e 598 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 867 time to evaluate : 5.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.9271 (m) cc_final: 0.8782 (t) REVERT: a 212 MET cc_start: 0.8830 (tpt) cc_final: 0.8566 (tpp) REVERT: a 231 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8828 (mtt90) REVERT: a 250 MET cc_start: 0.8862 (tpp) cc_final: 0.8597 (tpp) REVERT: a 336 MET cc_start: 0.9135 (tmm) cc_final: 0.8544 (tpp) REVERT: a 548 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8619 (pm20) REVERT: b 297 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8117 (tm-30) REVERT: b 299 GLU cc_start: 0.9027 (mp0) cc_final: 0.8760 (mp0) REVERT: b 370 LEU cc_start: 0.9524 (tp) cc_final: 0.9314 (tp) REVERT: b 541 ASP cc_start: 0.8879 (m-30) cc_final: 0.8665 (m-30) REVERT: b 548 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8418 (tm-30) REVERT: b 560 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8968 (mm-30) REVERT: C 12 ASN cc_start: 0.9175 (t0) cc_final: 0.8584 (t0) REVERT: C 25 GLU cc_start: 0.9177 (mp0) cc_final: 0.8917 (mp0) REVERT: C 27 SER cc_start: 0.9414 (OUTLIER) cc_final: 0.9054 (p) REVERT: C 33 SER cc_start: 0.9438 (p) cc_final: 0.9052 (t) REVERT: C 40 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7644 (ttt) REVERT: c 212 MET cc_start: 0.8870 (tpp) cc_final: 0.8647 (tpp) REVERT: c 294 THR cc_start: 0.9423 (m) cc_final: 0.9138 (p) REVERT: c 299 GLU cc_start: 0.9144 (mp0) cc_final: 0.8656 (pm20) REVERT: c 464 MET cc_start: 0.9595 (tpp) cc_final: 0.9279 (mmm) REVERT: c 495 MET cc_start: 0.9153 (tpp) cc_final: 0.8560 (tpp) REVERT: D 12 ASN cc_start: 0.9486 (t0) cc_final: 0.9025 (t0) REVERT: D 26 THR cc_start: 0.8917 (p) cc_final: 0.8432 (t) REVERT: d 176 ASP cc_start: 0.9110 (m-30) cc_final: 0.8837 (m-30) REVERT: d 226 ASP cc_start: 0.8804 (p0) cc_final: 0.8434 (p0) REVERT: d 250 MET cc_start: 0.8993 (tpt) cc_final: 0.8637 (tpp) REVERT: E 12 ASN cc_start: 0.9182 (t0) cc_final: 0.8679 (t0) REVERT: e 97 ASP cc_start: 0.8988 (p0) cc_final: 0.8558 (p0) REVERT: e 98 GLU cc_start: 0.8532 (pm20) cc_final: 0.8217 (pm20) REVERT: e 212 MET cc_start: 0.8641 (mmm) cc_final: 0.8189 (mpp) REVERT: e 223 LEU cc_start: 0.9759 (mt) cc_final: 0.9456 (mp) REVERT: e 336 MET cc_start: 0.9220 (tmm) cc_final: 0.8450 (tpp) REVERT: e 376 MET cc_start: 0.8805 (tpp) cc_final: 0.8478 (tpp) REVERT: F 35 SER cc_start: 0.8848 (t) cc_final: 0.8642 (p) REVERT: f 73 GLU cc_start: 0.8895 (mp0) cc_final: 0.8692 (mp0) REVERT: f 250 MET cc_start: 0.8848 (tpp) cc_final: 0.8425 (tpp) REVERT: f 251 ASP cc_start: 0.9080 (t70) cc_final: 0.8191 (t0) REVERT: f 254 GLU cc_start: 0.8775 (mp0) cc_final: 0.8190 (mp0) REVERT: f 287 GLU cc_start: 0.8946 (tp30) cc_final: 0.8532 (tp30) REVERT: f 632 LYS cc_start: 0.9408 (mtpp) cc_final: 0.9190 (mtpp) REVERT: f 669 SER cc_start: 0.9442 (m) cc_final: 0.9103 (p) REVERT: G 12 ASN cc_start: 0.9235 (t0) cc_final: 0.8750 (t0) REVERT: G 42 ASN cc_start: 0.8949 (t0) cc_final: 0.8685 (t0) REVERT: g 64 ARG cc_start: 0.8864 (ptm-80) cc_final: 0.7539 (mmt180) REVERT: g 260 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8397 (tp30) REVERT: g 502 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8793 (mp0) REVERT: H 21 LYS cc_start: 0.9168 (mttt) cc_final: 0.8695 (mmmm) REVERT: H 25 GLU cc_start: 0.9148 (mp0) cc_final: 0.8742 (pm20) REVERT: h 297 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8836 (tp30) REVERT: h 317 LYS cc_start: 0.8543 (mppt) cc_final: 0.8261 (mppt) REVERT: I 12 ASN cc_start: 0.9469 (t0) cc_final: 0.9071 (t0) REVERT: I 21 LYS cc_start: 0.9178 (mttp) cc_final: 0.8892 (mtpt) REVERT: i 95 TYR cc_start: 0.7623 (m-80) cc_final: 0.7402 (m-80) REVERT: i 126 ASP cc_start: 0.7426 (t0) cc_final: 0.6919 (m-30) REVERT: i 161 LYS cc_start: 0.9664 (mmmt) cc_final: 0.9384 (mmmm) REVERT: i 250 MET cc_start: 0.8903 (tmm) cc_final: 0.8679 (tmm) REVERT: i 251 ASP cc_start: 0.9109 (t0) cc_final: 0.8391 (t0) REVERT: i 254 GLU cc_start: 0.9061 (mp0) cc_final: 0.8572 (mp0) REVERT: i 287 GLU cc_start: 0.9149 (tt0) cc_final: 0.8820 (mt-10) REVERT: i 512 GLU cc_start: 0.8698 (pp20) cc_final: 0.8473 (pp20) REVERT: i 559 ASP cc_start: 0.8563 (m-30) cc_final: 0.8228 (t0) REVERT: J 12 ASN cc_start: 0.9284 (t0) cc_final: 0.8881 (t0) REVERT: j 54 GLU cc_start: 0.8584 (pp20) cc_final: 0.8302 (tm-30) REVERT: j 176 ASP cc_start: 0.9103 (m-30) cc_final: 0.8842 (m-30) REVERT: j 212 MET cc_start: 0.8788 (tpp) cc_final: 0.8488 (mpp) REVERT: j 250 MET cc_start: 0.9032 (ttp) cc_final: 0.8623 (tmm) REVERT: j 299 GLU cc_start: 0.5898 (tm-30) cc_final: 0.5391 (tm-30) REVERT: j 376 MET cc_start: 0.9068 (tpp) cc_final: 0.8681 (tpp) REVERT: j 456 GLN cc_start: 0.8398 (pp30) cc_final: 0.8180 (pp30) REVERT: j 539 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8829 (tpp) REVERT: j 632 LYS cc_start: 0.9462 (mtmm) cc_final: 0.9120 (tmtt) REVERT: j 636 ARG cc_start: 0.5360 (ttp-170) cc_final: 0.5079 (tmm160) REVERT: K 33 ASP cc_start: 0.9334 (m-30) cc_final: 0.8812 (m-30) REVERT: K 69 ASP cc_start: 0.8488 (t70) cc_final: 0.8170 (t0) REVERT: K 99 ARG cc_start: 0.4256 (mmt180) cc_final: 0.4042 (mpt180) REVERT: K 142 MET cc_start: 0.9187 (mmm) cc_final: 0.8930 (tpp) REVERT: K 182 ASP cc_start: 0.9015 (m-30) cc_final: 0.8107 (p0) REVERT: K 253 ASP cc_start: 0.9391 (m-30) cc_final: 0.9137 (m-30) REVERT: K 325 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8888 (ptp-110) REVERT: K 409 GLU cc_start: 0.8651 (tp30) cc_final: 0.8049 (tp30) REVERT: K 413 MET cc_start: 0.9076 (mmm) cc_final: 0.8522 (mmm) REVERT: K 537 LYS cc_start: 0.9459 (mmtm) cc_final: 0.9226 (mptt) REVERT: K 579 ASP cc_start: 0.7300 (p0) cc_final: 0.6596 (p0) REVERT: K 736 ASN cc_start: 0.8825 (m-40) cc_final: 0.8233 (m-40) REVERT: K 838 GLU cc_start: 0.8876 (tt0) cc_final: 0.8604 (pt0) REVERT: K 843 THR cc_start: 0.9455 (OUTLIER) cc_final: 0.9188 (p) REVERT: K 856 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8550 (mp10) REVERT: K 901 MET cc_start: 0.8273 (mtp) cc_final: 0.7724 (ttm) REVERT: K 963 MET cc_start: 0.8461 (mpp) cc_final: 0.8139 (mpp) REVERT: K 1072 MET cc_start: 0.8966 (mmm) cc_final: 0.8572 (mmm) REVERT: K 1235 MET cc_start: 0.9301 (mmt) cc_final: 0.9049 (mmm) outliers start: 178 outliers final: 109 residues processed: 988 average time/residue: 0.5419 time to fit residues: 933.6430 Evaluate side-chains 927 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 811 time to evaluate : 5.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain a residue 231 ARG Chi-restraints excluded: chain a residue 339 LYS Chi-restraints excluded: chain a residue 424 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain a residue 548 GLU Chi-restraints excluded: chain a residue 635 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 105 GLU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 179 GLN Chi-restraints excluded: chain b residue 221 ASP Chi-restraints excluded: chain b residue 275 SER Chi-restraints excluded: chain b residue 359 LEU Chi-restraints excluded: chain b residue 527 LEU Chi-restraints excluded: chain b residue 617 VAL Chi-restraints excluded: chain b residue 665 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain c residue 90 SER Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain c residue 169 THR Chi-restraints excluded: chain c residue 196 GLN Chi-restraints excluded: chain c residue 342 ASN Chi-restraints excluded: chain c residue 368 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain d residue 80 ASP Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain d residue 210 CYS Chi-restraints excluded: chain d residue 223 LEU Chi-restraints excluded: chain d residue 240 LEU Chi-restraints excluded: chain d residue 268 SER Chi-restraints excluded: chain d residue 359 LEU Chi-restraints excluded: chain d residue 403 VAL Chi-restraints excluded: chain d residue 457 LEU Chi-restraints excluded: chain d residue 546 ILE Chi-restraints excluded: chain d residue 669 SER Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain e residue 106 HIS Chi-restraints excluded: chain e residue 359 LEU Chi-restraints excluded: chain e residue 382 LEU Chi-restraints excluded: chain e residue 403 VAL Chi-restraints excluded: chain e residue 572 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain f residue 138 SER Chi-restraints excluded: chain f residue 234 LYS Chi-restraints excluded: chain f residue 253 SER Chi-restraints excluded: chain f residue 301 ILE Chi-restraints excluded: chain f residue 304 LEU Chi-restraints excluded: chain f residue 359 LEU Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 610 ILE Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 128 MET Chi-restraints excluded: chain g residue 328 ILE Chi-restraints excluded: chain g residue 359 LEU Chi-restraints excluded: chain g residue 541 ASP Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain h residue 280 GLU Chi-restraints excluded: chain h residue 292 LEU Chi-restraints excluded: chain h residue 359 LEU Chi-restraints excluded: chain h residue 527 LEU Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain i residue 130 VAL Chi-restraints excluded: chain i residue 403 VAL Chi-restraints excluded: chain i residue 471 THR Chi-restraints excluded: chain i residue 554 ASP Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain j residue 347 ILE Chi-restraints excluded: chain j residue 359 LEU Chi-restraints excluded: chain j residue 539 MET Chi-restraints excluded: chain j residue 600 MET Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 304 LEU Chi-restraints excluded: chain