Starting phenix.real_space_refine on Mon Feb 19 07:48:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qoo_14098/02_2024/7qoo_14098.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qoo_14098/02_2024/7qoo_14098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qoo_14098/02_2024/7qoo_14098.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qoo_14098/02_2024/7qoo_14098.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qoo_14098/02_2024/7qoo_14098.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qoo_14098/02_2024/7qoo_14098.pdb" } resolution = 4.6 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= 0.000 sd= 0.001 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 133 5.16 5 C 15411 2.51 5 N 4097 2.21 5 O 4444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24085 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "H" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1733 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 207} Chain: "I" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5042 Classifications: {'peptide': 618} Link IDs: {'PTRANS': 22, 'TRANS': 595} Chain breaks: 2 Chain: "K" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2100 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 242} Chain: "L" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2467 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 2 Chain: "M" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1350 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 167} Chain: "N" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2640 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Chain: "O" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1584 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 189} Chain: "P" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1891 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "U" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1535 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 180} Chain: "Q" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1667 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "R" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "T" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 878 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 575 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "X" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 76 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 12.38, per 1000 atoms: 0.51 Number of scatterers: 24085 At special positions: 0 Unit cell: (187.6, 155.4, 168.7, 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 133 16.00 O 4444 8.00 N 4097 7.00 C 15411 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 - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 8.33 Conformation dependent library (CDL) restraints added in 4.9 seconds 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5762 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 11 sheets defined 58.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'H' and resid 39 through 66 Processing helix chain 'H' and resid 74 through 118 removed outlier: 3.759A pdb=" N ILE H 78 " --> pdb=" O GLN H 74 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS H 118 " --> pdb=" O LYS H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 189 removed outlier: 4.457A pdb=" N ASP H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 224 removed outlier: 4.509A pdb=" N ILE H 198 " --> pdb=" O ARG H 194 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS H 207 " --> pdb=" O GLN H 203 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN H 217 " --> pdb=" O GLN H 213 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN H 218 " --> pdb=" O HIS H 214 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS H 224 " --> pdb=" O ILE H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 240 Processing helix chain 'I' and resid 60 through 74 removed outlier: 3.552A pdb=" N MET I 68 " --> pdb=" O ASP I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 100 removed outlier: 3.977A pdb=" N VAL I 95 " --> pdb=" O HIS I 91 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN I 97 " --> pdb=" O LYS I 93 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL I 98 " --> pdb=" O THR I 94 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA I 99 " --> pdb=" O VAL I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 117 removed outlier: 3.660A pdb=" N ASP I 110 " --> pdb=" O SER I 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN I 114 " --> pdb=" O ASP I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 132 removed outlier: 3.928A pdb=" N ASN I 126 " --> pdb=" O GLY I 122 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG I 128 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE I 129 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU I 130 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N CYS I 132 " --> pdb=" O ARG I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 152 removed outlier: 3.546A pdb=" N VAL I 148 " --> pdb=" O VAL I 144 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER I 149 " --> pdb=" O VAL I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 171 removed outlier: 3.887A pdb=" N LYS I 161 " --> pdb=" O SER I 157 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL I 162 " --> pdb=" O GLY I 158 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 183 No H-bonds generated for 'chain 'I' and resid 181 through 183' Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 197 through 207 removed outlier: 3.505A pdb=" N CYS I 202 " --> pdb=" O CYS I 198 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS I 203 " --> pdb=" O PRO I 199 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU I 204 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU I 207 " --> pdb=" O HIS I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 230 removed outlier: 3.718A pdb=" N LEU I 222 " --> pdb=" O ARG I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 246 removed outlier: 3.548A pdb=" N LEU I 238 " --> pdb=" O HIS I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 250 removed outlier: 3.680A pdb=" N ILE I 250 " --> pdb=" O PRO I 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 247 through 250' Processing helix chain 'I' and resid 267 through 274 Processing helix chain 'I' and resid 340 through 344 removed outlier: 3.518A pdb=" N GLN I 343 " --> pdb=" O PRO I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 353 removed outlier: 3.687A pdb=" N LEU I 351 " --> pdb=" O PHE I 347 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN I 352 " --> pdb=" O PRO I 348 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN I 353 " --> pdb=" O GLN I 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 347 through 353' Processing helix chain 'I' and resid 372 through 377 removed outlier: 3.567A pdb=" N ILE I 376 " --> pdb=" O LEU I 372 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN I 377 " --> pdb=" O LEU I 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 372 through 377' Processing helix chain 'I' and resid 382 through 399 removed outlier: 3.502A pdb=" N ARG I 387 " --> pdb=" O PRO I 383 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE I 388 " --> pdb=" O VAL I 384 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU I 392 " --> pdb=" O PHE I 388 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN I 394 " --> pdb=" O TYR I 390 " (cutoff:3.500A) Processing helix chain 'I' and resid 407 through 429 removed outlier: 3.608A pdb=" N THR I 420 " --> pdb=" O ASN I 416 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG I 423 " --> pdb=" O ASP I 419 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS I 426 " --> pdb=" O ILE I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 443 removed outlier: 3.500A pdb=" N GLU I 436 " --> pdb=" O PHE I 432 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA I 437 " --> pdb=" O TYR I 433 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS I 441 " --> pdb=" O ALA I 437 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU I 443 " --> pdb=" O LEU I 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 456 Processing helix chain 'I' and resid 466 through 474 removed outlier: 3.679A pdb=" N VAL I 470 " --> pdb=" O SER I 466 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS I 471 " --> pdb=" O PHE I 467 " (cutoff:3.500A) Proline residue: I 472 - end of helix No H-bonds generated for 'chain 'I' and resid 466 through 474' Processing helix chain 'I' and resid 474 through 483 removed outlier: 3.966A pdb=" N LEU I 481 " --> pdb=" O HIS I 477 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE I 483 " --> pdb=" O ALA I 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 511 removed outlier: 3.871A pdb=" N LEU I 494 " --> pdb=" O LYS I 490 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU I 499 " --> pdb=" O GLN I 495 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU I 505 " --> pdb=" O LEU I 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP I 507 " --> pdb=" O ASN I 503 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET I 510 " --> pdb=" O LEU I 506 " (cutoff:3.500A) Processing helix chain 'I' and resid 522 through 529 Processing helix chain 'I' and resid 529 through 552 removed outlier: 3.706A pdb=" N VAL I 533 " --> pdb=" O SER I 529 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU I 536 " --> pdb=" O SER I 532 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR I 546 " --> pdb=" O TRP I 542 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG I 549 " --> pdb=" O THR I 545 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 563 removed outlier: 3.613A pdb=" N LEU I 558 " --> pdb=" O ASN I 554 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE I 560 " --> pdb=" O PHE I 556 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU I 562 " --> pdb=" O LEU I 558 " (cutoff:3.500A) Processing helix chain 'I' and resid 563 through 569 removed outlier: 3.926A pdb=" N LYS I 567 " --> pdb=" O ASP I 563 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL I 568 " --> pdb=" O PHE I 564 " (cutoff:3.500A) Processing helix chain 'I' and resid 587 through 593 Processing helix chain 'I' and resid 596 through 624 removed outlier: 3.536A pdb=" N LEU I 600 " --> pdb=" O ASP I 596 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA I 616 " --> pdb=" O LYS I 612 " (cutoff:3.500A) Processing helix chain 'I' and resid 634 through 650 removed outlier: 3.667A pdb=" N GLN I 638 " --> pdb=" O SER I 634 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER I 646 " --> pdb=" O HIS I 642 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS I 650 " --> pdb=" O SER I 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 688 through 700 removed outlier: 3.716A pdb=" N LEU I 696 " --> pdb=" O ALA I 692 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER I 700 " --> pdb=" O LEU I 696 " (cutoff:3.500A) Processing helix chain 'I' and resid 713 through 726 removed outlier: 3.687A pdb=" N GLN I 726 " --> pdb=" O TYR I 722 " (cutoff:3.500A) Processing helix chain 'I' and resid 728 through 736 removed outlier: 3.623A pdb=" N ARG I 736 " --> pdb=" O LYS I 732 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 31 through 43 Processing helix chain 'K' and resid 56 through 70 removed outlier: 3.885A pdb=" N LEU K 60 " --> pdb=" O GLN K 56 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N MET K 62 " --> pdb=" O SER K 58 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN K 63 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA K 69 " --> pdb=" O LYS K 65 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU K 70 " --> pdb=" O CYS K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 77 Processing helix chain 'K' and resid 88 through 148 removed outlier: 3.540A pdb=" N LEU K 108 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU K 120 " --> pdb=" O GLU K 116 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU K 125 " --> pdb=" O ASP K 121 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN K 126 " --> pdb=" O LEU K 122 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL K 141 " --> pdb=" O GLU K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 188 removed outlier: 3.632A pdb=" N ILE K 158 " --> pdb=" O SER K 154 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN K 160 " --> pdb=" O SER K 156 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET K 166 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS K 170 " --> pdb=" O MET K 166 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU K 171 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU K 184 " --> pdb=" O LEU K 180 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU K 185 " --> pdb=" O GLY K 181 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS K 187 " --> pdb=" O PHE K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 226 removed outlier: 3.603A pdb=" N ILE K 218 " --> pdb=" O GLU K 214 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU K 223 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE K 224 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP K 225 " --> pdb=" O ASN K 221 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL K 226 " --> pdb=" O ARG K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 249 removed outlier: 3.673A pdb=" N LEU K 246 " --> pdb=" O TYR K 242 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN K 249 " --> pdb=" O LEU K 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 39 removed outlier: 3.661A pdb=" N VAL L 34 " --> pdb=" O ARG L 30 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS L 36 " --> pdb=" O GLU L 32 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN L 37 " --> pdb=" O SER L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 68 removed outlier: 3.625A pdb=" N VAL L 64 " --> pdb=" O ASP L 60 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA L 65 " --> pdb=" O PRO L 61 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE L 66 " --> pdb=" O GLN L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 106 removed outlier: 3.606A pdb=" N ARG L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL L 100 " --> pdb=" O ASN L 96 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA L 101 " --> pdb=" O ALA L 97 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS L 103 " --> pdb=" O ILE L 99 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 204 removed outlier: 3.502A pdb=" N ILE L 195 " --> pdb=" O SER L 191 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE L 196 " --> pdb=" O ASN L 192 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP L 199 " --> pdb=" O ILE L 195 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN L 201 " --> pdb=" O GLY L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 226 removed outlier: 4.008A pdb=" N TRP L 220 " --> pdb=" O PHE L 216 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET L 221 " --> pdb=" O ASN L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 269 removed outlier: 4.180A pdb=" N SER L 267 " --> pdb=" O ALA L 263 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 296 removed outlier: 3.842A pdb=" N VAL L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP L 281 " --> pdb=" O GLN L 277 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG L 293 " --> pdb=" O SER L 289 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N HIS L 294 " --> pdb=" O HIS L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 344 removed outlier: 3.951A pdb=" N VAL L 331 " --> pdb=" O TYR L 327 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR L 334 " --> pdb=" O GLY L 330 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE L 340 " --> pdb=" O THR L 336 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE L 341 " --> pdb=" O GLU L 337 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE L 343 " --> pdb=" O ALA L 339 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 35 removed outlier: 3.768A pdb=" N GLN M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU M 31 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET M 35 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 85 removed outlier: 3.615A pdb=" N THR M 81 " --> pdb=" O SER M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 94 removed outlier: 3.971A pdb=" N LEU M 94 " --> pdb=" O SER M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 123 removed outlier: 3.989A pdb=" N VAL M 117 " --> pdb=" O HIS M 113 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 154 removed outlier: 3.775A pdb=" N THR M 141 " --> pdb=" O GLY M 137 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG M 148 " --> pdb=" O GLN M 144 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL M 149 " --> pdb=" O ARG M 145 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE M 152 " --> pdb=" O ARG M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 removed outlier: 3.618A pdb=" N LEU M 166 " --> pdb=" O ALA M 162 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER M 167 " --> pdb=" O LEU M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 15 removed outlier: 3.973A pdb=" N PHE N 8 " --> pdb=" O THR N 4 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE N 9 " --> pdb=" O VAL N 5 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE N 13 " --> pdb=" O ILE N 9 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU N 14 " --> pdb=" O LYS N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 29 removed outlier: 3.597A pdb=" N ILE N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU N 25 " --> pdb=" O LEU N 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA N 27 " --> pdb=" O THR N 23 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP N 29 " --> pdb=" O LEU N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 37 removed outlier: 3.672A pdb=" N LEU N 36 " --> pdb=" O SER N 32 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN N 37 " --> pdb=" O GLU N 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 32 through 37' Processing helix chain 'N' and resid 44 through 59 removed outlier: 3.869A pdb=" N HIS N 54 " --> pdb=" O GLN N 50 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU N 55 " --> pdb=" O HIS N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 77 removed outlier: 3.544A pdb=" N ASP N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE N 71 " --> pdb=" O ALA N 67 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE N 72 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE N 76 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 108 removed outlier: 3.746A pdb=" N ASN N 106 " --> pdb=" O LYS N 102 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER N 107 " --> pdb=" O GLN N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 114 removed outlier: 3.608A pdb=" N ARG N 114 " --> pdb=" O LYS N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 170 No H-bonds generated for 'chain 'N' and resid 168 through 170' Processing helix chain 'N' and resid 171 through 183 removed outlier: 3.509A pdb=" N GLY N 176 " --> pdb=" O THR N 172 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA N 178 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU N 179 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA N 182 " --> pdb=" O ALA N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 197 through 205 removed outlier: 3.714A pdb=" N ALA N 203 " --> pdb=" O ASP N 199 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL N 205 " --> pdb=" O LEU N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 246 removed outlier: 4.425A pdb=" N GLU N 246 " --> pdb=" O ILE N 242 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 256 Processing helix chain 'N' and resid 305 through 309 removed outlier: 3.839A pdb=" N SER N 308 " --> pdb=" O ALA N 305 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU N 309 " --> pdb=" O LEU N 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 305 through 309' Processing helix chain 'N' and resid 325 through 330 removed outlier: 3.793A pdb=" N ARG N 330 " --> pdb=" O ILE N 326 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 111 removed outlier: 3.525A pdb=" N ILE O 104 " --> pdb=" O ASN O 100 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS O 109 " --> pdb=" O LEU O 105 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE O 110 " --> pdb=" O GLN O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 161 through 166 Processing helix chain 'O' and resid 167 through 172 removed outlier: 4.326A pdb=" N THR O 171 " --> pdb=" O LYS O 167 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN O 172 " --> pdb=" O TYR O 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 167 through 172' Processing helix chain 'O' and resid 173 through 198 removed outlier: 3.678A pdb=" N GLN O 193 " --> pdb=" O GLY O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 262 through 274 removed outlier: 3.585A pdb=" N THR O 273 " --> pdb=" O ALA O 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 279 through 288 removed outlier: 3.521A pdb=" N PHE O 284 " --> pdb=" O LEU O 280 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA O 285 " --> pdb=" O HIS O 281 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR O 288 " --> pdb=" O PHE O 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 Processing helix chain 'P' and resid 62 through 74 removed outlier: 3.658A pdb=" N THR P 72 " --> pdb=" O SER P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 161 removed outlier: 3.716A pdb=" N VAL P 154 " --> pdb=" O LEU P 150 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER P 155 " --> pdb=" O SER P 151 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU P 159 " --> pdb=" O SER P 155 " (cutoff:3.500A) Processing helix chain 'P' and resid 162 through 191 removed outlier: 3.607A pdb=" N PHE P 166 " --> pdb=" O ASP P 162 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU P 170 " --> pdb=" O PHE P 166 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS P 171 " --> pdb=" O PHE P 167 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR P 179 " --> pdb=" O GLU P 175 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG P 182 " --> pdb=" O GLU P 178 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS P 185 " --> pdb=" O LYS P 181 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS P 186 " --> pdb=" O ARG P 182 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR P 191 " --> pdb=" O LEU P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 199 through 203 removed outlier: 4.202A pdb=" N SER P 202 " --> pdb=" O GLU P 199 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER P 203 " --> pdb=" O GLY P 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 199 through 203' Processing helix chain 'P' and resid 243 through 247 removed outlier: 3.502A pdb=" N ALA P 246 " --> pdb=" O PRO P 243 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU P 247 " --> pdb=" O GLN P 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 243 through 247' Processing helix chain 'P' and resid 257 through 270 removed outlier: 3.688A pdb=" N THR P 264 " --> pdb=" O LEU P 260 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU P 265 " --> pdb=" O SER P 261 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL P 266 " --> pdb=" O PHE P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 281 removed outlier: 3.599A pdb=" N LEU P 278 " --> pdb=" O ALA P 274 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE P 279 " --> pdb=" O LEU P 275 " (cutoff:3.500A) Processing helix chain 'U' and resid 250 through 261 removed outlier: 4.049A pdb=" N VAL U 254 " --> pdb=" O GLU U 250 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU U 255 " --> pdb=" O LEU U 251 " (cutoff:3.500A) Proline residue: U 256 - end of helix removed outlier: 3.622A pdb=" N GLU U 259 " --> pdb=" O LEU U 255 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR U 261 " --> pdb=" O GLU U 257 " (cutoff:3.500A) Processing helix chain 'U' and resid 262 through 267 removed outlier: 3.584A pdb=" N GLN U 266 " --> pdb=" O HIS U 262 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN U 267 " --> pdb=" O LEU U 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 262 through 267' Processing helix chain 'U' and resid 271 through 331 removed outlier: 3.649A pdb=" N ALA U 277 " --> pdb=" O VAL U 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL U 285 " --> pdb=" O PHE U 281 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS U 286 " --> pdb=" O TYR U 282 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET U 298 " --> pdb=" O LYS U 294 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE U 310 " --> pdb=" O ASN U 306 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER U 311 " --> pdb=" O ALA U 307 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP U 312 " --> pdb=" O LYS U 308 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS U 315 " --> pdb=" O SER U 311 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS U 316 " --> pdb=" O ASP U 312 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU U 322 " --> pdb=" O GLN U 318 " (cutoff:3.500A) Processing helix chain 'U' and resid 331 through 370 removed outlier: 3.502A pdb=" N ASN U 353 " --> pdb=" O SER U 349 " (cutoff:3.500A) Processing helix chain 'U' and resid 386 through 394 Processing helix chain 'U' and resid 394 through 399 Processing helix chain 'U' and resid 399 through 418 removed outlier: 3.829A pdb=" N ARG U 405 " --> pdb=" O GLU U 401 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN U 410 " --> pdb=" O ASN U 406 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 99 removed outlier: 3.601A pdb=" N ARG Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS Q 83 " --> pdb=" O SER Q 79 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET Q 93 " --> pdb=" O GLU Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 124 removed outlier: 3.590A pdb=" N GLU Q 122 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 157 Processing helix chain 'Q' and resid 158 through 174 removed outlier: 3.709A pdb=" N GLU Q 167 " --> pdb=" O ASP Q 163 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU Q 171 " --> pdb=" O GLU Q 167 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET Q 172 " --> pdb=" O THR Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 182 removed outlier: 3.523A pdb=" N LYS Q 182 " --> pdb=" O SER Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 202 removed outlier: 3.516A pdb=" N GLU Q 192 " --> pdb=" O SER Q 188 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU Q 195 " --> pdb=" O GLU Q 191 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL Q 197 " --> pdb=" O GLU Q 193 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET Q 200 " --> pdb=" O ARG Q 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 230 removed outlier: 3.778A pdb=" N ALA Q 230 " --> pdb=" O LYS Q 226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 235 through 237 No H-bonds generated for 'chain 'Q' and resid 235 through 237' Processing helix chain 'Q' and resid 238 through 247 removed outlier: 3.654A pdb=" N LEU Q 245 " --> pdb=" O ASP Q 241 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 268 Processing helix chain 'R' and resid 87 through 96 Processing helix chain 'R' and resid 96 through 104 removed outlier: 3.693A pdb=" N ILE R 103 " --> pdb=" O GLU R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 114 Processing helix chain 'R' and resid 118 through 123 removed outlier: 4.018A pdb=" N LEU R 122 " --> pdb=" O GLU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 149 removed outlier: 3.663A pdb=" N GLN R 137 " --> pdb=" O LYS R 133 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET R 143 " --> pdb=" O THR R 139 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN R 147 " --> pdb=" O MET R 143 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN R 149 " --> pdb=" O LYS R 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 455 through 472 removed outlier: 3.959A pdb=" N HIS T 462 " --> pdb=" O ALA T 458 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR T 463 " --> pdb=" O GLY T 459 " (cutoff:3.500A) Processing helix chain 'T' and resid 476 through 504 removed outlier: 3.564A pdb=" N VAL T 500 " --> pdb=" O ASP T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 511 through 522 removed outlier: 4.044A pdb=" N LEU T 515 " --> pdb=" O LYS T 511 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET T 519 " --> pdb=" O LEU T 515 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG T 520 " --> pdb=" O GLU T 516 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 removed outlier: 4.037A pdb=" N LEU T 534 " --> pdb=" O SER T 530 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL T 535 " --> pdb=" O LEU T 531 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU T 536 " --> pdb=" O HIS T 532 " (cutoff:3.500A) Processing helix chain 'T' and resid 540 through 548 removed outlier: 3.694A pdb=" N LEU T 546 " --> pdb=" O GLU T 542 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU T 547 " --> pdb=" O TYR T 543 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 29 removed outlier: 3.710A pdb=" N LYS W 23 " --> pdb=" O ARG W 19 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG W 24 " --> pdb=" O GLY W 20 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS W 27 " --> pdb=" O LYS W 23 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG W 28 " --> pdb=" O ARG W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 65 removed outlier: 3.504A pdb=" N LEU W 49 " --> pdb=" O LEU W 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL W 51 " --> pdb=" O CYS W 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS W 52 " --> pdb=" O LEU W 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU W 57 " --> pdb=" O ARG W 53 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER W 65 " --> pdb=" O ASN W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 80 removed outlier: 3.607A pdb=" N VAL W 75 " --> pdb=" O ASN W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 81 through 87 removed outlier: 3.786A pdb=" N ARG W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 15 removed outlier: 3.684A pdb=" N UNK X 13 " --> pdb=" O UNK X 9 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N UNK X 14 " --> pdb=" O UNK X 10 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 232 through 233 Processing sheet with id=AA2, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'L' and resid 117 through 123 removed outlier: 3.535A pdb=" N PHE L 162 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP L 158 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N SER L 143 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL L 156 " --> pdb=" O SER L 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 117 through 123 removed outlier: 3.535A pdb=" N PHE L 162 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP L 158 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N SER L 143 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL L 156 " --> pdb=" O SER L 143 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS L 319 " --> pdb=" O HIS L 315 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU L 304 " --> pdb=" O SER L 242 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER L 242 " --> pdb=" O LEU L 304 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG L 306 " --> pdb=" O LEU L 240 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP L 241 " --> pdb=" O ILE L 252 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP L 251 " --> pdb=" O SER N 298 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER N 298 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU N 294 " --> pdb=" O ALA L 255 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA N 267 " --> pdb=" O PHE N 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 43 through 49 removed outlier: 7.052A pdb=" N ALA M 16 " --> pdb=" O LYS M 45 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N HIS M 47 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE M 18 " --> pdb=" O HIS M 47 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA M 49 " --> pdb=" O ILE M 18 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU M 20 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL M 67 " --> pdb=" O THR M 17 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU M 19 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL M 69 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL M 21 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASN M 71 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU M 129 " --> pdb=" O PHE M 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 119 through 122 removed outlier: 3.521A pdb=" N SER N 122 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TRP N 83 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU N 193 " --> pdb=" O TRP N 83 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL N 85 " --> pdb=" O MET N 191 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN N 187 " --> pdb=" O SER N 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 113 through 117 removed outlier: 3.854A pdb=" N LYS O 116 " --> pdb=" O CYS O 123 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS O 123 " --> pdb=" O LYS O 116 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N HIS O 152 " --> pdb=" O ASP O 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 217 through 224 removed outlier: 3.564A pdb=" N LEU O 224 " --> pdb=" O PHE O 231 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 77 through 87 removed outlier: 5.385A pdb=" N ILE P 78 " --> pdb=" O ASN P 110 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN P 110 " --> pdb=" O ILE P 78 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER P 82 " --> pdb=" O ARG P 106 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG P 106 " --> pdb=" O SER P 82 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE P 120 " --> pdb=" O HIS P 105 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY P 109 " --> pdb=" O PHE P 116 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLN P 121 " --> pdb=" O THR P 136 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER P 132 " --> pdb=" O ILE P 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 195 through 196 removed outlier: 3.564A pdb=" N TYR P 196 " --> pdb=" O GLY P 207 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY P 207 " --> pdb=" O TYR P 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 509 through 510 1143 hydrogen bonds defined for protein. 