Starting phenix.real_space_refine on Mon Sep 30 08:14:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6o_11101/09_2024/6z6o_11101.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6o_11101/09_2024/6z6o_11101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6o_11101/09_2024/6z6o_11101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6o_11101/09_2024/6z6o_11101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6o_11101/09_2024/6z6o_11101.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6o_11101/09_2024/6z6o_11101.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.361 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: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 356 5.16 5 C 49220 2.51 5 N 13136 2.21 5 O 14796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 393 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 77516 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5220 Classifications: {'peptide': 656} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 620} Chain breaks: 1 Chain: "B" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5245 Classifications: {'peptide': 661} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4472 Classifications: {'peptide': 548} Link IDs: {'CIS': 1, 'PTRANS': 20, 'TRANS': 526} Chain breaks: 6 Chain: "D" Number of atoms: 4440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4440 Classifications: {'peptide': 542} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 524} Chain breaks: 1 Chain: "E" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5220 Classifications: {'peptide': 656} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 620} Chain breaks: 1 Chain: "F" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5245 Classifications: {'peptide': 661} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4472 Classifications: {'peptide': 548} Link IDs: {'CIS': 1, 'PTRANS': 20, 'TRANS': 526} Chain breaks: 6 Chain: "H" Number of atoms: 4440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4440 Classifications: {'peptide': 542} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 524} Chain breaks: 1 Chain: "I" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5220 Classifications: {'peptide': 656} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 620} Chain breaks: 1 Chain: "J" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5245 Classifications: {'peptide': 661} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4472 Classifications: {'peptide': 548} Link IDs: {'CIS': 1, 'PTRANS': 20, 'TRANS': 526} Chain breaks: 6 Chain: "L" Number of atoms: 4440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4440 Classifications: {'peptide': 542} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 524} Chain breaks: 1 Chain: "M" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5220 Classifications: {'peptide': 656} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 620} Chain breaks: 1 Chain: "N" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5245 Classifications: {'peptide': 661} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "O" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4472 Classifications: {'peptide': 548} Link IDs: {'CIS': 1, 'PTRANS': 20, 'TRANS': 526} Chain breaks: 6 Chain: "P" Number of atoms: 4440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4440 Classifications: {'peptide': 542} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 524} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 31.03, per 1000 atoms: 0.40 Number of scatterers: 77516 At special positions: 0 Unit cell: (314.093, 231.526, 167.686, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 356 16.00 O 14796 8.00 N 13136 7.00 C 49220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 359 " - pdb=" SG CYS C 366 " distance=2.03 Simple disulfide: pdb=" SG CYS G 359 " - pdb=" SG CYS G 366 " distance=2.03 Simple disulfide: pdb=" SG CYS K 359 " - pdb=" SG CYS K 366 " distance=2.03 Simple disulfide: pdb=" SG CYS O 359 " - pdb=" SG CYS O 366 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.71 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" ND1 HIS A 247 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" ND1 HIS B 247 " pdb=" ZN E 801 " pdb="ZN ZN E 801 " - pdb=" ND1 HIS E 247 " pdb=" ZN F 801 " pdb="ZN ZN F 801 " - pdb=" ND1 HIS F 247 " pdb=" ZN I 801 " pdb="ZN ZN I 801 " - pdb=" ND1 HIS I 247 " pdb=" ZN J 801 " pdb="ZN ZN J 801 " - pdb=" ND1 HIS J 247 " pdb=" ZN M 801 " pdb="ZN ZN M 801 " - pdb=" ND1 HIS M 247 " pdb=" ZN N 801 " pdb="ZN ZN N 801 " - pdb=" ND1 HIS N 247 " 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18328 Finding SS restraints... Secondary structure from input PDB file: 324 helices and 32 sheets defined 51.9% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.88 Creating SS restraints... Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 89 through 99 Processing helix chain 'A' and resid 127 through 133 removed outlier: 3.697A pdb=" N ILE A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 147 removed outlier: 3.539A pdb=" N LEU A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 170 through 190 Proline residue: A 177 - end of helix removed outlier: 3.592A pdb=" N GLU A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 232 removed outlier: 3.562A pdb=" N ALA A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.595A pdb=" N GLY A 282 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 307 through 318 removed outlier: 4.082A pdb=" N TYR A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 336 through 340 removed outlier: 4.314A pdb=" N ALA A 339 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.657A pdb=" N TYR A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 396 Processing helix chain 'A' and resid 410 through 428 removed outlier: 3.719A pdb=" N ILE A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 474 removed outlier: 3.754A pdb=" N ILE A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 472 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 534 through 543 Processing helix chain 'A' and resid 562 through 580 Processing helix chain 'A' and resid 581 through 584 removed outlier: 3.510A pdb=" N PHE A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 598 through 609 removed outlier: 4.358A pdb=" N ILE A 602 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 645 removed outlier: 4.177A pdb=" N GLU A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 699 removed outlier: 6.096A pdb=" N GLU A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 69 removed outlier: 3.598A pdb=" N MET B 66 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR B 68 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS B 69 " --> pdb=" O MET B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 100 removed outlier: 4.098A pdb=" N TYR B 91 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.718A pdb=" N LEU B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 175 through 190 removed outlier: 3.730A pdb=" N GLY B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'B' and resid 307 through 318 removed outlier: 3.813A pdb=" N TYR B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 327 removed outlier: 3.508A pdb=" N MET B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 340 removed outlier: 4.265A pdb=" N ALA B 339 " --> pdb=" O GLY B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.758A pdb=" N TYR B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA B 366 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 396 Processing helix chain 'B' and resid 410 through 428 removed outlier: 3.575A pdb=" N ILE B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 473 Processing helix chain 'B' and resid 534 through 542 removed outlier: 4.403A pdb=" N ILE B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 580 Processing helix chain 'B' and resid 581 through 584 removed outlier: 3.632A pdb=" N PHE B 584 " --> pdb=" O ILE B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 584' Processing helix chain 'B' and resid 598 through 608 removed outlier: 4.103A pdb=" N ILE B 602 " --> pdb=" O SER B 598 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS B 608 " --> pdb=" O HIS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.869A pdb=" N GLU B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 700 removed outlier: 5.234A pdb=" N GLU B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLU B 690 " --> pdb=" O GLU B 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 42 removed outlier: 