K residue 325 ARG Chi-restraints excluded: chain K residue 603 MET Chi-restraints excluded: chain K residue 682 GLU Chi-restraints excluded: chain K residue 706 ILE Chi-restraints excluded: chain K residue 708 THR Chi-restraints excluded: chain K residue 712 GLU Chi-restraints excluded: chain K residue 824 VAL Chi-restraints excluded: chain K residue 843 THR Chi-restraints excluded: chain K residue 860 CYS Chi-restraints excluded: chain K residue 942 ILE Chi-restraints excluded: chain K residue 984 LEU Chi-restraints excluded: chain K residue 1018 ILE Chi-restraints excluded: chain K residue 1165 ILE Chi-restraints excluded: chain K residue 1222 LEU Chi-restraints excluded: chain K residue 1263 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 255 optimal weight: 7.9990 chunk 684 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 446 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 760 optimal weight: 30.0000 chunk 631 optimal weight: 0.0040 chunk 352 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 251 optimal weight: 8.9990 chunk 399 optimal weight: 0.0570 overall best weight: 4.0116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 81 ASN ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 160 GLN g 202 ASN ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 458 ASN ** i 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 458 ASN j 106 HIS j 196 GLN j 213 GLN ** j 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 61867 Z= 0.217 Angle : 0.632 12.395 84461 Z= 0.321 Chirality : 0.046 0.298 9924 Planarity : 0.005 0.057 10909 Dihedral : 4.991 58.937 8544 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 2.39 % Allowed : 17.06 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.10), residues: 7872 helix: 1.10 (0.10), residues: 2605 sheet: -1.20 (0.14), residues: 1335 loop : -0.74 (0.10), residues: 3932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 624 HIS 0.007 0.001 HIS f 106 PHE 0.021 0.001 PHE K 188 TYR 0.027 0.001 TYR K 744 ARG 0.006 0.000 ARG K 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 895 time to evaluate : 5.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.9217 (m) cc_final: 0.8724 (t) REVERT: a 212 MET cc_start: 0.8789 (tpt) cc_final: 0.8342 (tpp) REVERT: a 231 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8827 (mtt90) REVERT: a 250 MET cc_start: 0.8842 (tpp) cc_final: 0.8568 (tpp) REVERT: a 336 MET cc_start: 0.9166 (tmm) cc_final: 0.8764 (tpp) REVERT: a 376 MET cc_start: 0.8363 (tpt) cc_final: 0.7795 (tpt) REVERT: a 548 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8598 (pm20) REVERT: B 21 LYS cc_start: 0.9585 (ttmm) cc_final: 0.9385 (ttmm) REVERT: B 40 MET cc_start: 0.8787 (ttp) cc_final: 0.8356 (tmm) REVERT: b 115 GLU cc_start: 0.8569 (tt0) cc_final: 0.8191 (tm-30) REVERT: b 205 ILE cc_start: 0.9233 (tp) cc_final: 0.8986 (tt) REVERT: b 376 MET cc_start: 0.9306 (tpt) cc_final: 0.8725 (tpp) REVERT: b 464 MET cc_start: 0.9131 (tpp) cc_final: 0.8832 (tpp) REVERT: b 541 ASP cc_start: 0.8848 (m-30) cc_final: 0.8628 (m-30) REVERT: b 560 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8919 (mm-30) REVERT: C 12 ASN cc_start: 0.9168 (t0) cc_final: 0.8573 (t0) REVERT: C 25 GLU cc_start: 0.9201 (mp0) cc_final: 0.8881 (mp0) REVERT: C 27 SER cc_start: 0.9386 (OUTLIER) cc_final: 0.9015 (p) REVERT: C 33 SER cc_start: 0.9367 (p) cc_final: 0.8983 (t) REVERT: C 40 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7784 (ttt) REVERT: c 207 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8082 (tm-30) REVERT: c 212 MET cc_start: 0.8835 (tpp) cc_final: 0.8541 (tpp) REVERT: c 250 MET cc_start: 0.9020 (tmm) cc_final: 0.8676 (tmm) REVERT: c 287 GLU cc_start: 0.8578 (pp20) cc_final: 0.8364 (pp20) REVERT: c 294 THR cc_start: 0.9396 (m) cc_final: 0.9108 (p) REVERT: c 299 GLU cc_start: 0.9131 (mp0) cc_final: 0.8676 (pm20) REVERT: c 464 MET cc_start: 0.9595 (tpp) cc_final: 0.9311 (mmm) REVERT: c 600 MET cc_start: 0.9317 (ttp) cc_final: 0.9047 (ttp) REVERT: c 611 ILE cc_start: 0.9389 (mm) cc_final: 0.9119 (mm) REVERT: D 12 ASN cc_start: 0.9459 (t0) cc_final: 0.9030 (t0) REVERT: D 26 THR cc_start: 0.9000 (p) cc_final: 0.8446 (t) REVERT: d 115 GLU cc_start: 0.8718 (tt0) cc_final: 0.8239 (mm-30) REVERT: d 176 ASP cc_start: 0.9093 (m-30) cc_final: 0.8746 (m-30) REVERT: d 196 GLN cc_start: 0.8913 (mt0) cc_final: 0.8570 (mt0) REVERT: d 226 ASP cc_start: 0.8765 (p0) cc_final: 0.8472 (p0) REVERT: d 250 MET cc_start: 0.9000 (tpt) cc_final: 0.8650 (tpp) REVERT: d 606 ASP cc_start: 0.8685 (t0) cc_final: 0.8447 (t0) REVERT: E 12 ASN cc_start: 0.9156 (t0) cc_final: 0.8661 (t0) REVERT: e 89 GLU cc_start: 0.8536 (mp0) cc_final: 0.8193 (mp0) REVERT: e 97 ASP cc_start: 0.8940 (p0) cc_final: 0.8586 (p0) REVERT: e 98 GLU cc_start: 0.8502 (pm20) cc_final: 0.8292 (pm20) REVERT: e 189 GLU cc_start: 0.9000 (tp30) cc_final: 0.8569 (tm-30) REVERT: e 219 LEU cc_start: 0.9897 (mt) cc_final: 0.9663 (mt) REVERT: e 223 LEU cc_start: 0.9739 (mt) cc_final: 0.9429 (mp) REVERT: e 336 MET cc_start: 0.9221 (tmm) cc_final: 0.8437 (tpp) REVERT: F 35 SER cc_start: 0.8800 (t) cc_final: 0.8579 (p) REVERT: f 123 GLU cc_start: 0.8140 (pm20) cc_final: 0.7832 (pm20) REVERT: f 160 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8445 (mm110) REVERT: f 250 MET cc_start: 0.8889 (tpp) cc_final: 0.8638 (tpp) REVERT: f 251 ASP cc_start: 0.9104 (t70) cc_final: 0.8255 (t0) REVERT: f 254 GLU cc_start: 0.8778 (mp0) cc_final: 0.8161 (mp0) REVERT: f 336 MET cc_start: 0.8804 (tmm) cc_final: 0.8016 (tmm) REVERT: f 376 MET cc_start: 0.9376 (mmm) cc_final: 0.8730 (mmm) REVERT: f 632 LYS cc_start: 0.9427 (mtpp) cc_final: 0.9166 (mtpp) REVERT: G 12 ASN cc_start: 0.9265 (t0) cc_final: 0.8808 (t0) REVERT: g 64 ARG cc_start: 0.8869 (ptm-80) cc_final: 0.7544 (mmt180) REVERT: g 260 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8385 (tp30) REVERT: g 502 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8826 (mp0) REVERT: g 548 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8862 (tp30) REVERT: H 25 GLU cc_start: 0.9171 (mp0) cc_final: 0.8746 (pm20) REVERT: h 297 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8806 (tp30) REVERT: h 317 LYS cc_start: 0.8644 (mppt) cc_final: 0.8414 (mppt) REVERT: h 336 MET cc_start: 0.8932 (tmm) cc_final: 0.8371 (tmm) REVERT: I 12 ASN cc_start: 0.9509 (t0) cc_final: 0.9100 (t0) REVERT: I 21 LYS cc_start: 0.9179 (mttp) cc_final: 0.8876 (mtpt) REVERT: i 95 TYR cc_start: 0.7638 (m-80) cc_final: 0.7430 (m-80) REVERT: i 113 LYS cc_start: 0.9544 (mmtp) cc_final: 0.9295 (mmtp) REVERT: i 126 ASP cc_start: 0.7395 (t0) cc_final: 0.6890 (m-30) REVERT: i 161 LYS cc_start: 0.9646 (mmmt) cc_final: 0.9367 (mmmm) REVERT: i 179 GLN cc_start: 0.9079 (tt0) cc_final: 0.8861 (tt0) REVERT: i 189 GLU cc_start: 0.8904 (tp30) cc_final: 0.8571 (tp30) REVERT: i 250 MET cc_start: 0.8967 (tmm) cc_final: 0.8713 (tmm) REVERT: i 251 ASP cc_start: 0.9082 (t0) cc_final: 0.8295 (t0) REVERT: i 254 GLU cc_start: 0.9030 (mp0) cc_final: 0.8502 (mp0) REVERT: i 299 GLU cc_start: 0.8759 (mp0) cc_final: 0.8367 (tp30) REVERT: i 512 GLU cc_start: 0.8704 (pp20) cc_final: 0.8482 (pp20) REVERT: i 559 ASP cc_start: 0.8481 (m-30) cc_final: 0.8161 (t0) REVERT: J 12 ASN cc_start: 0.9264 (t0) cc_final: 0.8866 (t0) REVERT: J 40 MET cc_start: 0.8073 (ttt) cc_final: 0.7653 (tmm) REVERT: j 54 GLU cc_start: 0.8550 (pp20) cc_final: 0.8288 (tm-30) REVERT: j 176 ASP cc_start: 0.9088 (m-30) cc_final: 0.8769 (m-30) REVERT: j 183 LYS cc_start: 0.6478 (mttm) cc_final: 0.6213 (mttt) REVERT: j 250 MET cc_start: 0.9016 (ttp) cc_final: 0.8696 (tmm) REVERT: j 253 SER cc_start: 0.9443 (OUTLIER) cc_final: 0.8943 (p) REVERT: j 299 GLU cc_start: 0.5833 (tm-30) cc_final: 0.5377 (tm-30) REVERT: j 376 MET cc_start: 0.9063 (tpp) cc_final: 0.8247 (tpt) REVERT: j 539 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8844 (tpp) REVERT: j 572 LEU cc_start: 0.9784 (mt) cc_final: 0.9579 (mt) REVERT: j 632 LYS cc_start: 0.9473 (mtmm) cc_final: 0.9125 (tmtt) REVERT: j 636 ARG cc_start: 0.5575 (ttp-170) cc_final: 0.4880 (tmt-80) REVERT: K 33 ASP cc_start: 0.9354 (m-30) cc_final: 0.8853 (m-30) REVERT: K 69 ASP cc_start: 0.8418 (t70) cc_final: 0.8119 (t0) REVERT: K 93 LEU cc_start: 0.9624 (tp) cc_final: 0.9395 (tp) REVERT: K 142 MET cc_start: 0.9208 (mmm) cc_final: 0.8942 (tpp) REVERT: K 182 ASP cc_start: 0.9037 (m-30) cc_final: 0.8214 (p0) REVERT: K 253 ASP cc_start: 0.9370 (m-30) cc_final: 0.9102 (m-30) REVERT: K 325 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8834 (ptp-110) REVERT: K 409 GLU cc_start: 0.8628 (tp30) cc_final: 0.8040 (tp30) REVERT: K 413 MET cc_start: 0.9050 (mmm) cc_final: 0.8479 (mmm) REVERT: K 577 ASP cc_start: 0.8321 (t70) cc_final: 0.7975 (t0) REVERT: K 579 ASP cc_start: 0.7479 (p0) cc_final: 0.6410 (p0) REVERT: K 706 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9170 (pp) REVERT: K 736 ASN cc_start: 0.8767 (m-40) cc_final: 0.8101 (m-40) REVERT: K 781 GLU cc_start: 0.8609 (pm20) cc_final: 0.8287 (pm20) REVERT: K 838 GLU cc_start: 0.8860 (tt0) cc_final: 0.8649 (pt0) REVERT: K 856 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8539 (mp10) REVERT: K 901 MET cc_start: 0.8326 (mtp) cc_final: 0.7795 (ttm) REVERT: K 963 MET cc_start: 0.8476 (mpp) cc_final: 0.8138 (mpp) REVERT: K 1072 MET cc_start: 0.9005 (mmm) cc_final: 0.8667 (mmm) REVERT: K 1235 MET cc_start: 0.9310 (mmt) cc_final: 0.9066 (mmm) outliers start: 161 outliers final: 101 residues processed: 1001 average time/residue: 0.5534 time to fit residues: 969.0800 Evaluate side-chains 943 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 832 time to evaluate : 5.