3360 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: 6.66 Time building geometry restraints manager: 9.13 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: 7627 1.34 - 1.47: 5498 1.47 - 1.59: 11208 1.59 - 1.71: 0 1.71 - 1.84: 209 Bond restraints: 24542 Sorted by residual: bond pdb=" C LYS I 471 " pdb=" N PRO I 472 " ideal model delta sigma weight residual 1.337 1.398 -0.061 1.24e-02 6.50e+03 2.44e+01 bond pdb=" N ASP N 29 " pdb=" CA ASP N 29 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.50e+00 bond pdb=" C PHE I 347 " pdb=" N PRO I 348 " ideal model delta sigma weight residual 1.335 1.363 -0.028 9.40e-03 1.13e+04 8.81e+00 bond pdb=" C THR N 158 " pdb=" N PRO N 159 " ideal model delta sigma weight residual 1.331 1.354 -0.022 7.90e-03 1.60e+04 8.04e+00 bond pdb=" C GLU I 382 " pdb=" N PRO I 383 " ideal model delta sigma weight residual 1.337 1.364 -0.027 1.06e-02 8.90e+03 6.63e+00 ... (remaining 24537 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.34: 431 105.34 - 112.76: 12708 112.76 - 120.19: 10064 120.19 - 127.62: 9659 127.62 - 135.04: 234 Bond angle restraints: 33096 Sorted by residual: angle pdb=" C GLN I 278 " pdb=" N ARG I 279 " pdb=" CA ARG I 279 " ideal model delta sigma weight residual 122.08 130.76 -8.68 1.47e+00 4.63e-01 3.49e+01 angle pdb=" C ILE I 260 " pdb=" N TYR I 261 " pdb=" CA TYR I 261 " ideal model delta sigma weight residual 121.54 132.79 -11.25 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C TRP N 28 " pdb=" N ASP N 29 " pdb=" CA ASP N 29 " ideal model delta sigma weight residual 121.54 132.21 -10.67 1.91e+00 2.74e-01 3.12e+01 angle pdb=" CA CYS I 451 " pdb=" CB CYS I 451 " pdb=" SG CYS I 451 " ideal model delta sigma weight residual 114.40 127.08 -12.68 2.30e+00 1.89e-01 3.04e+01 angle pdb=" C TYR L 81 " pdb=" N LYS L 82 " pdb=" CA LYS L 82 " ideal model delta sigma weight residual 122.07 129.88 -7.81 1.43e+00 4.89e-01 2.98e+01 ... (remaining 33091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 14253 16.59 - 33.19: 610 33.19 - 49.78: 197 49.78 - 66.37: 6 66.37 - 82.96: 26 Dihedral angle restraints: 15092 sinusoidal: 6297 harmonic: 8795 Sorted by residual: dihedral pdb=" CA PHE T 558 " pdb=" C PHE T 558 " pdb=" N PRO T 559 " pdb=" CA PRO T 559 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ALA N 317 " pdb=" C ALA N 317 " pdb=" N PRO N 318 " pdb=" CA PRO N 318 " ideal model delta harmonic sigma weight residual 180.00 157.81 22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LYS N 143 " pdb=" C LYS N 143 " pdb=" N PRO N 144 " pdb=" CA PRO N 144 " ideal model delta harmonic sigma weight residual 180.00 -158.95 -21.05 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 15089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3331 0.077 - 0.155: 380 0.155 - 0.232: 36 0.232 - 0.310: 15 0.310 - 0.387: 4 Chirality restraints: 3766 Sorted by residual: chirality pdb=" CB ILE L 41 " pdb=" CA ILE L 41 " pdb=" CG1 ILE L 41 " pdb=" CG2 ILE L 41 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CB ILE N 188 " pdb=" CA ILE N 188 " pdb=" CG1 ILE N 188 " pdb=" CG2 ILE N 188 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CG LEU M 146 " pdb=" CB LEU M 146 " pdb=" CD1 LEU M 146 " pdb=" CD2 LEU M 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 3763 not shown) Planarity restraints: 4177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 240 " -0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO K 241 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO K 241 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO K 241 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 443 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.63e+00 pdb=" N PRO I 444 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO I 444 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 444 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE T 558 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO T 559 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO T 559 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO T 559 " -0.039 5.00e-02 4.00e+02 ... (remaining 4174 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 7595 2.87 - 3.38: 19883 3.38 - 3.89: 37250 3.89 - 4.39: 41221 4.39 - 4.90: 70856 Nonbonded interactions: 176805 Sorted by model distance: nonbonded pdb=" OD1 ASN L 217 " pdb=" OH TYR L 334 " model vdw 2.363 2.440 nonbonded pdb=" OG SER N 32 " pdb=" OD1 ASN N 34 " model vdw 2.367 2.440 nonbonded pdb=" OG SER L 76 " pdb=" OG SER L 209 " model vdw 2.372 2.440 nonbonded pdb=" O LEU I 205 " pdb=" OG1 THR I 209 " model vdw 2.374 2.440 nonbonded pdb=" O VAL L 165 " pdb=" OG1 THR L 336 " model vdw 2.381 2.440 ... (remaining 176800 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 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: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.250 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 59.400 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 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 : 0.005 0.061 24542 Z= 0.347 Angle : 0.994 13.882 33096 Z= 0.533 Chirality : 0.053 0.387 3766 Planarity : 0.008 0.084 4177 Dihedral : 11.191 82.963 9330 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.15 % Allowed : 2.99 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -5.80 (0.10), residues: 2920 helix: -4.95 (0.03), residues: 1604 sheet: -0.88 (0.30), residues: 254 loop : -2.35 (0.14), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 239 HIS 0.011 0.002 HIS O 271 PHE 0.030 0.002 PHE I 583 TYR 0.030 0.002 TYR O 183 ARG 0.009 0.001 ARG N 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 811 time to evaluate : 3.024 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: C 304 ILE cc_start: 0.5401 (OUTLIER) cc_final: 0.4622 (tp) REVERT: C 305 ILE cc_start: 0.6406 (mp) cc_final: 0.6156 (mp) REVERT: H 89 ILE cc_start: 0.8426 (tp) cc_final: 0.8161 (tp) REVERT: H 98 ILE cc_start: 0.8029 (mm) cc_final: 0.7799 (mm) REVERT: H 130 MET cc_start: 0.7999 (mmp) cc_final: 0.6993 (ptm) REVERT: H 137 ASN cc_start: 0.8161 (m-40) cc_final: 0.6436 (m-40) REVERT: I 88 LEU cc_start: 0.6904 (pp) cc_final: 0.5598 (pp) REVERT: I 334 ASN cc_start: 0.6712 (m-40) cc_final: 0.6088 (p0) REVERT: I 355 HIS cc_start: 0.7257 (p-80) cc_final: 0.6836 (p-80) REVERT: I 357 LEU cc_start: 0.7798 (tt) cc_final: 0.7446 (tt) REVERT: I 416 ASN cc_start: 0.7452 (t0) cc_final: 0.7200 (p0) REVERT: I 461 TRP cc_start: 0.6090 (m-90) cc_final: 0.5871 (m-90) REVERT: I 599 ILE cc_start: 0.8438 (mt) cc_final: 0.7912 (tp) REVERT: I 600 LEU cc_start: 0.9192 (mt) cc_final: 0.8728 (mt) REVERT: I 607 MET cc_start: 0.7129 (mmm) cc_final: 0.6710 (mmm) REVERT: I 620 ASN cc_start: 0.6532 (t0) cc_final: 0.5873 (t0) REVERT: I 683 VAL cc_start: 0.8354 (p) cc_final: 0.8138 (t) REVERT: K 31 MET cc_start: 0.8566 (ptp) cc_final: 0.8298 (ptp) REVERT: K 65 LYS cc_start: 0.8589 (mtmm) cc_final: 0.7827 (ttpt) REVERT: K 80 GLU cc_start: 0.5531 (mt-10) cc_final: 0.5306 (tp30) REVERT: K 82 ILE cc_start: 0.7286 (mt) cc_final: 0.7041 (mp) REVERT: K 103 ASP cc_start: 0.8549 (m-30) cc_final: 0.8127 (t0) REVERT: K 106 MET cc_start: 0.7515 (mtt) cc_final: 0.6887 (mtm) REVERT: K 122 LEU cc_start: 0.8189 (tp) cc_final: 0.7929 (tp) REVERT: K 135 ILE cc_start: 0.8383 (mm) cc_final: 0.8081 (mm) REVERT: K 215 MET cc_start: 0.5010 (mtt) cc_final: 0.4664 (mtt) REVERT: K 261 ARG cc_start: 0.9298 (mpt180) cc_final: 0.9079 (mmt90) REVERT: L 47 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7235 (mtp-110) REVERT: L 52 CYS cc_start: 0.4096 (t) cc_final: 0.3866 (p) REVERT: L 93 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7692 (mmm-85) REVERT: L 116 ASN cc_start: 0.7530 (p0) cc_final: 0.6766 (p0) REVERT: L 144 LYS cc_start: 0.2420 (mttt) cc_final: 0.1959 (tttp) REVERT: L 221 MET cc_start: 0.7990 (ptm) cc_final: 0.7662 (ptm) REVERT: L 226 THR cc_start: 0.8734 (p) cc_final: 0.8422 (p) REVERT: L 288 TYR cc_start: 0.7643 (m-10) cc_final: 0.7236 (m-80) REVERT: M 64 ASP cc_start: 0.7056 (m-30) cc_final: 0.6230 (m-30) REVERT: M 68 PHE cc_start: 0.7765 (m-80) cc_final: 0.7524 (m-80) REVERT: M 71 ASN cc_start: 0.7456 (t0) cc_final: 0.7102 (m110) REVERT: M 94 LEU cc_start: 0.7413 (mt) cc_final: 0.7147 (pp) REVERT: M 131 CYS cc_start: 0.7654 (t) cc_final: 0.7229 (t) REVERT: M 146 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7706 (mm) REVERT: M 166 LEU cc_start: 0.8201 (tp) cc_final: 0.7903 (pp) REVERT: N 18 MET cc_start: 0.7296 (pmm) cc_final: 0.6032 (tpt) REVERT: N 19 ASN cc_start: 0.8560 (p0) cc_final: 0.8226 (p0) REVERT: N 106 ASN cc_start: 0.7757 (p0) cc_final: 0.6896 (m-40) REVERT: N 145 ASN cc_start: 0.5944 (t0) cc_final: 0.5433 (t0) REVERT: N 151 TYR cc_start: 0.7658 (m-80) cc_final: 0.7400 (m-80) REVERT: N 271 LEU cc_start: 0.8606 (mp) cc_final: 0.8388 (mp) REVERT: O 128 THR cc_start: 0.7752 (p) cc_final: 0.6637 (p) REVERT: O 174 GLN cc_start: 0.7907 (pt0) cc_final: 0.7469 (tt0) REVERT: O 176 PHE cc_start: 0.7750 (t80) cc_final: 0.7413 (t80) REVERT: O 198 GLN cc_start: 0.7545 (pt0) cc_final: 0.6383 (tp40) REVERT: O 222 TYR cc_start: 0.7202 (p90) cc_final: 0.6726 (p90) REVERT: O 281 HIS cc_start: 0.7033 (p-80) cc_final: 0.6508 (p-80) REVERT: P 69 PHE cc_start: 0.7076 (t80) cc_final: 0.6516 (t80) REVERT: P 136 THR cc_start: 0.6681 (p) cc_final: 0.6179 (p) REVERT: P 162 ASP cc_start: 0.7635 (t0) cc_final: 0.7194 (m-30) REVERT: P 174 VAL cc_start: 0.8700 (t) cc_final: 0.8455 (t) REVERT: U 334 LEU cc_start: 0.7242 (pp) cc_final: 0.7027 (pt) REVERT: U 396 THR cc_start: 0.8454 (p) cc_final: 0.7878 (t) REVERT: Q 165 MET cc_start: 0.7658 (mtp) cc_final: 0.7282 (mmp) REVERT: W 72 LYS cc_start: 0.7409 (mptp) cc_final: 0.6867 (pttm) outliers start: 4 outliers final: 0 residues processed: 813 average time/residue: 0.4272 time to fit residues: 520.5773 Evaluate side-chains 457 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 455 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 GLN H 71 GLN ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 ASN I 410 HIS I 495 GLN I 559 HIS I 642 HIS I 685 HIS K 39 GLN K 168 ASN L 342 GLN M 115 HIS ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN ** N 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 ASN O 175 HIS ** O 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 353 ASN ** U 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 403 HIS U 409 HIS Q 246 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 24542 Z= 0.287 Angle : 0.723 9.610 33096 Z= 0.383 Chirality : 0.043 0.159 3766 Planarity : 0.006 0.099 4177 Dihedral : 5.125 86.507 3174 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.11 (0.13), residues: 2920 helix: -2.45 (0.10), residues: 1616 sheet: -0.08 (0.31), residues: 267 loop : -1.61 (0.17), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP I 167 HIS 0.008 0.002 HIS N 77 PHE 0.022 0.002 PHE I 640 TYR 0.026 0.002 TYR N 141 ARG 0.007 0.001 ARG P 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 560 time to evaluate : 2.930 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: H 98 ILE cc_start: 0.8161 (mm) cc_final: 0.7913 (mm) REVERT: H 105 ARG cc_start: 0.8478 (mmt-90) cc_final: 0.8216 (tpp80) REVERT: H 130 MET cc_start: 0.8094 (mmp) cc_final: 0.6960 (ptm) REVERT: H 141 MET cc_start: 0.8495 (mpp) cc_final: 0.8190 (mpp) REVERT: H 164 LEU cc_start: 0.7963 (tt) cc_final: 0.7221 (tp) REVERT: I 334 ASN cc_start: 0.6788 (m-40) cc_final: 0.6170 (p0) REVERT: I 339 PHE cc_start: 0.7182 (t80) cc_final: 0.6782 (t80) REVERT: I 355 HIS cc_start: 0.7466 (p-80) cc_final: 0.7059 (p-80) REVERT: I 369 ASN cc_start: 0.8001 (t0) cc_final: 0.7655 (t0) REVERT: I 372 LEU cc_start: 0.9100 (mt) cc_final: 0.8466 (mt) REVERT: I 399 GLU cc_start: 0.7636 (pp20) cc_final: 0.7356 (pp20) REVERT: I 499 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7350 (mt-10) REVERT: I 510 MET cc_start: 0.5794 (mtt) cc_final: 0.5547 (mtt) REVERT: I 646 SER cc_start: 0.7855 (t) cc_final: 0.7642 (p) REVERT: K 65 LYS cc_start: 0.8699 (mtmm) cc_final: 0.8087 (ttpt) REVERT: K 80 GLU cc_start: 0.5761 (mt-10) cc_final: 0.5378 (tp30) REVERT: K 103 ASP cc_start: 0.8564 (m-30) cc_final: 0.8237 (t0) REVERT: K 215 MET cc_start: 0.6264 (mtt) cc_final: 0.6013 (mtt) REVERT: L 93 ARG cc_start: 0.8446 (mtt-85) cc_final: 0.7646 (tpt90) REVERT: L 116 ASN cc_start: 0.7469 (p0) cc_final: 0.6512 (p0) REVERT: L 144 LYS cc_start: 0.2711 (mttt) cc_final: 0.1924 (tttp) REVERT: L 158 TRP cc_start: 0.7324 (t60) cc_final: 0.6729 (t60) REVERT: L 163 CYS cc_start: 0.8312 (p) cc_final: 0.8018 (t) REVERT: L 214 ASN cc_start: 0.8399 (m-40) cc_final: 0.7787 (p0) REVERT: L 238 GLU cc_start: 0.6915 (tp30) cc_final: 0.6666 (tp30) REVERT: L 253 SER cc_start: 0.8155 (m) cc_final: 0.7840 (m) REVERT: L 288 TYR cc_start: 0.7838 (m-10) cc_final: 0.7275 (m-80) REVERT: L 299 LEU cc_start: 0.8232 (mt) cc_final: 0.7835 (mt) REVERT: M 30 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7836 (mm-40) REVERT: M 45 LYS cc_start: 0.6345 (tttt) cc_final: 0.6028 (tttp) REVERT: M 64 ASP cc_start: 0.7064 (m-30) cc_final: 0.6561 (m-30) REVERT: M 94 LEU cc_start: 0.7803 (mt) cc_final: 0.7137 (pp) REVERT: M 102 THR cc_start: 0.7781 (p) cc_final: 0.7195 (t) REVERT: N 18 MET cc_start: 0.7606 (pmm) cc_final: 0.6048 (tpt) REVERT: N 19 ASN cc_start: 0.8627 (p0) cc_final: 0.8152 (p0) REVERT: N 197 TYR cc_start: 0.8397 (m-80) cc_final: 0.8180 (m-80) REVERT: N 211 GLN cc_start: 0.6496 (mp10) cc_final: 0.5648 (tp-100) REVERT: O 174 GLN cc_start: 0.8036 (pt0) cc_final: 0.7540 (pm20) REVERT: O 182 GLU cc_start: 0.7111 (mm-30) cc_final: 0.5144 (mm-30) REVERT: O 185 ASN cc_start: 0.8510 (m110) cc_final: 0.8178 (m110) REVERT: O 205 LEU cc_start: 0.7650 (tt) cc_final: 0.7011 (pp) REVERT: O 210 GLN cc_start: 0.7924 (pt0) cc_final: 0.7449 (pt0) REVERT: O 214 LEU cc_start: 0.8455 (tp) cc_final: 0.8160 (tt) REVERT: O 222 TYR cc_start: 0.7808 (p90) cc_final: 0.7269 (p90) REVERT: P 162 ASP cc_start: 0.7940 (t0) cc_final: 0.7488 (m-30) REVERT: P 165 MET cc_start: 0.8489 (mmp) cc_final: 0.8220 (mmp) REVERT: P 206 MET cc_start: 0.7880 (ppp) cc_final: 0.7500 (ppp) REVERT: P 244 GLN cc_start: 0.7985 (mt0) cc_final: 0.7567 (mm-40) REVERT: U 325 ASP cc_start: 0.8605 (t70) cc_final: 0.8279 (t0) REVERT: U 346 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8218 (tm-30) REVERT: U 396 THR cc_start: 0.8340 (p) cc_final: 0.7874 (t) REVERT: U 417 GLN cc_start: 0.5922 (mt0) cc_final: 0.5692 (pt0) REVERT: Q 201 HIS cc_start: 0.6269 (m90) cc_final: 0.5914 (m90) REVERT: Q 246 HIS cc_start: 0.8137 (m-70) cc_final: 0.7066 (t70) REVERT: R 143 MET cc_start: 0.6749 (ppp) cc_final: 0.6513 (mmt) REVERT: W 72 LYS cc_start: 0.7502 (mptt) cc_final: 0.7089 (mptt) REVERT: W 73 GLU cc_start: 0.8779 (tp30) cc_final: 0.7829 (mp0) REVERT: W 74 HIS cc_start: 0.7433 (m90) cc_final: 0.7028 (m170) outliers start: 3 outliers final: 1 residues processed: 563 average time/residue: 0.3713 time to fit residues: 325.2549 Evaluate side-chains 395 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 394 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 264 optimal weight: 0.0170 chunk 285 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 overall best weight: 3.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 GLN ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 406 ASN I 407 ASN I 454 GLN K 63 GLN K 148 ASN K 160 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 HIS M 29 GLN M 71 ASN M 115 HIS M 144 GLN M 164 ASN ** N 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN O 185 ASN ** O 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 403 HIS Q 151 ASN Q 246 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 24542 Z= 0.234 Angle : 0.633 9.639 33096 Z= 0.328 Chirality : 0.042 0.201 3766 Planarity : 0.005 0.059 4177 Dihedral : 4.830 74.443 3174 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.11 % Allowed : 2.69 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.25 (0.14), residues: 2920 helix: -0.61 (0.12), residues: 1625 sheet: 0.15 (0.31), residues: 264 loop : -1.23 (0.17), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 32 HIS 0.012 0.001 HIS P 171 PHE 0.023 0.002 PHE O 287 TYR 0.021 0.002 TYR Q 262 ARG 0.014 0.001 ARG K 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 517 time to evaluate : 2.976 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: H 128 ASP cc_start: 0.7891 (m-30) cc_final: 0.7641 (m-30) REVERT: H 130 MET cc_start: 0.8164 (mmp) cc_final: 0.7028 (ptm) REVERT: H 141 MET cc_start: 0.8296 (mpp) cc_final: 0.7929 (mpp) REVERT: I 171 MET cc_start: 0.6780 (tpp) cc_final: 0.6571 (tpp) REVERT: I 221 LYS cc_start: 0.6558 (tttt) cc_final: 0.6205 (tmtt) REVERT: I 334 ASN cc_start: 0.6792 (m-40) cc_final: 0.6201 (p0) REVERT: I 339 PHE cc_start: 0.7156 (t80) cc_final: 0.6766 (t80) REVERT: I 355 HIS cc_start: 0.7581 (p-80) cc_final: 0.7223 (p-80) REVERT: I 369 ASN cc_start: 0.8167 (t0) cc_final: 0.7643 (t0) REVERT: I 372 LEU cc_start: 0.9128 (mt) cc_final: 0.8412 (mt) REVERT: I 399 GLU cc_start: 0.7836 (pp20) cc_final: 0.6864 (pp20) REVERT: I 495 GLN cc_start: 0.7269 (pp30) cc_final: 0.6928 (pp30) REVERT: I 499 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7366 (mt-10) REVERT: I 575 TYR cc_start: 0.7499 (m-10) cc_final: 0.7210 (m-80) REVERT: I 588 PHE cc_start: 0.7554 (t80) cc_final: 0.7149 (t80) REVERT: I 613 ASN cc_start: 0.8852 (m-40) cc_final: 0.8594 (m-40) REVERT: I 646 SER cc_start: 0.8082 (t) cc_final: 0.7882 (p) REVERT: K 65 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8149 (ttpt) REVERT: K 80 GLU cc_start: 0.5883 (mt-10) cc_final: 0.5245 (tp30) REVERT: K 88 VAL cc_start: 0.8062 (m) cc_final: 0.7731 (m) REVERT: K 103 ASP cc_start: 0.8498 (m-30) cc_final: 0.8033 (t0) REVERT: K 145 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6305 (mp0) REVERT: K 215 MET cc_start: 0.6470 (mtt) cc_final: 0.6240 (mtt) REVERT: L 48 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7388 (mtpp) REVERT: L 93 ARG cc_start: 0.8527 (mtt-85) cc_final: 0.8153 (ttm110) REVERT: L 116 ASN cc_start: 0.7333 (p0) cc_final: 0.6398 (p0) REVERT: L 144 LYS cc_start: 0.2710 (mttt) cc_final: 0.1780 (tttm) REVERT: L 165 VAL cc_start: 0.8030 (t) cc_final: 0.7796 (t) REVERT: L 225 TRP cc_start: 0.8403 (m-10) cc_final: 0.8140 (m-10) REVERT: L 238 GLU cc_start: 0.6747 (tp30) cc_final: 0.6488 (tp30) REVERT: L 253 SER cc_start: 0.8182 (m) cc_final: 0.7945 (m) REVERT: L 288 TYR cc_start: 0.8014 (m-10) cc_final: 0.7441 (m-80) REVERT: L 299 LEU cc_start: 0.8238 (mt) cc_final: 0.7829 (mt) REVERT: M 33 ASP cc_start: 0.8127 (m-30) cc_final: 0.7810 (m-30) REVERT: M 38 GLU cc_start: 0.6898 (pt0) cc_final: 0.6591 (pt0) REVERT: M 45 LYS cc_start: 0.6613 (tttt) cc_final: 0.6201 (tttp) REVERT: M 64 ASP cc_start: 0.7444 (m-30) cc_final: 0.6872 (m-30) REVERT: M 94 LEU cc_start: 0.7685 (mt) cc_final: 0.7116 (pp) REVERT: M 144 GLN cc_start: 0.7668 (mm110) cc_final: 0.7420 (mm-40) REVERT: N 18 MET cc_start: 0.7764 (pmm) cc_final: 0.6155 (tpt) REVERT: N 19 ASN cc_start: 0.8712 (p0) cc_final: 0.8232 (p0) REVERT: N 211 GLN cc_start: 0.6792 (mp10) cc_final: 0.5925 (tp-100) REVERT: N 264 LEU cc_start: 0.8822 (mt) cc_final: 0.8588 (mp) REVERT: O 174 GLN cc_start: 0.8130 (pt0) cc_final: 0.7484 (pp30) REVERT: O 182 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6377 (mm-30) REVERT: O 205 LEU cc_start: 0.7790 (tt) cc_final: 0.7071 (pp) REVERT: O 210 GLN cc_start: 0.7982 (pt0) cc_final: 0.7488 (tt0) REVERT: O 214 LEU cc_start: 0.8810 (tp) cc_final: 0.8578 (tt) REVERT: O 222 TYR cc_start: 0.7835 (p90) cc_final: 0.7241 (p90) REVERT: P 162 ASP cc_start: 0.8086 (t0) cc_final: 0.7500 (m-30) REVERT: P 168 ARG cc_start: 0.6862 (ptm160) cc_final: 0.6178 (ptm160) REVERT: P 206 MET cc_start: 0.7889 (ppp) cc_final: 0.7608 (ppp) REVERT: P 244 GLN cc_start: 0.8119 (mt0) cc_final: 0.7907 (mt0) REVERT: U 329 ARG cc_start: 0.8690 (mmm160) cc_final: 0.8289 (tpp-160) REVERT: U 342 ASP cc_start: 0.8230 (t0) cc_final: 0.7760 (m-30) REVERT: U 383 ASP cc_start: 0.7195 (m-30) cc_final: 0.6930 (m-30) REVERT: U 396 THR cc_start: 0.8397 (p) cc_final: 0.7939 (t) REVERT: Q 201 HIS cc_start: 0.6334 (m90) cc_final: 0.6049 (m-70) REVERT: Q 246 HIS cc_start: 0.7420 (m90) cc_final: 0.7173 (t70) REVERT: R 87 MET cc_start: 0.4387 (ptp) cc_final: 0.4126 (ttm) REVERT: T 473 MET cc_start: -0.1113 (mtp) cc_final: -0.1314 (mtp) REVERT: W 72 LYS cc_start: 0.7444 (mptt) cc_final: 0.6686 (pttm) REVERT: W 74 HIS cc_start: 0.7567 (m90) cc_final: 0.7112 (m170) outliers start: 3 outliers final: 0 residues processed: 519 average time/residue: 0.3580 time to fit residues: 285.8350 Evaluate side-chains 371 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 20.0000 chunk 199 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 265 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 ASN I 406 ASN K 221 ASN ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 257 HIS L 277 GLN M 115 HIS ** N 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN O 133 ASN O 152 HIS O 175 HIS O 185 ASN ** O 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 284 ASN U 306 ASN ** U 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 ASN Q 151 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 24542 Z= 0.241 Angle : 0.634 10.048 33096 Z= 0.328 Chirality : 0.042 0.235 3766 Planarity : 0.004 0.042 4177 Dihedral : 4.702 44.235 3174 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.11 % Allowed : 2.92 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.32 (0.15), residues: 2920 helix: 0.31 (0.13), residues: 1653 sheet: 0.19 (0.31), residues: 263 loop : -1.06 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP P 222 HIS 0.015 0.001 HIS P 171 PHE 0.021 0.002 PHE O 287 TYR 0.021 0.002 TYR K 172 ARG 0.008 0.001 ARG N 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 475 time to evaluate : 3.006 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: H 98 ILE cc_start: 0.8368 (mm) cc_final: 0.8139 (mm) REVERT: H 100 LYS cc_start: 0.9259 (pttm) cc_final: 0.8931 (pttp) REVERT: H 105 ARG cc_start: 0.8448 (tpp-160) cc_final: 0.8038 (tpp80) REVERT: H 130 MET cc_start: 0.8294 (mmp) cc_final: 0.7178 (ptm) REVERT: H 169 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7828 (pp20) REVERT: I 334 ASN cc_start: 0.6798 (m-40) cc_final: 0.6105 (p0) REVERT: I 339 PHE cc_start: 0.7097 (t80) cc_final: 0.6696 (t80) REVERT: I 355 HIS cc_start: 0.7678 (p-80) cc_final: 0.7338 (p-80) REVERT: I 369 ASN cc_start: 0.8203 (t0) cc_final: 0.7646 (t0) REVERT: I 372 LEU cc_start: 0.9186 (mt) cc_final: 0.8464 (mp) REVERT: I 399 GLU cc_start: 0.7956 (pp20) cc_final: 0.7201 (pp20) REVERT: I 454 GLN cc_start: 0.7234 (mp-120) cc_final: 0.7017 (mp10) REVERT: I 494 LEU cc_start: 0.8781 (mt) cc_final: 0.8569 (mm) REVERT: I 537 ILE cc_start: 0.8904 (mm) cc_final: 0.8571 (mm) REVERT: I 588 PHE cc_start: 0.7548 (t80) cc_final: 0.7114 (t80) REVERT: I 603 LEU cc_start: 0.8086 (tp) cc_final: 0.7736 (tp) REVERT: I 607 MET cc_start: 0.8017 (mmm) cc_final: 0.7737 (mmm) REVERT: I 613 ASN cc_start: 0.8868 (m-40) cc_final: 0.8617 (m-40) REVERT: I 643 TYR cc_start: 0.7509 (m-80) cc_final: 0.7171 (m-80) REVERT: K 65 LYS cc_start: 0.8949 (mtmm) cc_final: 0.8285 (ttpt) REVERT: K 103 ASP cc_start: 0.8545 (m-30) cc_final: 0.8035 (t0) REVERT: K 215 MET cc_start: 0.6617 (mtt) cc_final: 0.6359 (mtt) REVERT: L 48 LYS cc_start: 0.7858 (mtpt) cc_final: 0.7654 (mtpp) REVERT: L 116 ASN cc_start: 0.7240 (p0) cc_final: 0.6268 (p0) REVERT: L 144 LYS cc_start: 0.2785 (mttt) cc_final: 0.1613 (tttp) REVERT: L 253 SER cc_start: 0.8254 (m) cc_final: 0.7996 (m) REVERT: L 281 ASP cc_start: 0.7783 (t0) cc_final: 0.7416 (p0) REVERT: L 284 MET cc_start: 0.8736 (tpt) cc_final: 0.8476 (tpp) REVERT: L 288 TYR cc_start: 0.8084 (m-10) cc_final: 0.7307 (m-80) REVERT: L 299 LEU cc_start: 0.8145 (mt) cc_final: 0.7918 (mt) REVERT: L 300 SER cc_start: 0.8433 (p) cc_final: 0.7994 (p) REVERT: M 33 ASP cc_start: 0.8272 (m-30) cc_final: 0.7998 (m-30) REVERT: M 38 GLU cc_start: 0.6857 (pt0) cc_final: 0.5997 (pt0) REVERT: M 45 LYS cc_start: 0.6710 (tttt) cc_final: 0.6287 (tttp) REVERT: M 64 ASP cc_start: 0.7390 (m-30) cc_final: 0.7003 (m-30) REVERT: M 94 LEU cc_start: 0.7956 (mt) cc_final: 0.7155 (pp) REVERT: N 19 ASN cc_start: 0.8782 (p0) cc_final: 0.8421 (p0) REVERT: N 154 TYR cc_start: 0.8772 (t80) cc_final: 0.8515 (t80) REVERT: N 264 LEU cc_start: 0.8767 (mt) cc_final: 0.8544 (mp) REVERT: O 130 PHE cc_start: 0.6637 (t80) cc_final: 0.5735 (t80) REVERT: O 174 GLN cc_start: 0.8267 (pt0) cc_final: 0.7692 (tt0) REVERT: O 176 PHE cc_start: 0.8400 (t80) cc_final: 0.8010 (t80) REVERT: O 180 LEU cc_start: 0.9004 (mt) cc_final: 0.8442 (mt) REVERT: O 182 GLU cc_start: 0.7338 (tp30) cc_final: 0.6917 (mm-30) REVERT: O 214 LEU cc_start: 0.8907 (tp) cc_final: 0.8609 (tt) REVERT: O 222 TYR cc_start: 0.7877 (p90) cc_final: 0.7361 (p90) REVERT: O 284 PHE cc_start: 0.7521 (m-10) cc_final: 0.7246 (m-80) REVERT: P 162 ASP cc_start: 0.8017 (t0) cc_final: 0.7462 (m-30) REVERT: P 168 ARG cc_start: 0.7210 (ptm160) cc_final: 0.6671 (ptm160) REVERT: P 206 MET cc_start: 0.7935 (ppp) cc_final: 0.7651 (ppp) REVERT: P 227 ASP cc_start: 0.5285 (p0) cc_final: 0.5058 (p0) REVERT: P 244 GLN cc_start: 0.8155 (mt0) cc_final: 0.7935 (mt0) REVERT: P 280 LYS cc_start: 0.5278 (tttm) cc_final: 0.4674 (tmtt) REVERT: U 329 ARG cc_start: 0.8765 (mmm160) cc_final: 0.8309 (tpp-160) REVERT: U 383 ASP cc_start: 0.7195 (m-30) cc_final: 0.6869 (m-30) REVERT: U 396 THR cc_start: 0.8381 (p) cc_final: 0.7901 (t) REVERT: Q 192 GLU cc_start: 0.8215 (tp30) cc_final: 0.7998 (tp30) REVERT: Q 226 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8262 (mttt) REVERT: Q 246 HIS cc_start: 0.7753 (m90) cc_final: 0.7386 (t70) REVERT: Q 252 LYS cc_start: 0.7793 (pttm) cc_final: 0.7418 (pttm) REVERT: R 87 MET cc_start: 0.4440 (ptp) cc_final: 0.4238 (mtt) REVERT: R 121 ASN cc_start: 0.8437 (t0) cc_final: 0.8204 (t0) REVERT: R 143 MET cc_start: 0.7233 (ppp) cc_final: 0.7021 (mmt) REVERT: W 72 LYS cc_start: 0.7580 (mptt) cc_final: 0.6716 (mmtt) REVERT: W 73 GLU cc_start: 0.8887 (tp30) cc_final: 0.7957 (mp0) REVERT: W 74 HIS cc_start: 0.7468 (m90) cc_final: 0.6959 (m90) outliers start: 3 outliers final: 1 residues processed: 478 average time/residue: 0.3453 time to fit residues: 256.6260 Evaluate side-chains 365 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 364 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 209 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 194 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN K 213 HIS ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 HIS M 144 GLN ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 185 ASN ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 GLN U 306 ASN ** U 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 417 GLN Q 151 ASN ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24542 Z= 0.212 Angle : 0.597 11.656 33096 Z= 0.306 Chirality : 0.042 0.195 3766 Planarity : 0.004 0.058 4177 Dihedral : 4.595 33.503 3174 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.19 (0.15), residues: 2920 helix: 0.75 (0.13), residues: 1659 sheet: 0.25 (0.31), residues: 263 loop : -0.85 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 461 HIS 0.013 0.001 HIS P 171 PHE 0.027 0.002 PHE L 98 TYR 0.021 0.001 TYR K 172 ARG 0.008 0.001 ARG P 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 460 time to evaluate : 2.954 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: H 98 ILE cc_start: 0.8422 (mm) cc_final: 0.8202 (mm) REVERT: H 130 MET cc_start: 0.8285 (mmp) cc_final: 0.7213 (ptm) REVERT: I 221 LYS cc_start: 0.6737 (tttt) cc_final: 0.6354 (tmtt) REVERT: I 229 MET cc_start: 0.7820 (ppp) cc_final: 0.7262 (ppp) REVERT: I 334 ASN cc_start: 0.6870 (m-40) cc_final: 0.6054 (p0) REVERT: I 339 PHE cc_start: 0.7092 (t80) cc_final: 0.6700 (t80) REVERT: I 355 HIS cc_start: 0.7752 (p-80) cc_final: 0.7405 (p-80) REVERT: I 369 ASN cc_start: 0.8208 (t0) cc_final: 0.7752 (t0) REVERT: I 372 LEU cc_start: 0.9124 (mt) cc_final: 0.8452 (mt) REVERT: I 399 GLU cc_start: 0.7882 (pp20) cc_final: 0.6988 (pp20) REVERT: I 454 GLN cc_start: 0.7170 (mp-120) cc_final: 0.6924 (mp10) REVERT: I 494 LEU cc_start: 0.8825 (mt) cc_final: 0.8514 (mm) REVERT: I 495 GLN cc_start: 0.7670 (pp30) cc_final: 0.7387 (pp30) REVERT: I 570 ASP cc_start: 0.7403 (t0) cc_final: 0.7075 (t0) REVERT: I 607 MET cc_start: 0.8050 (mmm) cc_final: 0.7812 (mmm) REVERT: I 613 ASN cc_start: 0.8835 (m-40) cc_final: 0.8551 (m110) REVERT: I 721 ASP cc_start: 0.7866 (m-30) cc_final: 0.7599 (t0) REVERT: K 103 ASP cc_start: 0.8492 (m-30) cc_final: 0.7996 (t0) REVERT: K 127 ARG cc_start: 0.8272 (tmm-80) cc_final: 0.7880 (tmm-80) REVERT: K 215 MET cc_start: 0.6729 (mtt) cc_final: 0.6431 (mtt) REVERT: L 48 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7509 (mtpp) REVERT: L 93 ARG cc_start: 0.8415 (mtt-85) cc_final: 0.8010 (ttm110) REVERT: L 116 ASN cc_start: 0.7161 (p0) cc_final: 0.6226 (p0) REVERT: L 144 LYS cc_start: 0.2585 (mttt) cc_final: 0.1322 (tttp) REVERT: L 253 SER cc_start: 0.8297 (m) cc_final: 0.7794 (p) REVERT: L 281 ASP cc_start: 0.7792 (t0) cc_final: 0.7441 (p0) REVERT: L 288 TYR cc_start: 0.7749 (m-10) cc_final: 0.7208 (m-80) REVERT: L 299 LEU cc_start: 0.8152 (mt) cc_final: 0.7920 (mt) REVERT: L 300 SER cc_start: 0.8550 (p) cc_final: 0.8044 (p) REVERT: M 33 ASP cc_start: 0.8232 (m-30) cc_final: 0.7939 (m-30) REVERT: M 38 GLU cc_start: 0.6935 (pt0) cc_final: 0.6050 (pt0) REVERT: M 45 LYS cc_start: 0.6804 (tttt) cc_final: 0.6365 (tttp) REVERT: M 64 ASP cc_start: 0.7209 (m-30) cc_final: 0.6887 (m-30) REVERT: M 94 LEU cc_start: 0.7750 (mt) cc_final: 0.7228 (pp) REVERT: M 144 GLN cc_start: 0.7720 (mm110) cc_final: 0.7506 (mm110) REVERT: N 19 ASN cc_start: 0.8817 (p0) cc_final: 0.8532 (p0) REVERT: N 154 TYR cc_start: 0.8760 (t80) cc_final: 0.8537 (t80) REVERT: O 174 GLN cc_start: 0.8203 (pt0) cc_final: 0.7550 (pm20) REVERT: O 176 PHE cc_start: 0.8399 (t80) cc_final: 0.7986 (t80) REVERT: O 180 LEU cc_start: 0.8973 (mt) cc_final: 0.8434 (mt) REVERT: O 182 GLU cc_start: 0.7337 (tp30) cc_final: 0.6704 (mm-30) REVERT: O 214 LEU cc_start: 0.8876 (tp) cc_final: 0.8646 (tt) REVERT: O 222 TYR cc_start: 0.7766 (p90) cc_final: 0.7230 (p90) REVERT: O 284 PHE cc_start: 0.7542 (m-10) cc_final: 0.7081 (m-10) REVERT: P 142 MET cc_start: 0.7651 (tpt) cc_final: 0.6939 (tpp) REVERT: P 162 ASP cc_start: 0.8113 (t0) cc_final: 0.7534 (m-30) REVERT: P 168 ARG cc_start: 0.7122 (ptm160) cc_final: 0.6284 (ptm160) REVERT: P 206 MET cc_start: 0.7953 (ppp) cc_final: 0.7670 (ppp) REVERT: P 227 ASP cc_start: 0.5417 (p0) cc_final: 0.5156 (p0) REVERT: P 232 VAL cc_start: 0.8853 (p) cc_final: 0.8587 (p) REVERT: P 253 ARG cc_start: 0.8108 (mmp80) cc_final: 0.7805 (mmm160) REVERT: P 280 LYS cc_start: 0.5441 (tttm) cc_final: 0.4831 (tmtt) REVERT: U 329 ARG cc_start: 0.8777 (mmm160) cc_final: 0.8440 (tpp-160) REVERT: U 396 THR cc_start: 0.8373 (p) cc_final: 0.7899 (t) REVERT: Q 192 GLU cc_start: 0.8325 (tp30) cc_final: 0.8053 (tp30) REVERT: Q 201 HIS cc_start: 0.6372 (m-70) cc_final: 0.6157 (m-70) REVERT: Q 215 SER cc_start: 0.7904 (p) cc_final: 0.7506 (t) REVERT: Q 226 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8293 (mttt) REVERT: Q 246 HIS cc_start: 0.7778 (m90) cc_final: 0.7384 (t70) REVERT: R 87 MET cc_start: 0.4510 (ptp) cc_final: 0.4304 (mtt) REVERT: R 121 ASN cc_start: 0.8540 (t0) cc_final: 0.8333 (t0) REVERT: W 72 LYS cc_start: 0.7570 (mptt) cc_final: 0.6749 (mmtt) REVERT: W 73 GLU cc_start: 0.8883 (tp30) cc_final: 0.7936 (mp0) REVERT: W 74 HIS cc_start: 0.7564 (m90) cc_final: 0.7073 (m90) outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.3564 time to fit residues: 254.7878 Evaluate side-chains 349 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 0.9980 chunk 253 optimal weight: 0.0000 chunk 55 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 69 optimal weight: 0.0770 chunk 281 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 147 optimal weight: 0.4980 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 213 HIS ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 HIS N 157 GLN N 177 GLN ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN O 175 HIS O 185 ASN P 103 GLN U 306 ASN ** U 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24542 Z= 0.145 Angle : 0.552 9.045 33096 Z= 0.278 Chirality : 0.041 0.157 3766 Planarity : 0.003 0.040 4177 Dihedral : 4.360 33.130 3174 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.57 (0.16), residues: 2920 helix: 1.10 (0.13), residues: 1656 sheet: 0.35 (0.31), residues: 263 loop : -0.73 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 222 HIS 0.010 0.001 HIS P 171 PHE 0.024 0.001 PHE L 98 TYR 0.020 0.001 TYR L 334 ARG 0.004 0.000 ARG M 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 3.276 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: H 130 MET cc_start: 0.8229 (mmp) cc_final: 0.7153 (ptm) REVERT: H 141 MET cc_start: 0.8441 (mpp) cc_final: 0.7889 (mpp) REVERT: I 221 LYS cc_start: 0.6663 (tttt) cc_final: 0.6292 (tmtt) REVERT: I 229 MET cc_start: 0.7872 (ppp) cc_final: 0.7374 (ppp) REVERT: I 334 ASN cc_start: 0.6979 (m-40) cc_final: 0.6070 (p0) REVERT: I 339 PHE cc_start: 0.7160 (t80) cc_final: 0.6745 (t80) REVERT: I 355 HIS cc_start: 0.7794 (p-80) cc_final: 0.7442 (p-80) REVERT: I 369 ASN cc_start: 0.8224 (t0) cc_final: 0.7754 (t0) REVERT: I 372 LEU cc_start: 0.9070 (mt) cc_final: 0.8354 (mt) REVERT: I 399 GLU cc_start: 0.7919 (pp20) cc_final: 0.6434 (pp20) REVERT: I 414 PHE cc_start: 0.8682 (t80) cc_final: 0.7923 (t80) REVERT: I 428 LEU cc_start: 0.8748 (mt) cc_final: 0.8471 (tp) REVERT: I 494 LEU cc_start: 0.8792 (mt) cc_final: 0.8489 (mm) REVERT: I 495 GLN cc_start: 0.7586 (pp30) cc_final: 0.7360 (pp30) REVERT: I 570 ASP cc_start: 0.7495 (t0) cc_final: 0.7213 (t0) REVERT: I 603 LEU cc_start: 0.8126 (tp) cc_final: 0.7896 (tp) REVERT: I 607 MET cc_start: 0.8103 (mmm) cc_final: 0.7878 (mmm) REVERT: I 613 ASN cc_start: 0.8782 (m-40) cc_final: 0.8488 (m110) REVERT: I 721 ASP cc_start: 0.7825 (m-30) cc_final: 0.7563 (t0) REVERT: K 103 ASP cc_start: 0.8453 (m-30) cc_final: 0.7970 (t0) REVERT: K 215 MET cc_start: 0.6759 (mtt) cc_final: 0.6443 (mtt) REVERT: L 48 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7596 (mtpp) REVERT: L 93 ARG cc_start: 0.8320 (mtt-85) cc_final: 0.7949 (ttm110) REVERT: L 99 ILE cc_start: 0.8907 (pt) cc_final: 0.8689 (pt) REVERT: L 116 ASN cc_start: 0.6840 (p0) cc_final: 0.6310 (p0) REVERT: L 144 LYS cc_start: 0.2628 (mttt) cc_final: 0.1239 (tttp) REVERT: L 238 GLU cc_start: 0.6967 (tp30) cc_final: 0.6765 (tp30) REVERT: L 253 SER cc_start: 0.8231 (m) cc_final: 0.7869 (p) REVERT: L 288 TYR cc_start: 0.8008 (m-10) cc_final: 0.7300 (m-80) REVERT: L 299 LEU cc_start: 0.8096 (mt) cc_final: 0.7819 (mt) REVERT: L 300 SER cc_start: 0.8507 (p) cc_final: 0.8022 (p) REVERT: M 33 ASP cc_start: 0.8175 (m-30) cc_final: 0.7917 (m-30) REVERT: M 38 GLU cc_start: 0.6883 (pt0) cc_final: 0.6030 (pt0) REVERT: M 45 LYS cc_start: 0.6809 (tttt) cc_final: 0.6384 (tttp) REVERT: M 64 ASP cc_start: 0.7378 (m-30) cc_final: 0.6923 (m-30) REVERT: M 115 HIS cc_start: 0.7144 (t-90) cc_final: 0.6875 (t-170) REVERT: M 119 LYS cc_start: 0.8138 (tttt) cc_final: 0.7842 (mtpt) REVERT: M 135 VAL cc_start: 0.8784 (t) cc_final: 0.8577 (t) REVERT: N 19 ASN cc_start: 0.8803 (p0) cc_final: 0.8548 (p0) REVERT: O 174 GLN cc_start: 0.8182 (pt0) cc_final: 0.7483 (pm20) REVERT: O 176 PHE cc_start: 0.8303 (t80) cc_final: 0.7932 (t80) REVERT: O 180 LEU cc_start: 0.8941 (mt) cc_final: 0.8350 (mt) REVERT: O 182 GLU cc_start: 0.7429 (tp30) cc_final: 0.6857 (mm-30) REVERT: O 214 LEU cc_start: 0.8800 (tp) cc_final: 0.8586 (tt) REVERT: O 222 TYR cc_start: 0.7665 (p90) cc_final: 0.7286 (p90) REVERT: O 284 PHE cc_start: 0.7401 (m-10) cc_final: 0.7170 (m-10) REVERT: P 142 MET cc_start: 0.7646 (tpt) cc_final: 0.6944 (tpp) REVERT: P 162 ASP cc_start: 0.8150 (t0) cc_final: 0.7551 (m-30) REVERT: P 168 ARG cc_start: 0.7215 (ptm160) cc_final: 0.6668 (ptm160) REVERT: P 206 MET cc_start: 0.7939 (ppp) cc_final: 0.7646 (ppp) REVERT: P 227 ASP cc_start: 0.5254 (p0) cc_final: 0.4941 (p0) REVERT: P 253 ARG cc_start: 0.8107 (mmp80) cc_final: 0.7877 (mmm160) REVERT: P 275 LEU cc_start: 0.8765 (mt) cc_final: 0.8512 (mp) REVERT: P 280 LYS cc_start: 0.5523 (tttm) cc_final: 0.5001 (tmtt) REVERT: U 329 ARG cc_start: 0.8733 (mmm160) cc_final: 0.8374 (tpp-160) REVERT: U 392 PHE cc_start: 0.6986 (m-10) cc_final: 0.6774 (m-10) REVERT: U 396 THR cc_start: 0.8363 (p) cc_final: 0.7896 (t) REVERT: Q 192 GLU cc_start: 0.8335 (tp30) cc_final: 0.8031 (tp30) REVERT: Q 201 HIS cc_start: 0.6440 (m-70) cc_final: 0.6158 (m-70) REVERT: Q 215 SER cc_start: 0.7845 (p) cc_final: 0.7420 (t) REVERT: Q 226 LYS cc_start: 0.9025 (mtmt) cc_final: 0.8272 (mttt) REVERT: Q 246 HIS cc_start: 0.7747 (m90) cc_final: 0.7323 (t70) REVERT: R 121 ASN cc_start: 0.8577 (t0) cc_final: 0.8015 (t0) REVERT: T 475 MET cc_start: 0.4110 (tpp) cc_final: 0.3537 (tmm) REVERT: W 72 LYS cc_start: 0.7597 (mptt) cc_final: 0.6682 (pttm) outliers start: 0 outliers final: 0 residues processed: 478 average time/residue: 0.3660 time to fit residues: 273.5097 Evaluate side-chains 356 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 237 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 280 optimal weight: 50.0000 chunk 175 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 232 HIS M 115 HIS ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 185 ASN P 126 GLN U 306 ASN ** U 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.6735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 24542 Z= 0.250 Angle : 0.652 10.609 33096 Z= 0.334 Chirality : 0.043 0.173 3766 Planarity : 0.004 0.039 4177 Dihedral : 4.652 34.769 3174 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.42 (0.15), residues: 2920 helix: 1.00 (0.13), residues: 1658 sheet: 0.10 (0.31), residues: 269 loop : -0.80 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 72 HIS 0.022 0.001 HIS P 171 PHE 0.015 0.002 PHE L 254 TYR 0.018 0.002 TYR I 610 ARG 0.012 0.001 ARG P 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 461 time to evaluate : 3.086 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: H 98 ILE cc_start: 0.8505 (mm) cc_final: 0.8297 (mm) REVERT: H 104 ASP cc_start: 0.8558 (t70) cc_final: 0.8249 (t0) REVERT: H 128 ASP cc_start: 0.7941 (m-30) cc_final: 0.7677 (m-30) REVERT: H 130 MET cc_start: 0.8305 (mmp) cc_final: 0.7257 (ptm) REVERT: H 141 MET cc_start: 0.8455 (mpp) cc_final: 0.7838 (mpp) REVERT: I 221 LYS cc_start: 0.6639 (tttt) cc_final: 0.6228 (tmtt) REVERT: I 334 ASN cc_start: 0.7115 (m-40) cc_final: 0.6196 (p0) REVERT: I 339 PHE cc_start: 0.7004 (t80) cc_final: 0.6608 (t80) REVERT: I 355 HIS cc_start: 0.7869 (p-80) cc_final: 0.7542 (p-80) REVERT: I 369 ASN cc_start: 0.8313 (t0) cc_final: 0.7896 (t0) REVERT: I 399 GLU cc_start: 0.7974 (pp20) cc_final: 0.7131 (pp20) REVERT: I 494 LEU cc_start: 0.8803 (mt) cc_final: 0.8492 (mm) REVERT: I 500 LEU cc_start: 0.8785 (tp) cc_final: 0.8571 (tp) REVERT: I 570 ASP cc_start: 0.7463 (t0) cc_final: 0.7242 (t0) REVERT: I 603 LEU cc_start: 0.8189 (tp) cc_final: 0.7973 (tp) REVERT: I 607 MET cc_start: 0.8110 (mmm) cc_final: 0.7845 (mmm) REVERT: I 613 ASN cc_start: 0.8804 (m-40) cc_final: 0.8598 (m-40) REVERT: I 721 ASP cc_start: 0.7973 (m-30) cc_final: 0.7707 (t0) REVERT: K 91 THR cc_start: 0.8299 (t) cc_final: 0.8025 (p) REVERT: K 96 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8316 (tm-30) REVERT: K 103 ASP cc_start: 0.8461 (m-30) cc_final: 0.7983 (t0) REVERT: K 127 ARG cc_start: 0.8262 (tmm-80) cc_final: 0.7900 (tmm-80) REVERT: K 215 MET cc_start: 0.6796 (mtt) cc_final: 0.6487 (mtt) REVERT: L 116 ASN cc_start: 0.6975 (p0) cc_final: 0.6247 (p0) REVERT: L 144 LYS cc_start: 0.2733 (mttt) cc_final: 0.2516 (mttp) REVERT: L 238 GLU cc_start: 0.7027 (tp30) cc_final: 0.6608 (tp30) REVERT: L 253 SER cc_start: 0.8348 (m) cc_final: 0.7631 (t) REVERT: L 288 TYR cc_start: 0.8082 (m-10) cc_final: 0.7311 (m-80) REVERT: L 300 SER cc_start: 0.8595 (p) cc_final: 0.7942 (t) REVERT: M 33 ASP cc_start: 0.8217 (m-30) cc_final: 0.7954 (m-30) REVERT: M 45 LYS cc_start: 0.6925 (tttt) cc_final: 0.6414 (tttp) REVERT: M 64 ASP cc_start: 0.7384 (m-30) cc_final: 0.6956 (m-30) REVERT: M 94 LEU cc_start: 0.8094 (mt) cc_final: 0.7624 (pp) REVERT: N 19 ASN cc_start: 0.8878 (p0) cc_final: 0.8563 (p0) REVERT: O 174 GLN cc_start: 0.8183 (pt0) cc_final: 0.7757 (pm20) REVERT: O 176 PHE cc_start: 0.8401 (t80) cc_final: 0.8027 (t80) REVERT: O 180 LEU cc_start: 0.9035 (mt) cc_final: 0.8642 (mm) REVERT: O 182 GLU cc_start: 0.7412 (tp30) cc_final: 0.7073 (mm-30) REVERT: O 222 TYR cc_start: 0.7801 (p90) cc_final: 0.7472 (p90) REVERT: O 284 PHE cc_start: 0.7505 (m-10) cc_final: 0.7279 (m-10) REVERT: P 127 ASN cc_start: 0.5947 (t0) cc_final: 0.5190 (p0) REVERT: P 142 MET cc_start: 0.7593 (tpt) cc_final: 0.6873 (tpp) REVERT: P 162 ASP cc_start: 0.8285 (t0) cc_final: 0.7625 (m-30) REVERT: P 206 MET cc_start: 0.8030 (ppp) cc_final: 0.7689 (ppp) REVERT: P 222 TRP cc_start: 0.7801 (t-100) cc_final: 0.7582 (t60) REVERT: P 227 ASP cc_start: 0.5663 (p0) cc_final: 0.5451 (p0) REVERT: P 244 GLN cc_start: 0.8221 (mt0) cc_final: 0.7865 (mt0) REVERT: P 253 ARG cc_start: 0.8135 (mmp80) cc_final: 0.7815 (mmm160) REVERT: U 319 ARG cc_start: 0.7690 (tpp80) cc_final: 0.7356 (tpp80) REVERT: U 329 ARG cc_start: 0.8757 (mmm160) cc_final: 0.8478 (tpp-160) REVERT: U 392 PHE cc_start: 0.7092 (m-10) cc_final: 0.6832 (m-10) REVERT: U 396 THR cc_start: 0.8357 (p) cc_final: 0.7943 (t) REVERT: U 397 LEU cc_start: 0.8974 (mt) cc_final: 0.8583 (mt) REVERT: Q 192 GLU cc_start: 0.8317 (tp30) cc_final: 0.8031 (tp30) REVERT: Q 201 HIS cc_start: 0.6538 (m-70) cc_final: 0.6057 (m-70) REVERT: Q 215 SER cc_start: 0.8139 (p) cc_final: 0.7795 (t) REVERT: Q 226 LYS cc_start: 0.9045 (mtmt) cc_final: 0.8284 (mttt) REVERT: Q 246 HIS cc_start: 0.7913 (m90) cc_final: 0.7459 (t70) REVERT: W 72 LYS cc_start: 0.7587 (mptt) cc_final: 0.6640 (pttm) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.3498 time to fit residues: 254.9384 Evaluate side-chains 356 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 84 optimal weight: 0.0470 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 191 optimal weight: 0.4980 chunk 138 optimal weight: 0.1980 chunk 26 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 GLN K 213 HIS L 71 GLN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 HIS M 115 HIS M 156 HIS ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN ** N 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 185 ASN U 306 ASN ** U 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Q 201 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.6601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24542 Z= 0.131 Angle : 0.563 10.790 33096 Z= 0.279 Chirality : 0.041 0.204 3766 Planarity : 0.003 0.041 4177 Dihedral : 4.278 36.788 3174 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.90 (0.16), residues: 2920 helix: 1.40 (0.13), residues: 1664 sheet: 0.22 (0.32), residues: 263 loop : -0.61 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 504 HIS 0.010 0.001 HIS P 171 PHE 0.015 0.001 PHE I 245 TYR 0.016 0.001 TYR K 172 ARG 0.004 0.000 ARG H 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 3.188 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: H 98 ILE cc_start: 0.8312 (mm) cc_final: 0.8109 (mm) REVERT: H 100 LYS cc_start: 0.9060 (pttm) cc_final: 0.8269 (pttm) REVERT: H 104 ASP cc_start: 0.8569 (t70) cc_final: 0.8229 (t0) REVERT: H 130 MET cc_start: 0.8142 (mmp) cc_final: 0.7102 (ptm) REVERT: I 88 LEU cc_start: 0.7042 (pp) cc_final: 0.5647 (pp) REVERT: I 221 LYS cc_start: 0.6791 (tttt) cc_final: 0.6388 (tttt) REVERT: I 334 ASN cc_start: 0.7137 (m-40) cc_final: 0.6182 (p0) REVERT: I 355 HIS cc_start: 0.7821 (p-80) cc_final: 0.7533 (p-80) REVERT: I 369 ASN cc_start: 0.8212 (t0) cc_final: 0.7771 (t0) REVERT: I 372 LEU cc_start: 0.8971 (mt) cc_final: 0.8206 (mt) REVERT: I 399 GLU cc_start: 0.7838 (pp20) cc_final: 0.6350 (pp20) REVERT: I 414 PHE cc_start: 0.8644 (t80) cc_final: 0.7806 (t80) REVERT: I 494 LEU cc_start: 0.8769 (mt) cc_final: 0.8421 (mm) REVERT: I 495 GLN cc_start: 0.7639 (pp30) cc_final: 0.7170 (pp30) REVERT: I 570 ASP cc_start: 0.7492 (t0) cc_final: 0.7222 (t0) REVERT: I 606 ILE cc_start: 0.9126 (mt) cc_final: 0.8880 (mm) REVERT: I 613 ASN cc_start: 0.8691 (m-40) cc_final: 0.8373 (m110) REVERT: I 721 ASP cc_start: 0.7844 (m-30) cc_final: 0.7588 (t0) REVERT: K 103 ASP cc_start: 0.8411 (m-30) cc_final: 0.7951 (t0) REVERT: K 215 MET cc_start: 0.6728 (mtt) cc_final: 0.6419 (mtt) REVERT: L 116 ASN cc_start: 0.6884 (p0) cc_final: 0.6080 (p0) REVERT: L 144 LYS cc_start: 0.2757 (mttt) cc_final: 0.2520 (mttp) REVERT: L 230 MET cc_start: 0.7315 (tmm) cc_final: 0.6936 (tmm) REVERT: L 238 GLU cc_start: 0.6955 (tp30) cc_final: 0.6728 (tp30) REVERT: L 281 ASP cc_start: 0.7917 (m-30) cc_final: 0.7712 (m-30) REVERT: L 288 TYR cc_start: 0.8015 (m-10) cc_final: 0.7309 (m-80) REVERT: L 299 LEU cc_start: 0.8166 (mt) cc_final: 0.7937 (mt) REVERT: L 300 SER cc_start: 0.8552 (p) cc_final: 0.7882 (p) REVERT: M 33 ASP cc_start: 0.8138 (m-30) cc_final: 0.7882 (m-30) REVERT: M 45 LYS cc_start: 0.6775 (tttt) cc_final: 0.6348 (tttp) REVERT: M 64 ASP cc_start: 0.7249 (m-30) cc_final: 0.6798 (m-30) REVERT: M 115 HIS cc_start: 0.7181 (t-90) cc_final: 0.6955 (t-170) REVERT: M 134 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7675 (mm-30) REVERT: N 19 ASN cc_start: 0.8834 (p0) cc_final: 0.8573 (p0) REVERT: N 211 GLN cc_start: 0.7248 (mp10) cc_final: 0.6726 (tp-100) REVERT: O 174 GLN cc_start: 0.8192 (pt0) cc_final: 0.7571 (pm20) REVERT: O 176 PHE cc_start: 0.8292 (t80) cc_final: 0.7891 (t80) REVERT: O 180 LEU cc_start: 0.8912 (mt) cc_final: 0.8407 (mt) REVERT: O 182 GLU cc_start: 0.7347 (tp30) cc_final: 0.6688 (mm-30) REVERT: O 222 TYR cc_start: 0.7567 (p90) cc_final: 0.7297 (p90) REVERT: O 265 GLU cc_start: 0.8137 (tp30) cc_final: 0.7389 (mp0) REVERT: P 142 MET cc_start: 0.7535 (tpt) cc_final: 0.6834 (tpp) REVERT: P 162 ASP cc_start: 0.8284 (t0) cc_final: 0.7555 (m-30) REVERT: P 168 ARG cc_start: 0.7106 (ptm160) cc_final: 0.6688 (ptm160) REVERT: P 206 MET cc_start: 0.7544 (ppp) cc_final: 0.7256 (ppp) REVERT: P 227 ASP cc_start: 0.5009 (p0) cc_final: 0.4715 (p0) REVERT: P 244 GLN cc_start: 0.8120 (mt0) cc_final: 0.7844 (mt0) REVERT: P 253 ARG cc_start: 0.8130 (mmp80) cc_final: 0.7811 (mmm160) REVERT: P 280 LYS cc_start: 0.5729 (tttm) cc_final: 0.5155 (tmtt) REVERT: U 319 ARG cc_start: 0.7583 (tpp80) cc_final: 0.7245 (tpp80) REVERT: U 329 ARG cc_start: 0.8659 (mmm160) cc_final: 0.8401 (tpp-160) REVERT: U 396 THR cc_start: 0.8286 (p) cc_final: 0.7860 (t) REVERT: Q 192 GLU cc_start: 0.8341 (tp30) cc_final: 0.8005 (tp30) REVERT: Q 215 SER cc_start: 0.8237 (p) cc_final: 0.7803 (t) REVERT: Q 226 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8251 (mttt) REVERT: Q 246 HIS cc_start: 0.7835 (m90) cc_final: 0.7388 (t70) REVERT: Q 252 LYS cc_start: 0.7818 (pttm) cc_final: 0.6860 (tmtt) REVERT: T 475 MET cc_start: 0.4068 (tpp) cc_final: 0.3691 (tmm) REVERT: W 72 LYS cc_start: 0.7672 (mptt) cc_final: 0.6838 (pttm) outliers start: 0 outliers final: 0 residues processed: 479 average time/residue: 0.3453 time to fit residues: 261.4111 Evaluate side-chains 371 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 chunk 247 optimal weight: 0.0980 chunk 260 optimal weight: 0.4980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 HIS ** M 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 185 ASN ** U 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 306 ASN ** U 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 417 GLN Q 151 ASN ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24542 Z= 0.149 Angle : 0.576 9.801 33096 Z= 0.287 Chirality : 0.041 0.208 3766 Planarity : 0.003 0.040 4177 Dihedral : 4.218 35.847 3174 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.96 (0.16), residues: 2920 helix: 1.47 (0.13), residues: 1659 sheet: 0.31 (0.32), residues: 256 loop : -0.62 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP P 222 HIS 0.011 0.001 HIS P 171 PHE 0.015 0.001 PHE I 245 TYR 0.015 0.001 TYR I 539 ARG 0.008 0.000 ARG U 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 3.023 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: H 104 ASP cc_start: 0.8548 (t70) cc_final: 0.8188 (t0) REVERT: H 105 ARG cc_start: 0.8785 (mmt180) cc_final: 0.8116 (tpp80) REVERT: H 128 ASP cc_start: 0.7989 (m-30) cc_final: 0.7749 (m-30) REVERT: H 130 MET cc_start: 0.8184 (mmp) cc_final: 0.7107 (ptm) REVERT: H 141 MET cc_start: 0.8219 (mpp) cc_final: 0.8013 (mpp) REVERT: I 221 LYS cc_start: 0.6818 (tttt) cc_final: 0.6416 (tttt) REVERT: I 229 MET cc_start: 0.8036 (ppp) cc_final: 0.7827 (ppp) REVERT: I 339 PHE cc_start: 0.6938 (t80) cc_final: 0.6710 (t80) REVERT: I 355 HIS cc_start: 0.7860 (p-80) cc_final: 0.7572 (p-80) REVERT: I 369 ASN cc_start: 0.8249 (t0) cc_final: 0.7781 (t0) REVERT: I 372 LEU cc_start: 0.8983 (mt) cc_final: 0.8270 (mt) REVERT: I 399 GLU cc_start: 0.7920 (pp20) cc_final: 0.6457 (pp20) REVERT: I 414 PHE cc_start: 0.8625 (t80) cc_final: 0.7930 (t80) REVERT: I 494 LEU cc_start: 0.8750 (mt) cc_final: 0.8389 (mm) REVERT: I 495 GLN cc_start: 0.7649 (pp30) cc_final: 0.7235 (pp30) REVERT: I 570 ASP cc_start: 0.7391 (t0) cc_final: 0.7096 (t0) REVERT: I 606 ILE cc_start: 0.9128 (mt) cc_final: 0.8912 (mm) REVERT: I 613 ASN cc_start: 0.8767 (m-40) cc_final: 0.8450 (m110) REVERT: I 643 TYR cc_start: 0.7264 (m-80) cc_final: 0.6362 (m-80) REVERT: I 721 ASP cc_start: 0.7901 (m-30) cc_final: 0.7630 (t0) REVERT: K 103 ASP cc_start: 0.8434 (m-30) cc_final: 0.7996 (t0) REVERT: K 215 MET cc_start: 0.6745 (mtt) cc_final: 0.6444 (mtt) REVERT: L 116 ASN cc_start: 0.6963 (p0) cc_final: 0.6127 (p0) REVERT: L 144 LYS cc_start: 0.2690 (mttt) cc_final: 0.2451 (mttp) REVERT: L 230 MET cc_start: 0.7331 (tmm) cc_final: 0.7010 (tmm) REVERT: L 238 GLU cc_start: 0.6985 (tp30) cc_final: 0.6763 (tp30) REVERT: L 288 TYR cc_start: 0.7994 (m-10) cc_final: 0.7249 (m-80) REVERT: L 299 LEU cc_start: 0.8234 (mt) cc_final: 0.7926 (mt) REVERT: L 300 SER cc_start: 0.8469 (p) cc_final: 0.7910 (p) REVERT: M 33 ASP cc_start: 0.8134 (m-30) cc_final: 0.7847 (m-30) REVERT: M 45 LYS cc_start: 0.6853 (tttt) cc_final: 0.6462 (tttp) REVERT: M 64 ASP cc_start: 0.7144 (m-30) cc_final: 0.6769 (m-30) REVERT: M 94 LEU cc_start: 0.7333 (mt) cc_final: 0.6821 (pp) REVERT: N 19 ASN cc_start: 0.8845 (p0) cc_final: 0.8573 (p0) REVERT: N 154 TYR cc_start: 0.8569 (t80) cc_final: 0.8216 (t80) REVERT: N 211 GLN cc_start: 0.7252 (mp10) cc_final: 0.6789 (tp-100) REVERT: O 174 GLN cc_start: 0.8193 (pt0) cc_final: 0.7562 (pm20) REVERT: O 176 PHE cc_start: 0.8262 (t80) cc_final: 0.7840 (t80) REVERT: O 180 LEU cc_start: 0.8963 (mt) cc_final: 0.8456 (mt) REVERT: O 182 GLU cc_start: 0.7340 (tp30) cc_final: 0.7000 (mm-30) REVERT: O 222 TYR cc_start: 0.7617 (p90) cc_final: 0.7359 (p90) REVERT: O 265 GLU cc_start: 0.8260 (tp30) cc_final: 0.7367 (mp0) REVERT: O 284 PHE cc_start: 0.7397 (m-80) cc_final: 0.6611 (m-80) REVERT: P 142 MET cc_start: 0.7573 (tpt) cc_final: 0.6861 (tpp) REVERT: P 162 ASP cc_start: 0.8340 (t0) cc_final: 0.7535 (m-30) REVERT: P 206 MET cc_start: 0.7609 (ppp) cc_final: 0.7345 (ppp) REVERT: P 227 ASP cc_start: 0.5163 (p0) cc_final: 0.4852 (p0) REVERT: P 244 GLN cc_start: 0.8125 (mt0) cc_final: 0.7835 (mt0) REVERT: P 253 ARG cc_start: 0.8155 (mmp80) cc_final: 0.7822 (mmm160) REVERT: P 280 LYS cc_start: 0.5657 (tttm) cc_final: 0.5174 (tmtt) REVERT: U 329 ARG cc_start: 0.8696 (mmm160) cc_final: 0.8477 (tpp-160) REVERT: U 392 PHE cc_start: 0.6933 (m-10) cc_final: 0.6640 (m-10) REVERT: U 396 THR cc_start: 0.8302 (p) cc_final: 0.7884 (t) REVERT: Q 215 SER cc_start: 0.8268 (p) cc_final: 0.7824 (t) REVERT: Q 226 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8241 (mttt) REVERT: Q 246 HIS cc_start: 0.7872 (m90) cc_final: 0.7356 (t70) REVERT: R 101 MET cc_start: 0.7400 (mmm) cc_final: 0.7174 (mtt) REVERT: T 475 MET cc_start: 0.4176 (tpp) cc_final: 0.3814 (tmm) REVERT: W 72 LYS cc_start: 0.7686 (mptt) cc_final: 0.6816 (pttm) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.3307 time to fit residues: 242.8535 Evaluate side-chains 370 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 9.9990 chunk 276 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 289 optimal weight: 8.9990 chunk 266 optimal weight: 0.9980 chunk 230 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 ASN K 63 GLN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 HIS ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN O 133 ASN O 185 ASN U 306 ASN ** U 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.7274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 24542 Z= 0.267 Angle : 0.691 9.777 33096 Z= 0.353 Chirality : 0.045 0.208 3766 Planarity : 0.004 0.061 4177 Dihedral : 4.691 38.158 3174 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.53 (0.16), residues: 2920 helix: 1.11 (0.13), residues: 1663 sheet: 0.07 (0.31), residues: 268 loop : -0.78 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 222 HIS 0.016 0.001 HIS P 171 PHE 0.021 0.002 PHE L 98 TYR 0.021 0.002 TYR H 57 ARG 0.010 0.001 ARG U 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 439 time to evaluate : 2.944 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: H 98 ILE cc_start: 0.8471 (mm) cc_final: 0.8262 (mm) REVERT: H 104 ASP cc_start: 0.8553 (t70) cc_final: 0.8206 (t0) REVERT: H 128 ASP cc_start: 0.8030 (m-30) cc_final: 0.7757 (m-30) REVERT: H 130 MET cc_start: 0.8350 (mmp) cc_final: 0.7316 (ptm) REVERT: H 141 MET cc_start: 0.8330 (mpp) cc_final: 0.7998 (mpp) REVERT: I 221 LYS cc_start: 0.6831 (tttt) cc_final: 0.6407 (tmtt) REVERT: I 355 HIS cc_start: 0.7885 (p-80) cc_final: 0.7552 (p-80) REVERT: I 369 ASN cc_start: 0.8338 (t0) cc_final: 0.7910 (t0) REVERT: I 399 GLU cc_start: 0.7999 (pp20) cc_final: 0.6375 (pp20) REVERT: I 414 PHE cc_start: 0.8612 (t80) cc_final: 0.7875 (t80) REVERT: I 494 LEU cc_start: 0.8768 (mt) cc_final: 0.8430 (mm) REVERT: I 495 GLN cc_start: 0.7760 (pp30) cc_final: 0.7364 (pp30) REVERT: I 606 ILE cc_start: 0.9133 (mt) cc_final: 0.8911 (mt) REVERT: I 607 MET cc_start: 0.8178 (mmm) cc_final: 0.7956 (mmm) REVERT: I 613 ASN cc_start: 0.8815 (m-40) cc_final: 0.8588 (m-40) REVERT: I 721 ASP cc_start: 0.7992 (m-30) cc_final: 0.7774 (t0) REVERT: K 59 LEU cc_start: 0.9167 (mt) cc_final: 0.8913 (mm) REVERT: K 103 ASP cc_start: 0.8481 (m-30) cc_final: 0.8014 (t0) REVERT: K 127 ARG cc_start: 0.8297 (tmm-80) cc_final: 0.7924 (tmm-80) REVERT: K 215 MET cc_start: 0.6902 (mtt) cc_final: 0.6566 (mtt) REVERT: L 116 ASN cc_start: 0.6976 (p0) cc_final: 0.6233 (p0) REVERT: L 230 MET cc_start: 0.7392 (tmm) cc_final: 0.7014 (tmm) REVERT: L 288 TYR cc_start: 0.8157 (m-10) cc_final: 0.7408 (m-80) REVERT: L 299 LEU cc_start: 0.8246 (mt) cc_final: 0.7998 (mt) REVERT: L 300 SER cc_start: 0.8513 (p) cc_final: 0.7975 (t) REVERT: M 33 ASP cc_start: 0.8227 (m-30) cc_final: 0.7884 (m-30) REVERT: M 45 LYS cc_start: 0.6966 (tttt) cc_final: 0.6694 (tttp) REVERT: M 64 ASP cc_start: 0.7383 (m-30) cc_final: 0.6864 (m-30) REVERT: M 115 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.7215 (t-170) REVERT: N 19 ASN cc_start: 0.8894 (p0) cc_final: 0.8619 (p0) REVERT: N 154 TYR cc_start: 0.8695 (t80) cc_final: 0.8199 (t80) REVERT: N 211 GLN cc_start: 0.7317 (mp10) cc_final: 0.6938 (tp-100) REVERT: O 174 GLN cc_start: 0.8139 (pt0) cc_final: 0.7756 (pm20) REVERT: O 176 PHE cc_start: 0.8480 (t80) cc_final: 0.8112 (t80) REVERT: O 180 LEU cc_start: 0.9016 (mt) cc_final: 0.8662 (mm) REVERT: O 182 GLU cc_start: 0.7363 (tp30) cc_final: 0.7043 (mm-30) REVERT: O 222 TYR cc_start: 0.7834 (p90) cc_final: 0.7599 (p90) REVERT: O 284 PHE cc_start: 0.7489 (m-80) cc_final: 0.6688 (m-80) REVERT: P 142 MET cc_start: 0.7530 (tpt) cc_final: 0.6903 (tpp) REVERT: P 227 ASP cc_start: 0.5878 (p0) cc_final: 0.5586 (p0) REVERT: P 244 GLN cc_start: 0.8196 (mt0) cc_final: 0.7873 (mt0) REVERT: P 253 ARG cc_start: 0.8174 (mmp80) cc_final: 0.7822 (mmm160) REVERT: U 319 ARG cc_start: 0.7773 (tpp80) cc_final: 0.7324 (tpp80) REVERT: U 396 THR cc_start: 0.8335 (p) cc_final: 0.7941 (t) REVERT: U 397 LEU cc_start: 0.8971 (mt) cc_final: 0.8558 (mt) REVERT: Q 215 SER cc_start: 0.8438 (p) cc_final: 0.7966 (t) REVERT: Q 226 LYS cc_start: 0.9083 (mtmt) cc_final: 0.8338 (mttt) REVERT: Q 246 HIS cc_start: 0.7975 (m90) cc_final: 0.7415 (t70) REVERT: Q 252 LYS cc_start: 0.7816 (pttm) cc_final: 0.7004 (tmtt) REVERT: T 475 MET cc_start: 0.4330 (tpp) cc_final: 0.4030 (tmm) REVERT: W 72 LYS cc_start: 0.7683 (mptt) cc_final: 0.6784 (pttm) outliers start: 1 outliers final: 0 residues processed: 439 average time/residue: 0.3387 time to fit residues: 237.6046 Evaluate side-chains 349 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 348 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 212 optimal weight: 0.0770 chunk 34 optimal weight: 30.0000 chunk 64 optimal weight: 0.6980 chunk 231 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 HIS M 115 HIS N 35 GLN ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 306 ASN U 353 ASN ** U 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Q 201 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.102215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.093217 restraints weight = 151705.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.093156 restraints weight = 125217.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.093473 restraints weight = 121092.481| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24542 Z= 0.146 Angle : 0.594 10.008 33096 Z= 0.295 Chirality : 0.042 0.194 3766 Planarity : 0.003 0.041 4177 Dihedral : 4.360 39.939 3174 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.92 (0.16), residues: 2920 helix: 1.44 (0.13), residues: 1655 sheet: 0.17 (0.32), residues: 257 loop : -0.60 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP P 222 HIS 0.007 0.001 HIS O 281 PHE 0.015 0.001 PHE N 334 TYR 0.018 0.001 TYR K 172 ARG 0.006 0.000 ARG U 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6666.48 seconds wall clock time: 121 minutes 23.77 seconds (7283.77 seconds total)