5.709A pdb=" N LYS C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 86 Processing helix chain 'C' and resid 87 through 92 removed outlier: 3.772A pdb=" N LEU C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 92 " --> pdb=" O SER C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 111 removed outlier: 3.626A pdb=" N SER C 109 " --> pdb=" O PRO C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 128 removed outlier: 3.518A pdb=" N GLN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.716A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 272 through 282 removed outlier: 3.611A pdb=" N ALA C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 removed outlier: 3.519A pdb=" N TYR C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU C 301 " --> pdb=" O PRO C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 341 Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 413 through 439 removed outlier: 3.592A pdb=" N GLY C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 509 removed outlier: 4.986A pdb=" N LYS C 476 " --> pdb=" O GLN C 472 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 601 removed outlier: 3.562A pdb=" N SER C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER C 561 " --> pdb=" O ASN C 557 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 52 Processing helix chain 'D' and resid 52 through 62 removed outlier: 3.594A pdb=" N GLU D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 87 removed outlier: 4.208A pdb=" N ILE D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 91 Processing helix chain 'D' and resid 104 through 113 removed outlier: 3.577A pdb=" N HIS D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 127 Processing helix chain 'D' and resid 140 through 151 removed outlier: 3.603A pdb=" N ASP D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 221 Processing helix chain 'D' and resid 243 through 252 Processing helix chain 'D' and resid 259 through 273 removed outlier: 4.259A pdb=" N VAL D 271 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE D 272 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 295 through 301 Processing helix chain 'D' and resid 318 through 327 removed outlier: 3.565A pdb=" N VAL D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 440 Processing helix chain 'D' and resid 448 through 515 removed outlier: 3.733A pdb=" N HIS D 452 " --> pdb=" O LEU D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 639 removed outlier: 3.956A pdb=" N LYS D 525 " --> pdb=" O ASP D 521 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) Proline residue: D 634 - end of helix removed outlier: 4.365A pdb=" N GLN D 639 " --> pdb=" O ARG D 635 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 80 Processing helix chain 'E' and resid 89 through 99 Processing helix chain 'E' and resid 127 through 133 removed outlier: 3.696A pdb=" N ILE E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 147 removed outlier: 3.542A pdb=" N LEU E 140 " --> pdb=" O THR E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 161 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 170 through 190 Proline residue: E 177 - end of helix removed outlier: 3.591A pdb=" N GLU E 190 " --> pdb=" O LYS E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 232 removed outlier: 3.558A pdb=" N ALA E 224 " --> pdb=" O ASN E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 256 Processing helix chain 'E' and resid 279 through 283 removed outlier: 3.594A pdb=" N GLY E 282 " --> pdb=" O THR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 293 Processing helix chain 'E' and resid 307 through 318 removed outlier: 4.069A pdb=" N TYR E 311 " --> pdb=" O GLY E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 327 Processing helix chain 'E' and resid 336 through 340 removed outlier: 4.315A pdb=" N ALA E 339 " --> pdb=" O GLY E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 366 removed outlier: 3.663A pdb=" N TYR E 355 " --> pdb=" O THR E 351 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA E 366 " --> pdb=" O LEU E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 396 Processing helix chain 'E' and resid 410 through 428 removed outlier: 3.720A pdb=" N ILE E 414 " --> pdb=" O LYS E 410 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU E 423 " --> pdb=" O LYS E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 474 removed outlier: 3.743A pdb=" N ILE E 461 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU E 472 " --> pdb=" O TYR E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 488 No H-bonds generated for 'chain 'E' and resid 486 through 488' Processing helix chain 'E' and resid 534 through 543 Processing helix chain 'E' and resid 562 through 580 Processing helix chain 'E' and resid 581 through 584 Processing helix chain 'E' and resid 598 through 609 removed outlier: 4.360A pdb=" N ILE E 602 " --> pdb=" O SER E 598 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 645 removed outlier: 4.166A pdb=" N GLU E 640 " --> pdb=" O GLU E 636 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 699 removed outlier: 6.101A pdb=" N GLU E 689 " --> pdb=" O GLU E 685 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU E 690 " --> pdb=" O GLU E 686 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE E 699 " --> pdb=" O ILE E 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 69 removed outlier: 3.593A pdb=" N MET F 66 " --> pdb=" O ASP F 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR F 68 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS F 69 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 100 removed outlier: 4.098A pdb=" N TYR F 91 " --> pdb=" O PRO F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 136 through 146 Processing helix chain 'F' and resid 150 through 161 removed outlier: 3.716A pdb=" N LEU F 154 " --> pdb=" O SER F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 174 Processing helix chain 'F' and resid 175 through 190 removed outlier: 3.754A pdb=" N GLY F 179 " --> pdb=" O ARG F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 232 Processing helix chain 'F' and resid 249 through 255 Processing helix chain 'F' and resid 279 through 283 Processing helix chain 'F' and resid 289 through 293 Processing helix chain 'F' and resid 307 through 318 removed outlier: 3.818A pdb=" N TYR F 311 " --> pdb=" O GLY F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 327 removed outlier: 3.513A pdb=" N MET F 322 " --> pdb=" O VAL F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 340 removed outlier: 4.266A pdb=" N ALA F 339 " --> pdb=" O GLY F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 366 removed outlier: 3.753A pdb=" N TYR F 355 " --> pdb=" O THR F 351 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA F 366 " --> pdb=" O LEU F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 396 Processing helix chain 'F' and resid 410 through 428 removed outlier: 3.573A pdb=" N ILE F 414 " --> pdb=" O LYS F 410 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU F 423 " --> pdb=" O LYS F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 473 Processing helix chain 'F' and resid 534 through 542 removed outlier: 4.411A pdb=" N ILE F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 580 Processing helix chain 'F' and resid 581 through 584 removed outlier: 3.645A pdb=" N PHE F 584 " --> pdb=" O ILE F 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 581 through 584' Processing helix chain 'F' and resid 598 through 608 removed outlier: 4.106A pdb=" N ILE F 602 " --> pdb=" O SER F 598 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS F 608 " --> pdb=" O HIS F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 645 removed outlier: 3.871A pdb=" N GLU F 640 " --> pdb=" O GLU F 636 " (cutoff:3.500A) Processing helix chain 'F' and resid 681 through 700 removed outlier: 5.229A pdb=" N GLU F 689 " --> pdb=" O GLU F 685 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLU F 690 " --> pdb=" O GLU F 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 42 removed outlier: 5.709A pdb=" N LYS G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N SER G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 86 Processing helix chain 'G' and resid 87 through 92 removed outlier: 3.772A pdb=" N LEU G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL G 92 " --> pdb=" O SER G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 111 removed outlier: 3.626A pdb=" N SER G 109 " --> pdb=" O PRO G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 