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain a residue 231 ARG Chi-restraints excluded: chain a residue 339 LYS Chi-restraints excluded: chain a residue 424 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain a residue 513 VAL Chi-restraints excluded: chain a residue 548 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain b residue 105 GLU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 179 GLN Chi-restraints excluded: chain b residue 221 ASP Chi-restraints excluded: chain b residue 275 SER Chi-restraints excluded: chain b residue 359 LEU Chi-restraints excluded: chain b residue 527 LEU Chi-restraints excluded: chain b residue 617 VAL Chi-restraints excluded: chain b residue 665 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain c residue 90 SER Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 207 GLU Chi-restraints excluded: chain c residue 265 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain d residue 210 CYS Chi-restraints excluded: chain d residue 223 LEU Chi-restraints excluded: chain d residue 240 LEU Chi-restraints excluded: chain d residue 359 LEU Chi-restraints excluded: chain d residue 403 VAL Chi-restraints excluded: chain d residue 457 LEU Chi-restraints excluded: chain d residue 546 ILE Chi-restraints excluded: chain d residue 669 SER Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain e residue 106 HIS Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 359 LEU Chi-restraints excluded: chain e residue 403 VAL Chi-restraints excluded: chain e residue 572 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain f residue 138 SER Chi-restraints excluded: chain f residue 160 GLN Chi-restraints excluded: chain f residue 186 GLU Chi-restraints excluded: chain f residue 234 LYS Chi-restraints excluded: chain f residue 253 SER Chi-restraints excluded: chain f residue 301 ILE Chi-restraints excluded: chain f residue 304 LEU Chi-restraints excluded: chain f residue 359 LEU Chi-restraints excluded: chain f residue 446 THR Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 610 ILE Chi-restraints excluded: chain g residue 359 LEU Chi-restraints excluded: chain g residue 424 VAL Chi-restraints excluded: chain g residue 541 ASP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain h residue 359 LEU Chi-restraints excluded: chain h residue 527 LEU Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain i residue 130 VAL Chi-restraints excluded: chain i residue 327 ARG Chi-restraints excluded: chain i residue 403 VAL Chi-restraints excluded: chain i residue 471 THR Chi-restraints excluded: chain i residue 554 ASP Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain j residue 115 GLU Chi-restraints excluded: chain j residue 123 GLU Chi-restraints excluded: chain j residue 253 SER Chi-restraints excluded: chain j residue 347 ILE Chi-restraints excluded: chain j residue 359 LEU Chi-restraints excluded: chain j residue 402 ILE Chi-restraints excluded: chain j residue 539 MET Chi-restraints excluded: chain j residue 562 SER Chi-restraints excluded: chain j residue 600 MET Chi-restraints excluded: chain j residue 617 VAL Chi-restraints excluded: chain j residue 651 LEU Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 249 ILE Chi-restraints excluded: chain K residue 325 ARG Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 603 MET Chi-restraints excluded: chain K residue 682 GLU Chi-restraints excluded: chain K residue 706 ILE Chi-restraints excluded: chain K residue 708 THR Chi-restraints excluded: chain K residue 712 GLU Chi-restraints excluded: chain K residue 824 VAL Chi-restraints excluded: chain K residue 860 CYS Chi-restraints excluded: chain K residue 942 ILE Chi-restraints excluded: chain K residue 984 LEU Chi-restraints excluded: chain K residue 1263 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 733 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 433 optimal weight: 10.0000 chunk 555 optimal weight: 20.0000 chunk 430 optimal weight: 8.9990 chunk 640 optimal weight: 30.0000 chunk 424 optimal weight: 0.7980 chunk 757 optimal weight: 9.9990 chunk 474 optimal weight: 8.9990 chunk 461 optimal weight: 7.9990 chunk 349 optimal weight: 9.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 162 GLN ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 369 ASN h 458 ASN ** i 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 576 GLN j 196 GLN ** j 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 61867 Z= 0.263 Angle : 0.652 13.425 84461 Z= 0.331 Chirality : 0.046 0.251 9924 Planarity : 0.005 0.059 10909 Dihedral : 4.983 57.437 8542 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.36 % Favored : 95.59 % Rotamer: Outliers : 2.36 % Allowed : 17.80 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.10), residues: 7872 helix: 1.17 (0.10), residues: 2575 sheet: -1.25 (0.13), residues: 1362 loop : -0.62 (0.10), residues: 3935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 624 HIS 0.014 0.001 HIS g 106 PHE 0.021 0.001 PHE K 188 TYR 0.016 0.001 TYR c 232 ARG 0.005 0.000 ARG K 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 848 time to evaluate : 5.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.9277 (m) cc_final: 0.8760 (t) REVERT: A 37 SER cc_start: 0.9563 (t) cc_final: 0.9353 (p) REVERT: a 212 MET cc_start: 0.8791 (tpt) cc_final: 0.8371 (tpp) REVERT: a 231 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8844 (mtt90) REVERT: a 336 MET cc_start: 0.9162 (tmm) cc_final: 0.8762 (tpp) REVERT: a 548 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8592 (pm20) REVERT: B 40 MET cc_start: 0.8815 (ttp) cc_final: 0.7882 (tmm) REVERT: b 98 GLU cc_start: 0.8031 (pm20) cc_final: 0.7706 (mp0) REVERT: b 205 ILE cc_start: 0.9247 (tp) cc_final: 0.9014 (tt) REVERT: b 483 MET cc_start: 0.8618 (mmm) cc_final: 0.8263 (mmm) REVERT: b 541 ASP cc_start: 0.8854 (m-30) cc_final: 0.8654 (m-30) REVERT: C 12 ASN cc_start: 0.9161 (t0) cc_final: 0.8555 (t0) REVERT: C 25 GLU cc_start: 0.9207 (mp0) cc_final: 0.8924 (mp0) REVERT: C 27 SER cc_start: 0.9445 (OUTLIER) cc_final: 0.9088 (p) REVERT: C 33 SER cc_start: 0.9402 (p) cc_final: 0.9000 (t) REVERT: C 40 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7910 (ttt) REVERT: c 207 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8051 (tm-30) REVERT: c 250 MET cc_start: 0.9026 (tmm) cc_final: 0.8659 (tmm) REVERT: c 254 GLU cc_start: 0.9124 (mp0) cc_final: 0.8862 (pm20) REVERT: c 287 GLU cc_start: 0.8678 (pp20) cc_final: 0.8450 (pp20) REVERT: c 294 THR cc_start: 0.9410 (m) cc_final: 0.9123 (p) REVERT: c 299 GLU cc_start: 0.9158 (mp0) cc_final: 0.8844 (pm20) REVERT: c 376 MET cc_start: 0.9371 (mmm) cc_final: 0.9030 (mmm) REVERT: c 464 MET cc_start: 0.9600 (tpp) cc_final: 0.9338 (mmm) REVERT: c 600 MET cc_start: 0.9306 (ttp) cc_final: 0.9048 (ttp) REVERT: c 611 ILE cc_start: 0.9409 (mm) cc_final: 0.9156 (mm) REVERT: D 12 ASN cc_start: 0.9436 (t0) cc_final: 0.9006 (t0) REVERT: D 26 THR cc_start: 0.8989 (p) cc_final: 0.8418 (t) REVERT: d 115 GLU cc_start: 0.8747 (tt0) cc_final: 0.8307 (mm-30) REVERT: d 176 ASP cc_start: 0.9084 (m-30) cc_final: 0.8701 (m-30) REVERT: d 196 GLN cc_start: 0.8773 (mt0) cc_final: 0.8528 (mt0) REVERT: d 226 ASP cc_start: 0.8782 (p0) cc_final: 0.8505 (p0) REVERT: d 250 MET cc_start: 0.8961 (tpt) cc_final: 0.8636 (tpp) REVERT: d 260 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8356 (mm-30) REVERT: d 606 ASP cc_start: 0.8724 (t0) cc_final: 0.8477 (t0) REVERT: E 12 ASN cc_start: 0.9148 (t0) cc_final: 0.8641 (t0) REVERT: e 97 ASP cc_start: 0.8925 (p0) cc_final: 0.8514 (p0) REVERT: e 98 GLU cc_start: 0.8489 (pm20) cc_final: 0.8217 (pm20) REVERT: e 189 GLU cc_start: 0.8997 (tp30) cc_final: 0.8590 (tm-30) REVERT: e 223 LEU cc_start: 0.9745 (mt) cc_final: 0.9425 (mp) REVERT: e 336 MET cc_start: 0.9233 (tmm) cc_final: 0.8376 (tpp) REVERT: f 123 GLU cc_start: 0.8257 (pm20) cc_final: 0.7913 (pm20) REVERT: f 250 MET cc_start: 0.8772 (tpp) cc_final: 0.8497 (tpp) REVERT: f 251 ASP cc_start: 0.9150 (t70) cc_final: 0.8272 (t0) REVERT: f 254 GLU cc_start: 0.8767 (mp0) cc_final: 0.8144 (mp0) REVERT: f 336 MET cc_start: 0.8803 (tmm) cc_final: 0.7910 (tmm) REVERT: f 376 MET cc_start: 0.9368 (mmm) cc_final: 0.8997 (mmm) REVERT: f 632 LYS cc_start: 0.9428 (mtpp) cc_final: 0.9186 (mtpp) REVERT: G 12 ASN cc_start: 0.9277 (t0) cc_final: 0.8781 (t0) REVERT: G 40 MET cc_start: 0.8759 (tmm) cc_final: 0.8472 (tmm) REVERT: g 64 ARG cc_start: 0.8946 (ptm-80) cc_final: 0.7603 (mmt180) REVERT: g 260 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8524 (tp30) REVERT: g 336 MET cc_start: 0.8642 (tpt) cc_final: 0.8411 (tpt) REVERT: g 502 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8808 (mp0) REVERT: g 548 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8855 (tp30) REVERT: H 25 GLU cc_start: 0.9208 (mp0) cc_final: 0.8755 (pm20) REVERT: h 317 LYS cc_start: 0.8751 (mppt) cc_final: 0.8526 (mppt) REVERT: h 336 MET cc_start: 0.8935 (tmm) cc_final: 0.8414 (tmm) REVERT: h 346 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8830 (mt0) REVERT: I 12 ASN cc_start: 0.9539 (t0) cc_final: 0.9164 (t0) REVERT: I 21 LYS cc_start: 0.9187 (mttp) cc_final: 0.8868 (mtpt) REVERT: i 95 TYR cc_start: 0.7605 (m-80) cc_final: 0.7366 (m-80) REVERT: i 113 LYS cc_start: 0.9522 (mmtp) cc_final: 0.9293 (mmtp) REVERT: i 126 ASP cc_start: 0.7419 (t0) cc_final: 0.6937 (m-30) REVERT: i 161 LYS cc_start: 0.9641 (mmmt) cc_final: 0.9367 (mmmm) REVERT: i 250 MET cc_start: 0.8999 (tmm) cc_final: 0.8726 (tmm) REVERT: i 251 ASP cc_start: 0.9089 (t0) cc_final: 0.8405 (t0) REVERT: i 254 GLU cc_start: 0.9025 (mp0) cc_final: 0.8547 (mp0) REVERT: i 290 MET cc_start: 0.9397 (tpp) cc_final: 0.8961 (mmm) REVERT: i 457 LEU cc_start: 0.9236 (mp) cc_final: 0.8928 (pp) REVERT: i 512 GLU cc_start: 0.8731 (pp20) cc_final: 0.8514 (pp20) REVERT: i 559 ASP cc_start: 0.8486 (m-30) cc_final: 0.8201 (t0) REVERT: J 12 ASN cc_start: 0.9258 (t0) cc_final: 0.8898 (t0) REVERT: J 21 LYS cc_start: 0.9285 (ttmm) cc_final: 0.9016 (mmmm) REVERT: J 40 MET cc_start: 0.8249 (ttt) cc_final: 0.7757 (tmm) REVERT: j 54 GLU cc_start: 0.8584 (pp20) cc_final: 0.8321 (tm-30) REVERT: j 176 ASP cc_start: 0.9088 (m-30) cc_final: 0.8752 (m-30) REVERT: j 182 LEU cc_start: 0.9759 (OUTLIER) cc_final: 0.9515 (mm) REVERT: j 183 LYS cc_start: 0.6239 (mttm) cc_final: 0.5899 (mttt) REVERT: j 250 MET cc_start: 0.9075 (ttp) cc_final: 0.8673 (tmm) REVERT: j 253 SER cc_start: 0.9475 (OUTLIER) cc_final: 0.8961 (p) REVERT: j 299 GLU cc_start: 0.5858 (tm-30) cc_final: 0.5407 (tm-30) REVERT: j 376 MET cc_start: 0.9087 (tpp) cc_final: 0.8290 (tpt) REVERT: j 572 LEU cc_start: 0.9783 (mt) cc_final: 0.9571 (mt) REVERT: j 632 LYS cc_start: 0.9484 (mtmm) cc_final: 0.9127 (tmtt) REVERT: K 69 ASP cc_start: 0.8413 (t70) cc_final: 0.8127 (t0) REVERT: K 142 MET cc_start: 0.9235 (mmm) cc_final: 0.8964 (tpp) REVERT: K 182 ASP cc_start: 0.9073 (m-30) cc_final: 0.8265 (p0) REVERT: K 253 ASP cc_start: 0.9391 (m-30) cc_final: 0.9147 (m-30) REVERT: K 325 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8753 (ptp-110) REVERT: K 375 LEU cc_start: 0.9616 (tt) cc_final: 0.9287 (tt) REVERT: K 409 GLU cc_start: 0.8654 (tp30) cc_final: 0.8085 (tp30) REVERT: K 413 MET cc_start: 0.9085 (mmm) cc_final: 0.8551 (mmm) REVERT: K 537 LYS cc_start: 0.9458 (mmtm) cc_final: 0.9221 (mptt) REVERT: K 577 ASP cc_start: 0.8554 (t70) cc_final: 0.8150 (t0) REVERT: K 579 ASP cc_start: 0.7586 (p0) cc_final: 0.7190 (p0) REVERT: K 706 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9175 (pp) REVERT: K 736 ASN cc_start: 0.8837 (m-40) cc_final: 0.8106 (m-40) REVERT: K 781 GLU cc_start: 0.8623 (pm20) cc_final: 0.8286 (pm20) REVERT: K 838 GLU cc_start: 0.8856 (tt0) cc_final: 0.8641 (pt0) REVERT: K 843 THR cc_start: 0.9502 (OUTLIER) cc_final: 0.9248 (p) REVERT: K 856 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8597 (mp10) REVERT: K 901 MET cc_start: 0.8274 (mtp) cc_final: 0.7716 (ttm) REVERT: K 963 MET cc_start: 0.8576 (mpp) cc_final: 0.8271 (mpp) REVERT: K 1019 MET cc_start: 0.9192 (mmm) cc_final: 0.8970 (mmm) REVERT: K 1072 MET cc_start: 0.9022 (mmm) cc_final: 0.8713 (mmm) outliers start: 159 outliers final: 118 residues processed: 952 average time/residue: 0.5318 time to fit residues: 882.5203 Evaluate side-chains 937 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 808 time to evaluate : 5.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain a residue 231 ARG Chi-restraints excluded: chain a residue 339 LYS Chi-restraints excluded: chain a residue 424 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain a residue 513 VAL Chi-restraints excluded: chain a residue 548 GLU Chi-restraints excluded: chain a residue 635 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain b residue 105 GLU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain b residue 179 GLN Chi-restraints excluded: chain b residue 221 ASP Chi-restraints excluded: chain b residue 275 SER Chi-restraints excluded: chain b residue 279 LEU Chi-restraints excluded: chain b residue 359 LEU Chi-restraints excluded: chain b residue 527 LEU Chi-restraints excluded: chain b residue 617 VAL Chi-restraints excluded: chain b residue 665 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain c residue 90 SER Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 207 GLU Chi-restraints excluded: chain c residue 265 VAL Chi-restraints excluded: chain c residue 342 ASN Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain d residue 210 CYS Chi-restraints excluded: chain d residue 223 LEU Chi-restraints excluded: chain d residue 268 SER Chi-restraints excluded: chain d residue 342 ASN Chi-restraints excluded: chain d residue 359 LEU Chi-restraints excluded: chain d residue 403 VAL Chi-restraints excluded: chain d residue 457 LEU Chi-restraints excluded: chain d residue 546 ILE Chi-restraints excluded: chain d residue 669 SER Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain e residue 66 MET Chi-restraints excluded: chain e residue 106 HIS Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain e residue 154 GLN Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 359 LEU Chi-restraints excluded: chain e residue 403 VAL Chi-restraints excluded: chain e residue 572 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 138 SER Chi-restraints excluded: chain f residue 234 LYS Chi-restraints excluded: chain f residue 253 SER Chi-restraints excluded: chain f residue 301 ILE Chi-restraints excluded: chain f residue 304 LEU Chi-restraints excluded: chain f residue 311 VAL Chi-restraints excluded: chain f residue 359 LEU Chi-restraints excluded: chain f residue 446 THR Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 610 ILE Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 328 ILE Chi-restraints excluded: chain g residue 359 LEU Chi-restraints excluded: chain g residue 424 VAL Chi-restraints excluded: chain g residue 541 ASP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain h residue 346 GLN Chi-restraints excluded: chain h residue 359 LEU Chi-restraints excluded: chain h residue 527 LEU Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain i residue 130 VAL Chi-restraints excluded: chain i residue 327 ARG Chi-restraints excluded: chain i residue 403 VAL Chi-restraints excluded: chain i residue 471 THR Chi-restraints excluded: chain i residue 554 ASP Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain j residue 115 GLU Chi-restraints excluded: chain j residue 182 LEU Chi-restraints excluded: chain j residue 253 SER Chi-restraints excluded: chain j residue 347 ILE Chi-restraints excluded: chain j residue 359 LEU Chi-restraints excluded: chain j residue 402 ILE Chi-restraints excluded: chain j residue 483 MET Chi-restraints excluded: chain j residue 562 SER Chi-restraints excluded: chain j residue 600 MET Chi-restraints excluded: chain j residue 617 VAL Chi-restraints excluded: chain j residue 651 LEU Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain K residue 249 ILE Chi-restraints excluded: chain K residue 304 LEU Chi-restraints excluded: chain K residue 325 ARG Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 603 MET Chi-restraints excluded: chain K residue 682 GLU Chi-restraints excluded: chain K residue 706 ILE Chi-restraints excluded: chain K residue 712 GLU Chi-restraints excluded: chain K residue 824 VAL Chi-restraints excluded: chain K residue 843 THR Chi-restraints excluded: chain K residue 860 CYS Chi-restraints excluded: chain K residue 942 ILE Chi-restraints excluded: chain K residue 982 VAL Chi-restraints excluded: chain K residue 984 LEU Chi-restraints excluded: chain K residue 1222 LEU Chi-restraints excluded: chain K residue 1263 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 468 optimal weight: 7.9990 chunk 302 optimal weight: 5.9990 chunk 452 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 481 optimal weight: 6.9990 chunk 516 optimal weight: 2.9990 chunk 374 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 595 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 106 HIS ** f 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 61867 Z= 0.206 Angle : 0.656 15.071 84461 Z= 0.331 Chirality : 0.046 0.233 9924 Planarity : 0.005 0.056 10909 Dihedral : 4.919 56.975 8542 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 2.21 % Allowed : 18.35 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.10), residues: 7872 helix: 1.22 (0.11), residues: 2568 sheet: -1.11 (0.14), residues: 1307 loop : -0.57 (0.10), residues: 3997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP K 624 HIS 0.007 0.001 HIS g 106 PHE 0.017 0.001 PHE j 124 TYR 0.016 0.001 TYR b 321 ARG 0.006 0.000 ARG K 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 878 time to evaluate : 5.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.9156 (m) cc_final: 0.8651 (t) REVERT: a 212 MET cc_start: 0.8787 (tpt) cc_final: 0.8414 (tpp) REVERT: a 231 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8848 (mtt90) REVERT: a 336 MET cc_start: 0.9166 (tmm) cc_final: 0.8816 (tpp) REVERT: B 40 MET cc_start: 0.8722 (ttp) cc_final: 0.7837 (tmm) REVERT: b 98 GLU cc_start: 0.8120 (pm20) cc_final: 0.7766 (mp0) REVERT: b 115 GLU cc_start: 0.8437 (tt0) cc_final: 0.7920 (tm-30) REVERT: b 176 ASP cc_start: 0.8732 (t0) cc_final: 0.8400 (t0) REVERT: b 205 ILE cc_start: 0.9276 (tp) cc_final: 0.9047 (tt) REVERT: b 464 MET cc_start: 0.9078 (tpp) cc_final: 0.8770 (tpp) REVERT: b 541 ASP cc_start: 0.8849 (m-30) cc_final: 0.8648 (m-30) REVERT: C 12 ASN cc_start: 0.9158 (t0) cc_final: 0.8579 (t0) REVERT: C 21 LYS cc_start: 0.9506 (ttmm) cc_final: 0.9071 (ttmm) REVERT: C 25 GLU cc_start: 0.9205 (mp0) cc_final: 0.8944 (mp0) REVERT: C 27 SER cc_start: 0.9412 (OUTLIER) cc_final: 0.9043 (p) REVERT: C 33 SER cc_start: 0.9350 (p) cc_final: 0.8957 (t) REVERT: C 40 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7840 (ttt) REVERT: c 207 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: c 250 MET cc_start: 0.9052 (tmm) cc_final: 0.8683 (tmm) REVERT: c 254 GLU cc_start: 0.9107 (mp0) cc_final: 0.8869 (pm20) REVERT: c 287 GLU cc_start: 0.8688 (pp20) cc_final: 0.8403 (pp20) REVERT: c 294 THR cc_start: 0.9390 (m) cc_final: 0.9095 (p) REVERT: c 299 GLU cc_start: 0.9158 (mp0) cc_final: 0.8849 (pm20) REVERT: c 376 MET cc_start: 0.9279 (mmm) cc_final: 0.8932 (mmm) REVERT: c 464 MET cc_start: 0.9594 (tpp) cc_final: 0.9346 (mmm) REVERT: c 600 MET cc_start: 0.9312 (ttp) cc_final: 0.9072 (ttp) REVERT: c 611 ILE cc_start: 0.9394 (mm) cc_final: 0.9150 (mm) REVERT: D 12 ASN cc_start: 0.9433 (t0) cc_final: 0.9022 (t0) REVERT: D 26 THR cc_start: 0.8946 (p) cc_final: 0.8370 (t) REVERT: d 115 GLU cc_start: 0.8712 (tt0) cc_final: 0.8252 (mm-30) REVERT: d 176 ASP cc_start: 0.9077 (m-30) cc_final: 0.8649 (m-30) REVERT: d 196 GLN cc_start: 0.8737 (mt0) cc_final: 0.8453 (mt0) REVERT: d 226 ASP cc_start: 0.8760 (p0) cc_final: 0.8532 (p0) REVERT: d 250 MET cc_start: 0.8933 (tpt) cc_final: 0.8583 (tpp) REVERT: d 260 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8552 (mm-30) REVERT: d 376 MET cc_start: 0.8887 (tpp) cc_final: 0.8148 (tmm) REVERT: d 606 ASP cc_start: 0.8677 (t0) cc_final: 0.8420 (t0) REVERT: e 97 ASP cc_start: 0.8907 (p0) cc_final: 0.8519 (p0) REVERT: e 98 GLU cc_start: 0.8438 (pm20) cc_final: 0.8192 (pm20) REVERT: e 189 GLU cc_start: 0.8986 (tp30) cc_final: 0.8576 (tm-30) REVERT: e 219 LEU cc_start: 0.9896 (mt) cc_final: 0.9664 (mt) REVERT: e 223 LEU cc_start: 0.9730 (mt) cc_final: 0.9399 (mp) REVERT: e 336 MET cc_start: 0.9232 (tmm) cc_final: 0.8424 (tpp) REVERT: f 123 GLU cc_start: 0.8231 (pm20) cc_final: 0.7848 (pm20) REVERT: f 250 MET cc_start: 0.8782 (tpp) cc_final: 0.8544 (tpp) REVERT: f 251 ASP cc_start: 0.9165 (t70) cc_final: 0.8282 (t0) REVERT: f 254 GLU cc_start: 0.8821 (mp0) cc_final: 0.8200 (mp0) REVERT: f 336 MET cc_start: 0.8769 (tmm) cc_final: 0.7788 (tmm) REVERT: f 376 MET cc_start: 0.9401 (mmm) cc_final: 0.9075 (mmm) REVERT: f 464 MET cc_start: 0.9025 (tpp) cc_final: 0.8694 (tpp) REVERT: f 632 LYS cc_start: 0.9428 (mtpp) cc_final: 0.9186 (mtpp) REVERT: G 12 ASN cc_start: 0.9249 (t0) cc_final: 0.8777 (t0) REVERT: g 64 ARG cc_start: 0.8938 (ptm-80) cc_final: 0.7594 (mmt180) REVERT: g 183 LYS cc_start: 0.9475 (tppt) cc_final: 0.9123 (tppt) REVERT: g 223 LEU cc_start: 0.9546 (mt) cc_final: 0.9343 (mp) REVERT: g 260 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8392 (tp30) REVERT: g 548 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8829 (tp30) REVERT: H 25 GLU cc_start: 0.9214 (mp0) cc_final: 0.8754 (pm20) REVERT: h 280 GLU cc_start: 0.8857 (pm20) cc_final: 0.8649 (pm20) REVERT: h 297 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8810 (tp30) REVERT: h 317 LYS cc_start: 0.8751 (mppt) cc_final: 0.8534 (mppt) REVERT: h 346 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8841 (mt0) REVERT: h 594 LYS cc_start: 0.9600 (mtpp) cc_final: 0.9354 (mtpp) REVERT: I 12 ASN cc_start: 0.9536 (t0) cc_final: 0.9124 (t0) REVERT: I 21 LYS cc_start: 0.9173 (mttp) cc_final: 0.8867 (mtpt) REVERT: i 95 TYR cc_start: 0.7598 (m-80) cc_final: 0.7355 (m-80) REVERT: i 126 ASP cc_start: 0.7379 (t0) cc_final: 0.6895 (m-30) REVERT: i 161 LYS cc_start: 0.9631 (mmmt) cc_final: 0.9357 (mmmm) REVERT: i 189 GLU cc_start: 0.8822 (tp30) cc_final: 0.8492 (tp30) REVERT: i 212 MET cc_start: 0.8805 (mmm) cc_final: 0.8590 (tpp) REVERT: i 250 MET cc_start: 0.8994 (tmm) cc_final: 0.8707 (tmm) REVERT: i 251 ASP cc_start: 0.9101 (t0) cc_final: 0.8403 (t0) REVERT: i 254 GLU cc_start: 0.9023 (mp0) cc_final: 0.8608 (mp0) REVERT: i 290 MET cc_start: 0.9388 (tpp) cc_final: 0.8961 (mmm) REVERT: i 299 GLU cc_start: 0.8815 (mp0) cc_final: 0.8382 (tp30) REVERT: i 457 LEU cc_start: 0.9205 (mp) cc_final: 0.8918 (pp) REVERT: i 512 GLU cc_start: 0.8698 (pp20) cc_final: 0.8483 (pp20) REVERT: i 553 ASP cc_start: 0.8148 (t0) cc_final: 0.7503 (t0) REVERT: i 554 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7192 (m-30) REVERT: J 12 ASN cc_start: 0.9273 (t0) cc_final: 0.8896 (t0) REVERT: J 21 LYS cc_start: 0.9232 (ttmm) cc_final: 0.8922 (mmmm) REVERT: J 40 MET cc_start: 0.8267 (ttt) cc_final: 0.7786 (tmm) REVERT: j 54 GLU cc_start: 0.8601 (pp20) cc_final: 0.8369 (tm-30) REVERT: j 176 ASP cc_start: 0.9090 (m-30) cc_final: 0.8710 (m-30) REVERT: j 182 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9522 (mm) REVERT: j 183 LYS cc_start: 0.6202 (mttm) cc_final: 0.5684 (ttmt) REVERT: j 250 MET cc_start: 0.9037 (ttp) cc_final: 0.8689 (tmm) REVERT: j 299 GLU cc_start: 0.5885 (tm-30) cc_final: 0.5409 (tm-30) REVERT: j 376 MET cc_start: 0.9084 (tpp) cc_final: 0.8481 (tmm) REVERT: j 539 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8851 (tpp) REVERT: j 572 LEU cc_start: 0.9779 (mt) cc_final: 0.9560 (mt) REVERT: j 600 MET cc_start: 0.8832 (tpp) cc_final: 0.8629 (tpp) REVERT: j 632 LYS cc_start: 0.9486 (mtmm) cc_final: 0.8963 (tptt) REVERT: K 69 ASP cc_start: 0.8377 (t70) cc_final: 0.7974 (t0) REVERT: K 142 MET cc_start: 0.9273 (mmm) cc_final: 0.8977 (tpp) REVERT: K 182 ASP cc_start: 0.9113 (m-30) cc_final: 0.8326 (p0) REVERT: K 253 ASP cc_start: 0.9379 (m-30) cc_final: 0.9128 (m-30) REVERT: K 325 ARG cc_start: 0.9140 (ptp-110) cc_final: 0.8631 (ptp-110) REVERT: K 375 LEU cc_start: 0.9620 (tt) cc_final: 0.9279 (tt) REVERT: K 409 GLU cc_start: 0.8639 (tp30) cc_final: 0.8037 (tp30) REVERT: K 413 MET cc_start: 0.9047 (mmm) cc_final: 0.8411 (mmm) REVERT: K 537 LYS cc_start: 0.9448 (mmtm) cc_final: 0.9236 (mptt) REVERT: K 577 ASP cc_start: 0.8524 (t70) cc_final: 0.8122 (t0) REVERT: K 579 ASP cc_start: 0.7715 (p0) cc_final: 0.6907 (p0) REVERT: K 736 ASN cc_start: 0.8801 (m-40) cc_final: 0.8005 (m-40) REVERT: K 778 ARG cc_start: 0.6309 (mtt180) cc_final: 0.5801 (tpt-90) REVERT: K 781 GLU cc_start: 0.8664 (pm20) cc_final: 0.8348 (pm20) REVERT: K 838 GLU cc_start: 0.8858 (tt0) cc_final: 0.8609 (pt0) REVERT: K 843 THR cc_start: 0.9499 (OUTLIER) cc_final: 0.9232 (p) REVERT: K 856 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8584 (mp10) REVERT: K 901 MET cc_start: 0.8290 (mtp) cc_final: 0.7757 (ttm) REVERT: K 963 MET cc_start: 0.8644 (mpp) cc_final: 0.8294 (mpp) REVERT: K 1019 MET cc_start: 0.9247 (mmm) cc_final: 0.9019 (mmm) REVERT: K 1072 MET cc_start: 0.8993 (mmm) cc_final: 0.8720 (mmm) outliers start: 149 outliers final: 104 residues processed: 977 average time/residue: 0.5459 time to fit residues: 930.5619 Evaluate side-chains 943 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 830 time to evaluate : 5.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain a residue 231 ARG Chi-restraints excluded: chain a residue 339 LYS Chi-restraints excluded: chain a residue 424 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain a residue 513 VAL Chi-restraints excluded: chain a residue 548 GLU Chi-restraints excluded: chain a residue 635 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain b residue 105 GLU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 221 ASP Chi-restraints excluded: chain b residue 275 SER Chi-restraints excluded: chain b residue 279 LEU Chi-restraints excluded: chain b residue 325 THR Chi-restraints excluded: chain b residue 359 LEU Chi-restraints excluded: chain b residue 527 LEU Chi-restraints excluded: chain b residue 617 VAL Chi-restraints excluded: chain b residue 644 VAL Chi-restraints excluded: chain b residue 665 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain c residue 196 GLN Chi-restraints excluded: chain c residue 207 GLU Chi-restraints excluded: chain c residue 265 VAL Chi-restraints excluded: chain c residue 301 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 223 LEU Chi-restraints excluded: chain d residue 268 SER Chi-restraints excluded: chain d residue 359 LEU Chi-restraints excluded: chain d residue 403 VAL Chi-restraints excluded: chain d residue 457 LEU Chi-restraints excluded: chain d residue 546 ILE Chi-restraints excluded: chain d residue 669 SER Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain e residue 66 MET Chi-restraints excluded: chain e residue 106 HIS Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain e residue 154 GLN Chi-restraints excluded: chain e residue 359 LEU Chi-restraints excluded: chain e residue 403 VAL Chi-restraints excluded: chain e residue 437 PHE Chi-restraints excluded: chain e residue 572 LEU Chi-restraints excluded: chain f residue 234 LYS Chi-restraints excluded: chain f residue 253 SER Chi-restraints excluded: chain f residue 301 ILE Chi-restraints excluded: chain f residue 304 LEU Chi-restraints excluded: chain f residue 311 VAL Chi-restraints excluded: chain f residue 359 LEU Chi-restraints excluded: chain f residue 446 THR Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 505 VAL Chi-restraints excluded: chain f residue 610 ILE Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 359 LEU Chi-restraints excluded: chain g residue 424 VAL Chi-restraints excluded: chain g residue 541 ASP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain h residue 346 GLN Chi-restraints excluded: chain h residue 359 LEU Chi-restraints excluded: chain h residue 527 LEU Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain i residue 130 VAL Chi-restraints excluded: chain i residue 327 ARG Chi-restraints excluded: chain i residue 403 VAL Chi-restraints excluded: chain i residue 471 THR Chi-restraints excluded: chain i residue 554 ASP Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain j residue 115 GLU Chi-restraints excluded: chain j residue 138 SER Chi-restraints excluded: chain j residue 182 LEU Chi-restraints excluded: chain j residue 347 ILE Chi-restraints excluded: chain