128 removed outlier: 3.519A pdb=" N GLN G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 159 removed outlier: 3.716A pdb=" N LEU G 151 " --> pdb=" O SER G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 226 Processing helix chain 'G' and resid 243 through 249 Processing helix chain 'G' and resid 272 through 282 removed outlier: 3.611A pdb=" N ALA G 282 " --> pdb=" O LEU G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 removed outlier: 3.518A pdb=" N TYR G 300 " --> pdb=" O SER G 296 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU G 301 " --> pdb=" O PRO G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 341 Processing helix chain 'G' and resid 353 through 363 Processing helix chain 'G' and resid 413 through 439 removed outlier: 3.594A pdb=" N GLY G 439 " --> pdb=" O GLU G 435 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 509 removed outlier: 4.987A pdb=" N LYS G 476 " --> pdb=" O GLN G 472 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER G 477 " --> pdb=" O GLU G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 518 through 601 removed outlier: 3.562A pdb=" N SER G 522 " --> pdb=" O ASN G 518 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER G 561 " --> pdb=" O ASN G 557 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS G 562 " --> pdb=" O ALA G 558 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS G 577 " --> pdb=" O ILE G 573 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 52 Processing helix chain 'H' and resid 52 through 62 removed outlier: 3.593A pdb=" N GLU H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR H 62 " --> pdb=" O ARG H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 87 removed outlier: 4.208A pdb=" N ILE H 70 " --> pdb=" O LYS H 66 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER H 73 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET H 74 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR H 86 " --> pdb=" O SER H 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 91 Processing helix chain 'H' and resid 104 through 113 removed outlier: 3.577A pdb=" N HIS H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 127 Processing helix chain 'H' and resid 140 through 151 removed outlier: 3.603A pdb=" N ASP H 144 " --> pdb=" O GLY H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 221 Processing helix chain 'H' and resid 243 through 252 Processing helix chain 'H' and resid 259 through 273 removed outlier: 4.259A pdb=" N VAL H 271 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE H 272 " --> pdb=" O ALA H 268 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU H 273 " --> pdb=" O ALA H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 290 Processing helix chain 'H' and resid 292 through 294 No H-bonds generated for 'chain 'H' and resid 292 through 294' Processing helix chain 'H' and resid 295 through 301 Processing helix chain 'H' and resid 318 through 327 removed outlier: 3.565A pdb=" N VAL H 322 " --> pdb=" O THR H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 440 Processing helix chain 'H' and resid 448 through 515 removed outlier: 3.732A pdb=" N HIS H 452 " --> pdb=" O LEU H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 521 through 639 removed outlier: 3.958A pdb=" N LYS H 525 " --> pdb=" O ASP H 521 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN H 528 " --> pdb=" O VAL H 524 " (cutoff:3.500A) Proline residue: H 634 - end of helix removed outlier: 4.366A pdb=" N GLN H 639 " --> pdb=" O ARG H 635 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 80 Processing helix chain 'I' and resid 89 through 99 Processing helix chain 'I' and resid 127 through 133 removed outlier: 3.695A pdb=" N ILE I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 147 removed outlier: 3.546A pdb=" N LEU I 140 " --> pdb=" O THR I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 161 Processing helix chain 'I' and resid 167 through 169 No H-bonds generated for 'chain 'I' and resid 167 through 169' Processing helix chain 'I' and resid 170 through 190 Proline residue: I 177 - end of helix removed outlier: 3.593A pdb=" N GLU I 190 " --> pdb=" O LYS I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 232 removed outlier: 3.555A pdb=" N ALA I 224 " --> pdb=" O ASN I 220 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 256 Processing helix chain 'I' and resid 279 through 283 removed outlier: 3.595A pdb=" N GLY I 282 " --> pdb=" O THR I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 293 Processing helix chain 'I' and resid 307 through 318 removed outlier: 4.091A pdb=" N TYR I 311 " --> pdb=" O GLY I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 336 through 340 removed outlier: 4.313A pdb=" N ALA I 339 " --> pdb=" O GLY I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 366 removed outlier: 3.657A pdb=" N TYR I 355 " --> pdb=" O THR I 351 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA I 366 " --> pdb=" O LEU I 362 " (cutoff:3.500A) Processing helix chain 'I' and resid 379 through 396 Processing helix chain 'I' and resid 410 through 428 removed outlier: 3.722A pdb=" N ILE I 414 " --> pdb=" O LYS I 410 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU I 423 " --> pdb=" O LYS I 419 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 474 removed outlier: 3.749A pdb=" N ILE I 461 " --> pdb=" O LEU I 457 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU I 472 " --> pdb=" O TYR I 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 488 No H-bonds generated for 'chain 'I' and resid 486 through 488' Processing helix chain 'I' and resid 534 through 543 Processing helix chain 'I' and resid 562 through 580 Processing helix chain 'I' and resid 581 through 584 removed outlier: 3.514A pdb=" N PHE I 584 " --> pdb=" O ILE I 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 581 through 584' Processing helix chain 'I' and resid 598 through 609 removed outlier: 4.360A pdb=" N ILE I 602 " --> pdb=" O SER I 598 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG I 609 " --> pdb=" O LEU I 605 " (cutoff:3.500A) Processing helix chain 'I' and resid 636 through 645 removed outlier: 4.175A pdb=" N GLU I 640 " --> pdb=" O GLU I 636 " (cutoff:3.500A) Processing helix chain 'I' and resid 679 through 699 removed outlier: 6.094A pdb=" N GLU I 689 " --> pdb=" O GLU I 685 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU I 690 " --> pdb=" O GLU I 686 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE I 699 " --> pdb=" O ILE I 695 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 69 removed outlier: 3.597A pdb=" N MET J 66 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR J 68 " --> pdb=" O ARG J 65 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS J 69 " --> pdb=" O MET J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 100 removed outlier: 4.088A pdb=" N TYR J 91 " --> pdb=" O PRO J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 136 through 146 Processing helix chain 'J' and resid 150 through 161 removed outlier: 3.715A pdb=" N LEU J 154 " --> pdb=" O SER J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 174 Processing helix chain 'J' and resid 175 through 190 removed outlier: 3.748A pdb=" N GLY J 179 " --> pdb=" O ARG J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 219 through 232 Processing helix chain 'J' and resid 249 through 255 Processing helix chain 'J' and resid 279 through 283 Processing helix chain 'J' and resid 289 through 293 Processing helix chain 'J' and resid 307 through 318 removed outlier: 3.814A pdb=" N TYR J 311 " --> pdb=" O GLY J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 318 through 327 removed outlier: 3.509A pdb=" N MET J 322 " --> pdb=" O VAL J 318 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 340 removed outlier: 4.267A pdb=" N ALA J 339 " --> pdb=" O GLY J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 366 removed outlier: 3.751A pdb=" N TYR J 355 " --> pdb=" O THR J 351 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA J 366 " --> pdb=" O LEU J 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 396 Processing helix chain 'J' and resid 410 through 428 removed outlier: 3.572A pdb=" N ILE J 414 " --> pdb=" O LYS J 410 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU J 423 " --> pdb=" O LYS J 419 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 473 Processing helix chain 'J' and resid 534 through 542 removed outlier: 4.404A pdb=" N ILE J 538 " --> pdb=" O SER J 534 " (cutoff:3.500A) Processing