j residue 359 LEU Chi-restraints excluded: chain j residue 402 ILE Chi-restraints excluded: chain j residue 483 MET Chi-restraints excluded: chain j residue 539 MET Chi-restraints excluded: chain j residue 562 SER Chi-restraints excluded: chain j residue 651 LEU Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 249 ILE Chi-restraints excluded: chain K residue 603 MET Chi-restraints excluded: chain K residue 712 GLU Chi-restraints excluded: chain K residue 824 VAL Chi-restraints excluded: chain K residue 843 THR Chi-restraints excluded: chain K residue 860 CYS Chi-restraints excluded: chain K residue 942 ILE Chi-restraints excluded: chain K residue 982 VAL Chi-restraints excluded: chain K residue 984 LEU Chi-restraints excluded: chain K residue 1165 ILE Chi-restraints excluded: chain K residue 1222 LEU Chi-restraints excluded: chain K residue 1263 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 689 optimal weight: 0.9980 chunk 725 optimal weight: 10.0000 chunk 662 optimal weight: 4.9990 chunk 705 optimal weight: 9.9990 chunk 424 optimal weight: 7.9990 chunk 307 optimal weight: 5.9990 chunk 554 optimal weight: 20.0000 chunk 216 optimal weight: 6.9990 chunk 637 optimal weight: 7.9990 chunk 667 optimal weight: 5.9990 chunk 703 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 179 GLN ** c 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 106 HIS e 288 GLN ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 GLN ** K 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 61867 Z= 0.245 Angle : 0.670 15.056 84461 Z= 0.338 Chirality : 0.046 0.224 9924 Planarity : 0.005 0.057 10909 Dihedral : 4.926 58.375 8542 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 2.23 % Allowed : 18.66 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.10), residues: 7872 helix: 1.21 (0.10), residues: 2613 sheet: -1.12 (0.14), residues: 1311 loop : -0.53 (0.10), residues: 3948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP K 624 HIS 0.029 0.001 HIS e 106 PHE 0.014 0.001 PHE b 401 TYR 0.037 0.001 TYR g 95 ARG 0.007 0.000 ARG K 757 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 841 time to evaluate : 5.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.9207 (m) cc_final: 0.8720 (t) REVERT: a 212 MET cc_start: 0.8814 (tpt) cc_final: 0.8425 (tpp) REVERT: a 231 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8861 (mtt90) REVERT: a 336 MET cc_start: 0.9158 (tmm) cc_final: 0.8815 (tpp) REVERT: a 548 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8568 (pm20) REVERT: B 40 MET cc_start: 0.8794 (ttp) cc_final: 0.7898 (tmm) REVERT: b 115 GLU cc_start: 0.8494 (tt0) cc_final: 0.8164 (tp30) REVERT: b 176 ASP cc_start: 0.8735 (t0) cc_final: 0.8402 (t0) REVERT: b 205 ILE cc_start: 0.9276 (tp) cc_final: 0.9052 (tt) REVERT: b 464 MET cc_start: 0.9070 (tpp) cc_final: 0.8754 (tpp) REVERT: b 483 MET cc_start: 0.8623 (mmm) cc_final: 0.8237 (mmm) REVERT: b 560 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8245 (mp0) REVERT: C 12 ASN cc_start: 0.9156 (t0) cc_final: 0.8542 (t0) REVERT: C 21 LYS cc_start: 0.9501 (ttmm) cc_final: 0.9068 (ttmm) REVERT: C 25 GLU cc_start: 0.9206 (mp0) cc_final: 0.8942 (mp0) REVERT: C 27 SER cc_start: 0.9421 (OUTLIER) cc_final: 0.9054 (p) REVERT: C 33 SER cc_start: 0.9352 (p) cc_final: 0.8971 (t) REVERT: C 40 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7906 (ttt) REVERT: c 66 MET cc_start: 0.8532 (mtp) cc_final: 0.7993 (ttm) REVERT: c 207 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: c 212 MET cc_start: 0.8917 (mmm) cc_final: 0.8553 (tpp) REVERT: c 250 MET cc_start: 0.9035 (tmm) cc_final: 0.8793 (tmm) REVERT: c 254 GLU cc_start: 0.9080 (mp0) cc_final: 0.8854 (pm20) REVERT: c 287 GLU cc_start: 0.8751 (pp20) cc_final: 0.8455 (pp20) REVERT: c 294 THR cc_start: 0.9400 (m) cc_final: 0.9122 (p) REVERT: c 376 MET cc_start: 0.9238 (mmm) cc_final: 0.8894 (mmm) REVERT: c 464 MET cc_start: 0.9579 (tpp) cc_final: 0.9354 (mmm) REVERT: c 600 MET cc_start: 0.9318 (ttp) cc_final: 0.9085 (ttp) REVERT: c 611 ILE cc_start: 0.9422 (mm) cc_final: 0.9195 (mm) REVERT: D 12 ASN cc_start: 0.9414 (t0) cc_final: 0.9020 (t0) REVERT: D 26 THR cc_start: 0.8929 (p) cc_final: 0.8350 (t) REVERT: d 82 SER cc_start: 0.9058 (p) cc_final: 0.8856 (p) REVERT: d 115 GLU cc_start: 0.8739 (tt0) cc_final: 0.8288 (mm-30) REVERT: d 176 ASP cc_start: 0.9068 (m-30) cc_final: 0.8654 (m-30) REVERT: d 196 GLN cc_start: 0.8741 (mt0) cc_final: 0.8436 (mt0) REVERT: d 226 ASP cc_start: 0.8775 (p0) cc_final: 0.8542 (p0) REVERT: d 250 MET cc_start: 0.8940 (tpt) cc_final: 0.8605 (tpp) REVERT: d 258 MET cc_start: 0.8469 (ttm) cc_final: 0.7803 (ttt) REVERT: d 260 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8355 (mm-30) REVERT: d 606 ASP cc_start: 0.8690 (t0) cc_final: 0.8412 (t0) REVERT: d 655 GLU cc_start: 0.8449 (pp20) cc_final: 0.8233 (tm-30) REVERT: E 12 ASN cc_start: 0.9150 (t0) cc_final: 0.8686 (t0) REVERT: e 97 ASP cc_start: 0.8887 (p0) cc_final: 0.8548 (p0) REVERT: e 189 GLU cc_start: 0.8983 (tp30) cc_final: 0.8594 (tm-30) REVERT: e 219 LEU cc_start: 0.9889 (mt) cc_final: 0.9668 (mt) REVERT: e 223 LEU cc_start: 0.9731 (mt) cc_final: 0.9402 (mp) REVERT: e 336 MET cc_start: 0.9238 (tmm) cc_final: 0.8386 (tpp) REVERT: F 40 MET cc_start: 0.8065 (tmm) cc_final: 0.7795 (tmm) REVERT: f 123 GLU cc_start: 0.8324 (pm20) cc_final: 0.7943 (pm20) REVERT: f 250 MET cc_start: 0.8756 (tpp) cc_final: 0.8540 (tpp) REVERT: f 251 ASP cc_start: 0.9180 (t70) cc_final: 0.8283 (t0) REVERT: f 254 GLU cc_start: 0.8807 (mp0) cc_final: 0.8173 (mp0) REVERT: f 336 MET cc_start: 0.8769 (tmm) cc_final: 0.7863 (tmm) REVERT: f 464 MET cc_start: 0.9043 (tpp) cc_final: 0.8723 (tpp) REVERT: G 12 ASN cc_start: 0.9289 (t0) cc_final: 0.8789 (t0) REVERT: g 64 ARG cc_start: 0.8972 (ptm-80) cc_final: 0.7600 (mmt180) REVERT: g 183 LYS cc_start: 0.9487 (tppt) cc_final: 0.9137 (tppt) REVERT: g 260 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8399 (tp30) REVERT: g 548 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8823 (tp30) REVERT: H 25 GLU cc_start: 0.9239 (mp0) cc_final: 0.8761 (pm20) REVERT: h 297 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8850 (tp30) REVERT: h 317 LYS cc_start: 0.8753 (mppt) cc_final: 0.8543 (mppt) REVERT: h 346 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8819 (mt0) REVERT: h 594 LYS cc_start: 0.9603 (mtpp) cc_final: 0.9365 (mtpp) REVERT: I 12 ASN cc_start: 0.9553 (t0) cc_final: 0.9170 (t0) REVERT: I 21 LYS cc_start: 0.9190 (mttp) cc_final: 0.8883 (mtpt) REVERT: i 95 TYR cc_start: 0.7628 (m-80) cc_final: 0.7390 (m-80) REVERT: i 126 ASP cc_start: 0.7272 (t0) cc_final: 0.6960 (m-30) REVERT: i 161 LYS cc_start: 0.9634 (mmmt) cc_final: 0.9358 (mmmm) REVERT: i 189 GLU cc_start: 0.8840 (tp30) cc_final: 0.8507 (tp30) REVERT: i 212 MET cc_start: 0.8789 (mmm) cc_final: 0.8528 (tpp) REVERT: i 251 ASP cc_start: 0.9084 (t0) cc_final: 0.8239 (t0) REVERT: i 254 GLU cc_start: 0.9019 (mp0) cc_final: 0.8591 (mp0) REVERT: i 290 MET cc_start: 0.9398 (tpp) cc_final: 0.8969 (mmm) REVERT: i 457 LEU cc_start: 0.9212 (mp) cc_final: 0.8927 (pp) REVERT: i 512 GLU cc_start: 0.8698 (pp20) cc_final: 0.8486 (pp20) REVERT: i 553 ASP cc_start: 0.8183 (t0) cc_final: 0.7662 (t0) REVERT: i 554 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7244 (m-30) REVERT: J 12 ASN cc_start: 0.9260 (t0) cc_final: 0.8887 (t0) REVERT: J 21 LYS cc_start: 0.9195 (ttmm) cc_final: 0.8872 (mmmm) REVERT: J 40 MET cc_start: 0.8361 (ttt) cc_final: 0.7799 (tmm) REVERT: j 54 GLU cc_start: 0.8649 (pp20) cc_final: 0.8366 (tm-30) REVERT: j 176 ASP cc_start: 0.9091 (m-30) cc_final: 0.8677 (m-30) REVERT: j 182 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9500 (mm) REVERT: j 183 LYS cc_start: 0.6161 (mttm) cc_final: 0.5836 (mttt) REVERT: j 250 MET cc_start: 0.9078 (ttp) cc_final: 0.8601 (tmm) REVERT: j 299 GLU cc_start: 0.5907 (tm-30) cc_final: 0.5423 (tm-30) REVERT: j 376 MET cc_start: 0.9056 (tpp) cc_final: 0.8438 (tmm) REVERT: j 572 LEU cc_start: 0.9773 (mt) cc_final: 0.9569 (mt) REVERT: j 600 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8640 (tpp) REVERT: j 632 LYS cc_start: 0.9510 (mtmm) cc_final: 0.8972 (tptt) REVERT: K 69 ASP cc_start: 0.8455 (t70) cc_final: 0.8184 (t0) REVERT: K 93 LEU cc_start: 0.9631 (tp) cc_final: 0.9419 (tp) REVERT: K 142 MET cc_start: 0.9284 (mmm) cc_final: 0.9001 (tpp) REVERT: K 182 ASP cc_start: 0.9172 (m-30) cc_final: 0.8664 (p0) REVERT: K 253 ASP cc_start: 0.9391 (m-30) cc_final: 0.9127 (m-30) REVERT: K 258 GLU cc_start: 0.8996 (tp30) cc_final: 0.8698 (mm-30) REVERT: K 325 ARG cc_start: 0.9170 (ptp-110) cc_final: 0.8956 (ptp-110) REVERT: K 375 LEU cc_start: 0.9633 (tt) cc_final: 0.9305 (tt) REVERT: K 409 GLU cc_start: 0.8645 (tp30) cc_final: 0.8061 (tp30) REVERT: K 413 MET cc_start: 0.9067 (mmm) cc_final: 0.8453 (mmm) REVERT: K 577 ASP cc_start: 0.8582 (t70) cc_final: 0.8165 (t0) REVERT: K 579 ASP cc_start: 0.7979 (p0) cc_final: 0.7409 (p0) REVERT: K 736 ASN cc_start: 0.8809 (m-40) cc_final: 0.7988 (m-40) REVERT: K 778 ARG cc_start: 0.6327 (mtt180) cc_final: 0.5793 (tpt-90) REVERT: K 781 GLU cc_start: 0.8663 (pm20) cc_final: 0.8355 (pm20) REVERT: K 796 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8137 (mp0) REVERT: K 843 THR cc_start: 0.9498 (OUTLIER) cc_final: 0.9217 (p) REVERT: K 856 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8600 (mp10) REVERT: K 901 MET cc_start: 0.8343 (mtp) cc_final: 0.7798 (ttm) REVERT: K 963 MET cc_start: 0.8650 (mpp) cc_final: 0.8327 (mpp) REVERT: K 1019 MET cc_start: 0.9259 (mmm) cc_final: 0.9019 (mmm) REVERT: K 1072 MET cc_start: 0.8997 (mmm) cc_final: 0.8734 (mmm) REVERT: K 1154 MET cc_start: 0.9034 (tpt) cc_final: 0.8703 (tpt) outliers start: 150 outliers final: 115 residues processed: 939 average time/residue: 0.5351 time to fit residues: 876.4907 Evaluate side-chains 937 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 812 time to evaluate : 5.