helix chain 'J' and resid 564 through 580 Processing helix chain 'J' and resid 581 through 584 removed outlier: 3.619A pdb=" N PHE J 584 " --> pdb=" O ILE J 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 581 through 584' Processing helix chain 'J' and resid 598 through 608 removed outlier: 4.106A pdb=" N ILE J 602 " --> pdb=" O SER J 598 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS J 608 " --> pdb=" O HIS J 604 " (cutoff:3.500A) Processing helix chain 'J' and resid 636 through 645 removed outlier: 3.865A pdb=" N GLU J 640 " --> pdb=" O GLU J 636 " (cutoff:3.500A) Processing helix chain 'J' and resid 681 through 700 removed outlier: 5.254A pdb=" N GLU J 689 " --> pdb=" O GLU J 685 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU J 690 " --> pdb=" O GLU J 686 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 42 removed outlier: 5.709A pdb=" N LYS K 35 " --> pdb=" O SER K 31 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER K 36 " --> pdb=" O LEU K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 86 Processing helix chain 'K' and resid 87 through 92 removed outlier: 3.772A pdb=" N LEU K 91 " --> pdb=" O PRO K 88 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL K 92 " --> pdb=" O SER K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 111 removed outlier: 3.627A pdb=" N SER K 109 " --> pdb=" O PRO K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 128 removed outlier: 3.518A pdb=" N GLN K 117 " --> pdb=" O SER K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 159 removed outlier: 3.716A pdb=" N LEU K 151 " --> pdb=" O SER K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 Processing helix chain 'K' and resid 243 through 249 Processing helix chain 'K' and resid 272 through 282 removed outlier: 3.610A pdb=" N ALA K 282 " --> pdb=" O LEU K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 306 removed outlier: 3.518A pdb=" N TYR K 300 " --> pdb=" O SER K 296 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU K 301 " --> pdb=" O PRO K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 341 Processing helix chain 'K' and resid 353 through 363 Processing helix chain 'K' and resid 413 through 439 removed outlier: 3.593A pdb=" N GLY K 439 " --> pdb=" O GLU K 435 " (cutoff:3.500A) Processing helix chain 'K' and resid 440 through 509 removed outlier: 4.987A pdb=" N LYS K 476 " --> pdb=" O GLN K 472 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER K 477 " --> pdb=" O GLU K 473 " (cutoff:3.500A) Processing helix chain 'K' and resid 518 through 601 removed outlier: 3.562A pdb=" N SER K 522 " --> pdb=" O ASN K 518 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER K 561 " --> pdb=" O ASN K 557 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS K 562 " --> pdb=" O ALA K 558 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS K 577 " --> pdb=" O ILE K 573 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 52 Processing helix chain 'L' and resid 52 through 62 removed outlier: 3.593A pdb=" N GLU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR L 62 " --> pdb=" O ARG L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 87 removed outlier: 4.208A pdb=" N ILE L 70 " --> pdb=" O LYS L 66 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU L 71 " --> pdb=" O GLU L 67 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU L 72 " --> pdb=" O ASP L 68 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET L 74 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR L 86 " --> pdb=" O SER L 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS L 87 " --> pdb=" O LEU L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 91 Processing helix chain 'L' and resid 104 through 113 removed outlier: 3.576A pdb=" N HIS L 108 " --> pdb=" O ASP L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 127 Processing helix chain 'L' and resid 140 through 151 removed outlier: 3.603A pdb=" N ASP L 144 " --> pdb=" O GLY L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 221 Processing helix chain 'L' and resid 243 through 252 Processing helix chain 'L' and resid 259 through 273 removed outlier: 4.259A pdb=" N VAL L 271 " --> pdb=" O THR L 267 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE L 272 " --> pdb=" O ALA L 268 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU L 273 " --> pdb=" O ALA L 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 290 Processing helix chain 'L' and resid 292 through 294 No H-bonds generated for 'chain 'L' and resid 292 through 294' Processing helix chain 'L' and resid 295 through 301 Processing helix chain 'L' and resid 318 through 327 removed outlier: 3.565A pdb=" N VAL L 322 " --> pdb=" O THR L 318 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 440 Processing helix chain 'L' and resid 448 through 515 removed outlier: 3.733A pdb=" N HIS L 452 " --> pdb=" O LEU L 448 " (cutoff:3.500A) Processing helix chain 'L' and resid 521 through 639 removed outlier: 3.957A pdb=" N LYS L 525 " --> pdb=" O ASP L 521 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN L 528 " --> pdb=" O VAL L 524 " (cutoff:3.500A) Proline residue: L 634 - end of helix removed outlier: 4.365A pdb=" N GLN L 639 " --> pdb=" O ARG L 635 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 80 Processing helix chain 'M' and resid 89 through 99 Processing helix chain 'M' and resid 127 through 133 removed outlier: 3.686A pdb=" N ILE M 131 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 147 removed outlier: 3.547A pdb=" N LEU M 140 " --> pdb=" O THR M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 161 Processing helix chain 'M' and resid 167 through 169 No H-bonds generated for 'chain 'M' and resid 167 through 169' Processing helix chain 'M' and resid 170 through 190 Proline residue: M 177 - end of helix removed outlier: 3.594A pdb=" N GLU M 190 " --> pdb=" O LYS M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 232 removed outlier: 3.562A pdb=" N ALA M 224 " --> pdb=" O ASN M 220 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 256 Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.598A pdb=" N GLY M 282 " --> pdb=" O THR M 279 " (cutoff:3.500A) Processing helix chain 'M' and resid 289 through 293 Processing helix chain 'M' and resid 307 through 318 removed outlier: 4.092A pdb=" N TYR M 311 " --> pdb=" O GLY M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 318 through 327 Processing helix chain 'M' and resid 336 through 340 removed outlier: 4.313A pdb=" N ALA M 339 " --> pdb=" O GLY M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 366 removed outlier: 3.657A pdb=" N TYR M 355 " --> pdb=" O THR M 351 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA M 366 " --> pdb=" O LEU M 362 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 396 Processing helix chain 'M' and resid 410 through 428 removed outlier: 3.722A pdb=" N ILE M 414 " --> pdb=" O LYS M 410 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU M 423 " --> pdb=" O LYS M 419 " (cutoff:3.500A) Processing helix chain 'M' and resid 457 through 474 removed outlier: 3.747A pdb=" N ILE M 461 " --> pdb=" O LEU M 457 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU M 472 " --> pdb=" O TYR M 468 " (cutoff:3.500A) Processing helix chain 'M' and resid 486 through 488 No H-bonds generated for 'chain 'M' and resid 486 through 488' Processing helix chain 'M' and resid 534 through 543 Processing helix chain 'M' and resid 562 through 580 Processing helix chain 'M' and resid 581 through 584 removed outlier: 3.504A pdb=" N PHE M 584 " --> pdb=" O ILE M 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 581 through 584' Processing helix chain 'M' and resid 598 through 609 removed outlier: 4.361A pdb=" N ILE M 602 " --> pdb=" O SER M 598 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG M 609 " --> pdb=" O LEU M 605 " (cutoff:3.500A) Processing helix chain 'M' and resid 636 through 645 removed outlier: 4.176A pdb=" N GLU M 640 " --> pdb=" O GLU M 636 " (cutoff:3.500A) Processing helix chain 'M' and resid 679 through 699 removed outlier: 6.093A pdb=" N GLU M 689 " --> pdb=" O GLU M 685 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU M 690 " --> pdb=" O GLU M 686 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE M 699 " --> pdb=" O ILE M 695 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 69 removed outlier: 3.604A pdb=" N MET N 66 " --> pdb=" O ASP N 63 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR N 68 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS N 69 " --> pdb=" O MET N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 100 removed outlier: 4.096A pdb=" N TYR N 91 " --> pdb=" O PRO N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 132 Processing helix chain 'N' and resid 136 through 146 Processing helix chain 'N' and resid 150 through 161 removed outlier: 3.716A pdb=" N LEU N 154 " --> pdb=" O SER N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 174 Processing helix chain 'N' and resid 175 through 190 removed outlier: 3.752A pdb=" N GLY N 179 " --> pdb=" O ARG N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 232 Processing helix chain 'N' and resid 249 through 255 Processing helix chain 'N' and resid 279 through 283 Processing helix chain 'N' and resid 289 through 293 Processing helix chain 'N' and resid 307 through 318 removed outlier: 3.814A pdb=" N TYR N 311 " --> pdb=" O GLY N 307 " (cutoff:3.500A) Processing helix chain 'N' and resid 318 through 327 removed outlier: 3.509A pdb=" N MET N 322 " --> pdb=" O VAL N 318 " (cutoff:3.500A) Processing helix chain 'N' and resid 336 through 340 removed outlier: 4.267A pdb=" N ALA N 339 " --> pdb=" O GLY N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 351 through 366 removed outlier: 3.751A pdb=" N TYR N 355 " --> pdb=" O THR N 351 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA N 366 " --> pdb=" O LEU N 362 " (cutoff:3.500A) Processing helix chain 'N' and resid 379 through 396 Processing helix chain 'N' and resid 410 through 428 removed outlier: 3.572A pdb=" N ILE N 414 " --> pdb=" O LYS N 410 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU N 423 " --> pdb=" O LYS N 419 " (cutoff:3.500A) Processing helix chain 'N' and resid 457 through 473 Processing helix chain 'N' and resid 534 through 542 removed outlier: 4.404A pdb=" N ILE N 538 " --> pdb=" O SER N 534 " (cutoff:3.500A) Processing helix chain 'N' and resid 564 through 580 Processing helix chain 'N' and resid 581 through 584 removed outlier: 3.636A pdb=" N PHE N 584 " --> pdb=" O ILE N 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 581 through 584' Processing helix chain 'N' and resid 598 through 608 removed outlier: 4.105A pdb=" N ILE N 602 " --> pdb=" O SER N 598 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS N 608 " --> pdb=" O HIS N 604 " (cutoff:3.500A) Processing helix chain 'N' and resid 636 through 645 removed outlier: 3.867A pdb=" N GLU N 640 " --> pdb=" O GLU N 636 " (cutoff:3.500A) Processing helix chain 'N' and resid 681 through 700 removed outlier: 5.259A pdb=" N GLU N 689 " --> pdb=" O GLU N 685 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU N 690 " --> pdb=" O GLU N 686 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 42 removed outlier: 5.709A pdb=" N LYS O 35 " --> pdb=" O SER O 31 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER O 36 " --> pdb=" O LEU O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 86 Processing helix chain 'O' and resid 87 through 92 removed outlier: 3.772A pdb=" N LEU O 91 " --> pdb=" O PRO O 88 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL O 92 " --> pdb=" O SER O 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 111 removed outlier: 3.627A pdb=" N SER O 109 " --> pdb=" O PRO O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 128 removed outlier: 3.518A pdb=" N GLN O 117 " --> pdb=" O SER O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 159 removed outlier: 3.716A pdb=" N LEU O 151 " --> pdb=" O SER O 147 " (cutoff:3.500A) Processing helix chain 'O' and resid 221 through 226 Processing helix chain 'O' and resid 243 through 249 Processing helix chain 'O' and resid 272 through 282 removed outlier: 3.610A pdb=" N ALA O 282 " --> pdb=" O LEU O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 296 through 306 removed outlier: 3.519A pdb=" N TYR O 300 " --> pdb=" O SER O 296 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU O 301 " --> pdb=" O PRO O 297 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 341 Processing helix chain 'O' and resid 353 through 363 Processing helix chain 'O' and resid 413 through 439 removed outlier: 3.593A pdb=" N GLY O 439 " --> pdb=" O GLU O 435 " (cutoff:3.500A) Processing helix chain 'O' and resid 440 through 509 removed outlier: 4.987A pdb=" N LYS O 476 " --> pdb=" O GLN O 472 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER O 477 " --> pdb=" O GLU O 473 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 601 removed outlier: 3.563A pdb=" N SER O 522 " --> pdb=" O ASN O 518 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER O 561 " --> pdb=" O ASN O 557 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS O 562 " --> pdb=" O ALA O 558 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS O 577 " --> pdb=" O ILE O 573 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 52 Processing helix chain 'P' and resid 52 through 62 removed outlier: 3.594A pdb=" N GLU P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR P 62 " --> pdb=" O ARG P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 87 removed outlier: 4.208A pdb=" N ILE P 70 " --> pdb=" O LYS P 66 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU P 71 " --> pdb=" O GLU P 67 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER P 73 " --> pdb=" O VAL P 69 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET P 74 " --> pdb=" O ILE P 70 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR P 86 " --> pdb=" O SER P 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS P 87 " --> pdb=" O LEU P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 91 Processing helix chain 'P' and resid 104 through 113 removed outlier: 3.577A pdb=" N HIS P 108 " --> pdb=" O ASP P 104 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 127 Processing helix chain 'P' and resid 140 through 151 removed outlier: 3.604A pdb=" N ASP P 144 " --> pdb=" O GLY P 140 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 221 Processing helix chain 'P' and resid 243 through 252 Processing helix chain 'P' and resid 259 through 273 removed outlier: 4.259A pdb=" N VAL P 271 " --> pdb=" O THR P 267 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE P 272 " --> pdb=" O ALA P 268 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU P 273 " --> pdb=" O ALA P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 284 through 290 Processing helix chain 'P' and resid 292 through 294 No H-bonds generated for 'chain 'P' and resid 292 through 294' Processing helix chain 'P' and resid 295 through 301 Processing helix chain 'P' and resid 318 through 327 removed outlier: 3.564A pdb=" N VAL P 322 " --> pdb=" O THR P 318 " (cutoff:3.500A) Processing helix chain 'P' and resid 405 through 440 Processing helix chain 'P' and resid 448 through 515 removed outlier: 3.732A pdb=" N HIS P 452 " --> pdb=" O LEU P 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 521 through 639 removed outlier: 3.957A pdb=" N LYS P 525 " --> pdb=" O ASP P 521 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN P 528 " --> pdb=" O VAL P 524 " (cutoff:3.500A) Proline residue: P 634 - end of helix removed outlier: 4.365A pdb=" N GLN P 639 " --> pdb=" O ARG P 635 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 120 removed outlier: 5.991A pdb=" N THR A 58 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY A 59 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 374 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS A 371 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N MET A 240 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N SER A 334 " --> pdb=" O MET A 240 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 242 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 490 through 492 removed outlier: 6.779A pdb=" N ILE A 502 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ILE A 593 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 504 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE A 595 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 506 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE A 590 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 617 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 647 " --> pdb=" O VAL A 618 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 511 through 516 removed outlier: 11.099A pdb=" N ASP A 511 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N SER A 528 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N TRP A 513 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N SER A 526 " --> pdb=" O TRP A 513 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS A 515 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 121 removed outlier: 6.130A pdb=" N THR B 58 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 121 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU B 60 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLY B 59 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 374 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET B 240 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N SER B 334 " --> pdb=" O MET B 240 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 242 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE B 239 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL B 265 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE B 241 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N LEU B 267 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASP B 243 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N ARG B 269 " --> pdb=" O ASP B 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 476 through 478 removed outlier: 4.766A pdb=" N VAL B 490 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B 553 " --> pdb=" O HIS B 507 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP B 508 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE B 590 " --> pdb=" O THR B 615 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR B 617 " --> pdb=" O ILE B 590 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU B 673 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE B 648 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 16 removed outlier: 3.608A pdb=" N LYS C 290 " --> pdb=" O TYR C 12 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 14 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE C 261 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU C 291 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N SER C 263 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N VAL C 293 " --> pdb=" O SER C 263 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 140 through 145 removed outlier: 6.230A pdb=" N ARG C 164 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LEU C 240 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS C 166 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N THR C 242 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 35 removed outlier: 7.177A pdb=" N TYR D 31 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL D 239 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU D 33 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU D 202 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU D 238 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS D 204 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ALA D 240 " --> pdb=" O CYS D 204 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N ILE D 203 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA D 134 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR D 133 " --> pdb=" O HIS D 179 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N PHE D 181 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE D 135 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N HIS D 156 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU D 180 " --> pdb=" O HIS D 156 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS D 158 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N SER D 182 " --> pdb=" O LYS D 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 120 removed outlier: 5.982A pdb=" N THR E 58 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY E 59 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU E 374 " --> pdb=" O ALA E 198 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS E 371 " --> pdb=" O VAL E 331 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET E 240 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER E 334 " --> pdb=" O MET E 240 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU E 242 " --> pdb=" O SER E 334 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 490 through 492 removed outlier: 6.782A pdb=" N ILE E 502 " --> pdb=" O ALA E 591 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ILE E 593 " --> pdb=" O ILE E 502 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE E 504 " --> pdb=" O ILE E 593 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE E 595 " --> pdb=" O ILE E 504 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL E 506 " --> pdb=" O ILE E 595 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE E 590 " --> pdb=" O THR E 615 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR E 617 " --> pdb=" O ILE E 590 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 647 " --> pdb=" O VAL E 618 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 511 through 516 removed outlier: 11.039A pdb=" N ASP E 511 " --> pdb=" O SER E 528 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N SER E 528 " --> pdb=" O ASP E 511 " (cutoff:3.500A) removed outlier: 10.168A pdb=" N TRP E 513 " --> pdb=" O SER E 526 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N SER E 526 " --> pdb=" O TRP E 513 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS E 515 " --> pdb=" O ASP E 524 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 118 through 121 removed outlier: 6.144A pdb=" N THR F 58 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE F 121 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU F 60 " --> pdb=" O ILE F 121 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY F 59 " --> pdb=" O LEU F 197 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU F 374 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET F 240 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N SER F 334 " --> pdb=" O MET F 240 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU F 242 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE F 239 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL F 265 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE F 241 " --> pdb=" O VAL F 265 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N LEU F 267 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP F 243 " --> pdb=" O LEU F 267 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ARG F 269 " --> pdb=" O ASP F 243 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 476 through 478 removed outlier: 4.767A pdb=" N VAL F 490 " --> pdb=" O LEU F 478 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE F 553 " --> pdb=" O HIS F 507 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP F 508 " --> pdb=" O ILE F 595 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE F 590 " --> pdb=" O THR F 615 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR F 617 " --> pdb=" O ILE F 590 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU F 673 " --> pdb=" O SER F 646 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE F 648 " --> pdb=" O LEU F 673 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 11 through 16 removed outlier: 3.607A pdb=" N LYS G 290 " --> pdb=" O TYR G 12 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU G 14 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE G 261 " --> pdb=" O ILE G 289 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU G 291 " --> pdb=" O ILE G 261 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N SER G 263 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N VAL G 293 " --> pdb=" O SER G 263 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 140 through 145 removed outlier: 6.230A pdb=" N ARG G 164 " --> pdb=" O LEU G 238 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LEU G 240 " --> pdb=" O ARG G 164 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS G 166 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N THR G 242 " --> pdb=" O LYS G 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 30 through 35 removed outlier: 7.177A pdb=" N TYR H 31 " --> pdb=" O ARG H 237 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL H 239 " --> pdb=" O TYR H 31 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU H 33 " --> pdb=" O VAL H 239 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU H 202 " --> pdb=" O VAL H 236 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU H 238 " --> pdb=" O LEU H 202 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS H 204 " --> pdb=" O LEU H 238 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ALA H 240 " --> pdb=" O CYS H 204 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ILE H 203 " --> pdb=" O GLU H 132 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA H 134 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR H 133 " --> pdb=" O HIS H 179 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N PHE H 181 " --> pdb=" O THR H 133 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE H 135 " --> pdb=" O PHE H 181 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N HIS H 156 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU H 180 " --> pdb=" O HIS H 156 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS H 158 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N SER H 182 " --> pdb=" O LYS H 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'I' and resid 118 through 120 removed outlier: 5.983A pdb=" N THR I 58 " --> pdb=" O LEU I 119 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLY I 59 " --> pdb=" O LEU I 197 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU I 374 " --> pdb=" O ALA I 198 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS I 371 " --> pdb=" O VAL I 331 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET I 240 " --> pdb=" O ILE I 332 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER I 334 " --> pdb=" O MET I 240 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU I 242 " --> pdb=" O SER I 334 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 490 through 492 removed outlier: 6.779A pdb=" N ILE I 502 " --> pdb=" O ALA I 591 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ILE I 593 " --> pdb=" O ILE I 502 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE I 504 " --> pdb=" O ILE I 593 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE I 595 " --> pdb=" O ILE I 504 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL I 506 " --> pdb=" O ILE I 595 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE I 590 " --> pdb=" O THR I 615 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR I 617 " --> pdb=" O ILE I 590 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU I 647 " --> pdb=" O VAL I 618 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 511 through 516 removed outlier: 11.050A pdb=" N ASP I 511 " --> pdb=" O SER I 528 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N SER I 528 " --> pdb=" O ASP I 511 " (cutoff:3.500A) removed outlier: 10.160A pdb=" N TRP I 513 " --> pdb=" O SER I 526 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N SER I 526 " --> pdb=" O TRP I 513 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS I 515 " --> pdb=" O ASP I 524 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 118 through 121 removed outlier: 6.141A pdb=" N THR J 58 " --> pdb=" O LEU J 119 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE J 121 " --> pdb=" O THR J 58 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU J 60 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY J 59 " --> pdb=" O LEU J 197 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU J 374 " --> pdb=" O ALA J 198 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N MET J 240 " --> pdb=" O ILE J 332 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N SER J 334 " --> pdb=" O MET J 240 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU J 242 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE J 239 " --> pdb=" O LEU J 263 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL J 265 " --> pdb=" O ILE J 239 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE J 241 " --> pdb=" O VAL J 265 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N LEU J 267 " --> pdb=" O ILE J 241 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP J 243 " --> pdb=" O LEU J 267 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N ARG J 269 " --> pdb=" O ASP J 243 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 476 through 478 removed outlier: 4.769A pdb=" N VAL J 490 " --> pdb=" O LEU J 478 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE J 553 " --> pdb=" O HIS J 507 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP J 508 " --> pdb=" O ILE J 595 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE J 590 " --> pdb=" O THR J 615 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR J 617 " --> pdb=" O ILE J 590 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU J 673 " --> pdb=" O SER J 646 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE J 648 " --> pdb=" O LEU J 673 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 11 through 16 removed outlier: 3.607A pdb=" N LYS K 290 " --> pdb=" O TYR K 12 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU K 14 " --> pdb=" O LYS K 290 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE K 261 " --> pdb=" O ILE K 289 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU K 291 " --> pdb=" O ILE K 261 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N SER K 263 " --> pdb=" O LEU K 291 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N VAL K 293 " --> pdb=" O SER K 263 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 140 through 145 removed outlier: 6.231A pdb=" N ARG K 164 " --> pdb=" O LEU K 238 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU K 240 " --> pdb=" O ARG K 164 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS K 166 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N THR K 242 " --> pdb=" O LYS K 166 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 30 through 35 removed outlier: 7.176A pdb=" N TYR L 31 " --> pdb=" O ARG L 237 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL L 239 " --> pdb=" O TYR L 31 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU L 33 " --> pdb=" O VAL L 239 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU L 202 " --> pdb=" O VAL L 236 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU L 238 " --> pdb=" O LEU L 202 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS L 204 " --> pdb=" O LEU L 238 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ALA L 240 " --> pdb=" O CYS L 204 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ILE L 203 " --> pdb=" O GLU L 132 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA L 134 " --> pdb=" O ILE L 203 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR L 133 " --> pdb=" O HIS L 179 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N PHE L 181 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE L 135 " --> pdb=" O PHE L 181 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N HIS L 156 " --> pdb=" O VAL L 178 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU L 180 " --> pdb=" O HIS L 156 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS L 158 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N SER L 182 " --> pdb=" O LYS L 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'M' and resid 118 through 120 removed outlier: 5.986A pdb=" N THR M 58 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY M 59 " --> pdb=" O LEU M 197 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU M 374 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS M 371 " --> pdb=" O VAL M 331 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET M 240 " --> pdb=" O ILE M 332 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N SER M 334 " --> pdb=" O MET M 240 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU M 242 " --> pdb=" O SER M 334 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 490 through 492 removed outlier: 6.782A pdb=" N ILE M 502 " --> pdb=" O ALA M 591 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ILE M 593 " --> pdb=" O ILE M 502 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE M 504 " --> pdb=" O ILE M 593 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE M 595 " --> pdb=" O ILE M 504 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL M 506 " --> pdb=" O ILE M 595 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE M 590 " --> pdb=" O THR M 615 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR M 617 " --> pdb=" O ILE M 590 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU M 647 " --> pdb=" O VAL M 618 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 511 through 516 removed outlier: 11.102A pdb=" N ASP M 511 " --> pdb=" O SER M 528 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N SER M 528 " --> pdb=" O ASP M 511 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N TRP M 513 " --> pdb=" O SER M 526 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N SER M 526 " --> pdb=" O TRP M 513 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS M 515 " --> pdb=" O ASP M 524 