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain a residue 231 ARG Chi-restraints excluded: chain a residue 339 LYS Chi-restraints excluded: chain a residue 424 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain a residue 513 VAL Chi-restraints excluded: chain a residue 548 GLU Chi-restraints excluded: chain a residue 635 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 105 GLU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain b residue 179 GLN Chi-restraints excluded: chain b residue 221 ASP Chi-restraints excluded: chain b residue 275 SER Chi-restraints excluded: chain b residue 325 THR Chi-restraints excluded: chain b residue 359 LEU Chi-restraints excluded: chain b residue 527 LEU Chi-restraints excluded: chain b residue 617 VAL Chi-restraints excluded: chain b residue 644 VAL Chi-restraints excluded: chain b residue 665 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain c residue 90 SER Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain c residue 207 GLU Chi-restraints excluded: chain c residue 265 VAL Chi-restraints excluded: chain c residue 301 ILE Chi-restraints excluded: chain c residue 342 ASN Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain d residue 182 LEU Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain d residue 223 LEU Chi-restraints excluded: chain d residue 268 SER Chi-restraints excluded: chain d residue 359 LEU Chi-restraints excluded: chain d residue 403 VAL Chi-restraints excluded: chain d residue 457 LEU Chi-restraints excluded: chain d residue 546 ILE Chi-restraints excluded: chain d residue 669 SER Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain e residue 66 MET Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain e residue 154 GLN Chi-restraints excluded: chain e residue 288 GLN Chi-restraints excluded: chain e residue 359 LEU Chi-restraints excluded: chain e residue 403 VAL Chi-restraints excluded: chain e residue 437 PHE Chi-restraints excluded: chain e residue 572 LEU Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 234 LYS Chi-restraints excluded: chain f residue 253 SER Chi-restraints excluded: chain f residue 301 ILE Chi-restraints excluded: chain f residue 304 LEU Chi-restraints excluded: chain f residue 311 VAL Chi-restraints excluded: chain f residue 359 LEU Chi-restraints excluded: chain f residue 446 THR Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 505 VAL Chi-restraints excluded: chain f residue 610 ILE Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 359 LEU Chi-restraints excluded: chain g residue 424 VAL Chi-restraints excluded: chain g residue 541 ASP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain h residue 346 GLN Chi-restraints excluded: chain h residue 359 LEU Chi-restraints excluded: chain h residue 527 LEU Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain i residue 130 VAL Chi-restraints excluded: chain i residue 327 ARG Chi-restraints excluded: chain i residue 403 VAL Chi-restraints excluded: chain i residue 554 ASP Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 115 GLU Chi-restraints excluded: chain j residue 138 SER Chi-restraints excluded: chain j residue 182 LEU Chi-restraints excluded: chain j residue 209 SER Chi-restraints excluded: chain j residue 253 SER Chi-restraints excluded: chain j residue 347 ILE Chi-restraints excluded: chain j residue 359 LEU Chi-restraints excluded: chain j residue 402 ILE Chi-restraints excluded: chain j residue 562 SER Chi-restraints excluded: chain j residue 600 MET Chi-restraints excluded: chain j residue 651 LEU Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain K residue 249 ILE Chi-restraints excluded: chain K residue 603 MET Chi-restraints excluded: chain K residue 682 GLU Chi-restraints excluded: chain K residue 712 GLU Chi-restraints excluded: chain K residue 824 VAL Chi-restraints excluded: chain K residue 843 THR Chi-restraints excluded: chain K residue 860 CYS Chi-restraints excluded: chain K residue 942 ILE Chi-restraints excluded: chain K residue 982 VAL Chi-restraints excluded: chain K residue 984 LEU Chi-restraints excluded: chain K residue 1165 ILE Chi-restraints excluded: chain K residue 1222 LEU Chi-restraints excluded: chain K residue 1263 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 463 optimal weight: 0.9980 chunk 746 optimal weight: 20.0000 chunk 455 optimal weight: 20.0000 chunk 354 optimal weight: 10.0000 chunk 518 optimal weight: 10.0000 chunk 783 optimal weight: 20.0000 chunk 720 optimal weight: 1.9990 chunk 623 optimal weight: 20.0000 chunk 64 optimal weight: 0.2980 chunk 481 optimal weight: 8.9990 chunk 382 optimal weight: 10.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 288 GLN ** f 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 61867 Z= 0.234 Angle : 0.688 15.536 84461 Z= 0.346 Chirality : 0.046 0.395 9924 Planarity : 0.005 0.057 10909 Dihedral : 4.927 59.614 8542 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 1.95 % Allowed : 19.21 % Favored : 78.84 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.10), residues: 7872 helix: 1.19 (0.10), residues: 2621 sheet: -1.04 (0.14), residues: 1372 loop : -0.51 (0.10), residues: 3879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP K 624 HIS 0.008 0.001 HIS g 106 PHE 0.013 0.001 PHE b 401 TYR 0.022 0.001 TYR c 232 ARG 0.006 0.000 ARG K 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 840 time to evaluate : 5.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.9224 (m) cc_final: 0.8745 (t) REVERT: a 212 MET cc_start: 0.8814 (tpt) cc_final: 0.8434 (tpp) REVERT: a 231 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8866 (mtt90) REVERT: a 336 MET cc_start: 0.9157 (tmm) cc_final: 0.8778 (tpp) REVERT: a 548 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8571 (pm20) REVERT: B 40 MET cc_start: 0.8752 (ttp) cc_final: 0.7866 (tmm) REVERT: b 115 GLU cc_start: 0.8458 (tt0) cc_final: 0.8162 (tp30) REVERT: b 176 ASP cc_start: 0.8696 (t0) cc_final: 0.8403 (t0) REVERT: b 205 ILE cc_start: 0.9275 (tp) cc_final: 0.9053 (tt) REVERT: b 464 MET cc_start: 0.9074 (tpp) cc_final: 0.8755 (tpp) REVERT: b 483 MET cc_start: 0.8683 (mmm) cc_final: 0.8300 (mmm) REVERT: b 560 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8202 (mp0) REVERT: C 12 ASN cc_start: 0.9168 (t0) cc_final: 0.8565 (t0) REVERT: C 21 LYS cc_start: 0.9491 (ttmm) cc_final: 0.9064 (ttmm) REVERT: C 25 GLU cc_start: 0.9208 (mp0) cc_final: 0.8957 (mp0) REVERT: C 27 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.9072 (p) REVERT: C 33 SER cc_start: 0.9334 (p) cc_final: 0.8953 (t) REVERT: C 40 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7906 (ttt) REVERT: c 66 MET cc_start: 0.8559 (mtp) cc_final: 0.8161 (ttm) REVERT: c 207 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: c 212 MET cc_start: 0.8964 (mmm) cc_final: 0.8588 (tpp) REVERT: c 250 MET cc_start: 0.9015 (tmm) cc_final: 0.8314 (tmm) REVERT: c 254 GLU cc_start: 0.9074 (mp0) cc_final: 0.8852 (pm20) REVERT: c 287 GLU cc_start: 0.8763 (pp20) cc_final: 0.8464 (pp20) REVERT: c 294 THR cc_start: 0.9376 (m) cc_final: 0.9083 (p) REVERT: c 376 MET cc_start: 0.9234 (mmm) cc_final: 0.8894 (mmm) REVERT: c 464 MET cc_start: 0.9583 (tpp) cc_final: 0.9341 (mmm) REVERT: c 600 MET cc_start: 0.9318 (ttp) cc_final: 0.9092 (ttp) REVERT: c 611 ILE cc_start: 0.9420 (mm) cc_final: 0.9191 (mm) REVERT: D 12 ASN cc_start: 0.9417 (t0) cc_final: 0.9041 (t0) REVERT: D 26 THR cc_start: 0.8914 (p) cc_final: 0.8331 (t) REVERT: d 115 GLU cc_start: 0.8709 (tt0) cc_final: 0.8263 (mm-30) REVERT: d 226 ASP cc_start: 0.8774 (p0) cc_final: 0.8529 (p0) REVERT: d 250 MET cc_start: 0.8927 (tpt) cc_final: 0.8586 (tpp) REVERT: d 258 MET cc_start: 0.8438 (ttm) cc_final: 0.7825 (ttt) REVERT: d 260 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8342 (mm-30) REVERT: d 606 ASP cc_start: 0.8677 (t0) cc_final: 0.8399 (t0) REVERT: d 655 GLU cc_start: 0.8533 (pp20) cc_final: 0.8309 (tm-30) REVERT: E 12 ASN cc_start: 0.9150 (t0) cc_final: 0.8670 (t0) REVERT: e 189 GLU cc_start: 0.8974 (tp30) cc_final: 0.8587 (tm-30) REVERT: e 212 MET cc_start: 0.8968 (tpp) cc_final: 0.8451 (mpp) REVERT: e 219 LEU cc_start: 0.9886 (mt) cc_final: 0.9669 (mt) REVERT: e 223 LEU cc_start: 0.9724 (mt) cc_final: 0.9384 (mp) REVERT: e 287 GLU cc_start: 0.9142 (pt0) cc_final: 0.8800 (pp20) REVERT: e 288 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.8771 (mt0) REVERT: e 336 MET cc_start: 0.9218 (tmm) cc_final: 0.8361 (tpp) REVERT: F 40 MET cc_start: 0.7884 (tmm) cc_final: 0.7574 (tmm) REVERT: f 123 GLU cc_start: 0.8314 (pm20) cc_final: 0.7942 (pm20) REVERT: f 250 MET cc_start: 0.8767 (tpp) cc_final: 0.8518 (tpp) REVERT: f 251 ASP cc_start: 0.9203 (t70) cc_final: 0.8286 (t0) REVERT: f 254 GLU cc_start: 0.8809 (mp0) cc_final: 0.8186 (mp0) REVERT: f 336 MET cc_start: 0.8778 (tmm) cc_final: 0.7873 (tmm) REVERT: f 464 MET cc_start: 0.9037 (tpp) cc_final: 0.8719 (tpp) REVERT: G 12 ASN cc_start: 0.9306 (t0) cc_final: 0.8805 (t0) REVERT: g 64 ARG cc_start: 0.8994 (ptm-80) cc_final: 0.7603 (mmt180) REVERT: g 260 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8416 (tp30) REVERT: g 548 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8820 (tp30) REVERT: H 25 GLU cc_start: 0.9252 (mp0) cc_final: 0.8761 (pm20) REVERT: h 297 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8841 (tp30) REVERT: h 346 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8827 (mt0) REVERT: h 594 LYS cc_start: 0.9628 (mtpp) cc_final: 0.9388 (mtpp) REVERT: I 12 ASN cc_start: 0.9562 (t0) cc_final: 0.9174 (t0) REVERT: I 21 LYS cc_start: 0.9195 (mttp) cc_final: 0.8883 (mtpt) REVERT: i 95 TYR cc_start: 0.7642 (m-80) cc_final: 0.7398 (m-80) REVERT: i 126 ASP cc_start: 0.7341 (t0) cc_final: 0.6892 (m-30) REVERT: i 161 LYS cc_start: 0.9627 (mmmt) cc_final: 0.9369 (mmmm) REVERT: i 189 GLU cc_start: 0.8854 (tp30) cc_final: 0.8521 (tp30) REVERT: i 212 MET cc_start: 0.8773 (mmm) cc_final: 0.8493 (tpp) REVERT: i 250 MET cc_start: 0.8835 (tmm) cc_final: 0.8625 (tmm) REVERT: i 251 ASP cc_start: 0.9084 (t0) cc_final: 0.8370 (t0) REVERT: i 254 GLU cc_start: 0.9024 (mp0) cc_final: 0.8480 (mp0) REVERT: i 290 MET cc_start: 0.9374 (tpp) cc_final: 0.8947 (mmm) REVERT: i 299 GLU cc_start: 0.8804 (mp0) cc_final: 0.8386 (tp30) REVERT: i 457 LEU cc_start: 0.9169 (mp) cc_final: 0.8888 (pp) REVERT: i 512 GLU cc_start: 0.8690 (pp20) cc_final: 0.8482 (pp20) REVERT: i 553 ASP cc_start: 0.8153 (t0) cc_final: 0.7458 (t0) REVERT: i 554 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7211 (m-30) REVERT: J 12 ASN cc_start: 0.9244 (t0) cc_final: 0.8853 (t0) REVERT: J 21 LYS cc_start: 0.9179 (ttmm) cc_final: 0.8872 (mmmm) REVERT: J 40 MET cc_start: 0.8359 (ttt) cc_final: 0.7815 (tmm) REVERT: j 54 GLU cc_start: 0.8658 (pp20) cc_final: 0.8348 (tm-30) REVERT: j 176 ASP cc_start: 0.9086 (m-30) cc_final: 0.8670 (m-30) REVERT: j 182 LEU cc_start: 0.9761 (OUTLIER) cc_final: 0.9507 (mm) REVERT: j 299 GLU cc_start: 0.5947 (tm-30) cc_final: 0.5458 (tm-30) REVERT: j 376 MET cc_start: 0.9079 (tpp) cc_final: 0.8517 (mmm) REVERT: j 572 LEU cc_start: 0.9771 (mt) cc_final: 0.9560 (mt) REVERT: j 600 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8636 (tpp) REVERT: j 632 LYS cc_start: 0.9517 (mtmm) cc_final: 0.8973 (tptt) REVERT: K 69 ASP cc_start: 0.8433 (t70) cc_final: 0.8161 (t0) REVERT: K 93 LEU cc_start: 0.9631 (tp) cc_final: 0.9415 (tp) REVERT: K 142 MET cc_start: 0.9291 (mmm) cc_final: 0.9001 (tpp) REVERT: K 182 ASP cc_start: 0.9202 (m-30) cc_final: 0.8363 (p0) REVERT: K 325 ARG cc_start: 0.9201 (ptp-110) cc_final: 0.8643 (ptp-110) REVERT: K 375 LEU cc_start: 0.9638 (tt) cc_final: 0.9314 (tt) REVERT: K 409 GLU cc_start: 0.8638 (tp30) cc_final: 0.8090 (tp30) REVERT: K 413 MET cc_start: 0.9075 (mmm) cc_final: 0.8450 (mmm) REVERT: K 577 ASP cc_start: 0.8575 (t70) cc_final: 0.8166 (t0) REVERT: K 579 ASP cc_start: 0.8002 (p0) cc_final: 0.7424 (p0) REVERT: K 778 ARG cc_start: 0.6289 (mtt180) cc_final: 0.5810 (tpt-90) REVERT: K 781 GLU cc_start: 0.8643 (pm20) cc_final: 0.8346 (pm20) REVERT: K 796 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8096 (mp0) REVERT: K 843 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.9213 (p) REVERT: K 856 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8591 (mp10) REVERT: K 901 MET cc_start: 0.8423 (mtp) cc_final: 0.7886 (ttm) REVERT: K 963 MET cc_start: 0.8688 (mpp) cc_final: 0.8382 (mpp) REVERT: K 1019 MET cc_start: 0.9298 (mmm) cc_final: 0.9058 (mmm) REVERT: K 1072 MET cc_start: 0.8977 (mmm) cc_final: 0.8722 (mmm) outliers start: 131 outliers final: 115 residues processed: 929 average time/residue: 0.5408 time to fit residues: 875.3432 Evaluate side-chains 935 residues out of total 6735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 809 time to evaluate : 6.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain a residue 231 ARG Chi-restraints excluded: chain a residue 339 LYS Chi-restraints excluded: chain a residue 424 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain a residue 513 VAL Chi-restraints excluded: chain a residue 548 GLU Chi-restraints excluded: chain a residue 635 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 105 GLU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 179 GLN Chi-restraints excluded: chain b residue 221 ASP Chi-restraints excluded: chain b residue 275 SER Chi-restraints excluded: chain b residue 325 THR Chi-restraints excluded: chain b residue 359 LEU Chi-restraints excluded: chain b residue 527 LEU Chi-restraints excluded: chain b residue 617 VAL Chi-restraints excluded: chain b residue 644 VAL Chi-restraints excluded: chain b residue 665 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain c residue 90 SER Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain c residue 182 LEU Chi-restraints excluded: chain c residue 207 GLU Chi-restraints excluded: chain c residue 265 VAL Chi-restraints excluded: chain c residue 342 ASN Chi-restraints excluded: chain c residue 617 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 182 LEU Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain d residue 223 LEU Chi-restraints excluded: chain d residue 268 SER Chi-restraints excluded: chain d residue 359 LEU Chi-restraints excluded: chain d residue 403 VAL Chi-restraints excluded: chain d residue 457 LEU Chi-restraints excluded: chain d residue 546 ILE Chi-restraints excluded: chain d residue 669 SER Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain e residue 66 MET Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain e residue 154 GLN Chi-restraints excluded: chain e residue 288 GLN Chi-restraints excluded: chain e residue 359 LEU Chi-restraints excluded: chain e residue 403 VAL Chi-restraints excluded: chain e residue 437 PHE Chi-restraints excluded: chain e residue 572 LEU Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 234 LYS Chi-restraints excluded: chain f residue 253 SER Chi-restraints excluded: chain f residue 301 ILE Chi-restraints excluded: chain f residue 304 LEU Chi-restraints excluded: chain f residue 311 VAL Chi-restraints excluded: chain f residue 359 LEU Chi-restraints excluded: chain f residue 446 THR Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 505 VAL Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 359 LEU Chi-restraints excluded: chain g residue 424 VAL Chi-restraints excluded: chain g residue 541 ASP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain h residue 292 LEU Chi-restraints excluded: chain h residue 346 GLN Chi-restraints excluded: chain h residue 359 LEU Chi-restraints excluded: chain h residue 527 LEU Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain i residue 130 VAL Chi-restraints excluded: chain i residue 327 ARG Chi-restraints excluded: chain i residue 403 VAL Chi-restraints excluded: chain i residue 554 ASP Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 115 GLU Chi-restraints excluded: chain j residue 138 SER Chi-restraints excluded: chain j residue 182 LEU Chi-restraints excluded: chain j residue 196 GLN Chi-restraints excluded: chain j residue 209 SER Chi-restraints excluded: chain j residue 347 ILE Chi-restraints excluded: chain j residue 359 LEU Chi-restraints excluded: chain j residue 402 ILE Chi-restraints excluded: chain j residue 483 MET Chi-restraints excluded: chain j residue 562 SER Chi-restraints excluded: chain j residue 600 MET Chi-restraints excluded: chain j residue 651 LEU Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain K residue 249 ILE Chi-restraints excluded: chain K residue 603 MET Chi-restraints excluded: chain K residue 682 GLU Chi-restraints excluded: chain K residue 712 GLU Chi-restraints excluded: chain K residue 824 VAL Chi-restraints excluded: chain K residue 837 LEU Chi-restraints excluded: chain K residue 843 THR Chi-restraints excluded: chain K residue 860 CYS Chi-restraints excluded: chain K residue 942 ILE Chi-restraints excluded: chain K residue 982 VAL Chi-restraints excluded: chain K residue 984 LEU Chi-restraints excluded: chain K residue 1222 LEU Chi-restraints excluded: chain K residue 1263 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 495 optimal weight: 0.9990 chunk 664 optimal weight: 7.9990 chunk 191 optimal weight: 0.0040 chunk 574 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 173 optimal weight: 40.0000 chunk 624 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 641 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 179 GLN ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 196 GLN ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.054240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.045284 restraints weight = 254773.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.046875 restraints weight = 126943.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.047963 restraints weight = 79758.429| |-----------------------------------------------------------------------------| r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 61867 Z= 0.241 Angle : 0.693 15.363 84461 Z= 0.347 Chirality : 0.046 0.417 9924 Planarity : 0.005 0.060 10909 Dihedral : 4.939 57.767 8542 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.36 % Favored : 95.59 % Rotamer: Outliers : 2.06 % Allowed : 19.20 % Favored : 78.74 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.18 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.10), residues: 7872 helix: 1.21 (0.10), residues: 2620 sheet: -1.02 (0.14), residues: 1372 loop : -0.49 (0.10), residues: 3880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP K 624 HIS 0.009 0.001 HIS g 106 PHE 0.014 0.001 PHE b 401 TYR 0.030 0.001 TYR K 178 ARG 0.006 0.000 ARG K 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15163.92 seconds wall clock time: 266 minutes 28.86 seconds (15988.86 seconds total)