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 118 through 121 removed outlier: 6.143A pdb=" N THR N 58 " --> pdb=" O LEU N 119 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE N 121 " --> pdb=" O THR N 58 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU N 60 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY N 59 " --> pdb=" O LEU N 197 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU N 374 " --> pdb=" O ALA N 198 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N MET N 240 " --> pdb=" O ILE N 332 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N SER N 334 " --> pdb=" O MET N 240 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU N 242 " --> pdb=" O SER N 334 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE N 239 " --> pdb=" O LEU N 263 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL N 265 " --> pdb=" O ILE N 239 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE N 241 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU N 267 " --> pdb=" O ILE N 241 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP N 243 " --> pdb=" O LEU N 267 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ARG N 269 " --> pdb=" O ASP N 243 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 476 through 478 removed outlier: 4.763A pdb=" N VAL N 490 " --> pdb=" O LEU N 478 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE N 553 " --> pdb=" O HIS N 507 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP N 508 " --> pdb=" O ILE N 595 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE N 590 " --> pdb=" O THR N 615 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR N 617 " --> pdb=" O ILE N 590 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU N 673 " --> pdb=" O SER N 646 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE N 648 " --> pdb=" O LEU N 673 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 11 through 16 removed outlier: 3.607A pdb=" N LYS O 290 " --> pdb=" O TYR O 12 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU O 14 " --> pdb=" O LYS O 290 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE O 261 " --> pdb=" O ILE O 289 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU O 291 " --> pdb=" O ILE O 261 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N SER O 263 " --> pdb=" O LEU O 291 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N VAL O 293 " --> pdb=" O SER O 263 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 140 through 145 removed outlier: 6.231A pdb=" N ARG O 164 " --> pdb=" O LEU O 238 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU O 240 " --> pdb=" O ARG O 164 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS O 166 " --> pdb=" O LEU O 240 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N THR O 242 " --> pdb=" O LYS O 166 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 30 through 35 removed outlier: 7.177A pdb=" N TYR P 31 " --> pdb=" O ARG P 237 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL P 239 " --> pdb=" O TYR P 31 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU P 33 " --> pdb=" O VAL P 239 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU P 202 " --> pdb=" O VAL P 236 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU P 238 " --> pdb=" O LEU P 202 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS P 204 " --> pdb=" O LEU P 238 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ALA P 240 " --> pdb=" O CYS P 204 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ILE P 203 " --> pdb=" O GLU P 132 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA P 134 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR P 133 " --> pdb=" O HIS P 179 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N PHE P 181 " --> pdb=" O THR P 133 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE P 135 " --> pdb=" O PHE P 181 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N HIS P 156 " --> pdb=" O VAL P 178 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU P 180 " --> pdb=" O HIS P 156 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS P 158 " --> pdb=" O LEU P 180 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N SER P 182 " --> pdb=" O LYS P 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 3749 hydrogen bonds defined for protein. 11028 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: 35.60 Time building geometry restraints manager: 16.64 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: 23746 1.34 - 1.46: 14285 1.46 - 1.58: 40505 1.58 - 1.69: 0 1.69 - 1.81: 548 Bond restraints: 79084 Sorted by residual: bond pdb=" C VAL D 105 " pdb=" N PRO D 106 " ideal model delta sigma weight residual 1.336 1.373 -0.038 1.23e-02 6.61e+03 9.43e+00 bond pdb=" C VAL P 105 " pdb=" N PRO P 106 " ideal model delta sigma weight residual 1.336 1.373 -0.037 1.23e-02 6.61e+03 9.17e+00 bond pdb=" C VAL L 105 " pdb=" N PRO L 106 " ideal model delta sigma weight residual 1.336 1.373 -0.037 1.23e-02 6.61e+03 9.02e+00 bond pdb=" C VAL H 105 " pdb=" N PRO H 106 " ideal model delta sigma weight residual 1.336 1.372 -0.037 1.23e-02 6.61e+03 8.91e+00 bond pdb=" C GLU A 444 " pdb=" N PRO A 445 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.82e+00 ... (remaining 79079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 105179 2.91 - 5.82: 1481 5.82 - 8.73: 227 8.73 - 11.64: 44 11.64 - 14.55: 9 Bond angle restraints: 106940 Sorted by residual: angle pdb=" N PRO B 55 " pdb=" CA PRO B 55 " pdb=" C PRO B 55 " ideal model delta sigma weight residual 114.98 107.77 7.21 1.46e+00 4.69e-01 2.44e+01 angle pdb=" N PRO J 55 " pdb=" CA PRO J 55 " pdb=" C PRO J 55 " ideal model delta sigma weight residual 114.98 107.78 7.20 1.46e+00 4.69e-01 2.43e+01 angle pdb=" N PRO N 55 " pdb=" CA PRO N 55 " pdb=" C PRO N 55 " ideal model delta sigma weight residual 114.98 107.79 7.19 1.46e+00 4.69e-01 2.42e+01 angle pdb=" CG1 ILE E 450 " pdb=" CB ILE E 450 " pdb=" CG2 ILE E 450 " ideal model delta sigma weight residual 110.70 96.15 14.55 3.00e+00 1.11e-01 2.35e+01 angle pdb=" CG1 ILE A 450 " pdb=" CB ILE A 450 " pdb=" CG2 ILE A 450 " ideal model delta sigma weight residual 110.70 96.16 14.54 3.00e+00 1.11e-01 2.35e+01 ... (remaining 106935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 42499 17.77 - 35.54: 4618 35.54 - 53.31: 882 53.31 - 71.09: 165 71.09 - 88.86: 92 Dihedral angle restraints: 48256 sinusoidal: 19956 harmonic: 28300 Sorted by residual: dihedral pdb=" CA SER N 54 " pdb=" C SER N 54 " pdb=" N PRO N 55 " pdb=" CA PRO N 55 " ideal model delta harmonic sigma weight residual 180.00 132.12 47.88 0 5.00e+00 4.00e-02 9.17e+01 dihedral pdb=" CA SER B 54 " pdb=" C SER B 54 " pdb=" N PRO B 55 " pdb=" CA PRO B 55 " ideal model delta harmonic sigma weight residual 180.00 132.16 47.84 0 5.00e+00 4.00e-02 9.15e+01 dihedral pdb=" CA SER F 54 " pdb=" C SER F 54 " pdb=" N PRO F 55 " pdb=" CA PRO F 55 " ideal model delta harmonic sigma weight residual 180.00 132.19 47.81 0 5.00e+00 4.00e-02 9.14e+01 ... (remaining 48253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 9815 0.071 - 0.142: 1896 0.142 - 0.213: 191 0.213 - 0.284: 14 0.284 - 0.355: 12 Chirality restraints: 11928 Sorted by residual: chirality pdb=" CB ILE E 450 " pdb=" CA ILE E 450 " pdb=" CG1 ILE E 450 " pdb=" CG2 ILE E 450 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB ILE I 450 " pdb=" CA ILE I 450 " pdb=" CG1 ILE I 450 " pdb=" CG2 ILE I 450 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CB ILE A 450 " pdb=" CA ILE A 450 " pdb=" CG1 ILE A 450 " pdb=" CG2 ILE A 450 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 11925 not shown) Planarity restraints: 13768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 54 " 0.064 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO B 55 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 54 " -0.064 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO F 55 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO F 55 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO F 55 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 54 " 0.064 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO N 55 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO N 55 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO N 55 " 0.053 5.00e-02 4.00e+02 ... (remaining 13765 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1778 2.66 - 3.22: 72623 3.22 - 3.78: 126748 3.78 - 4.34: 160128 4.34 - 4.90: 254858 Nonbonded interactions: 616135 Sorted by model distance: nonbonded pdb=" OD2 ASP B 338 " pdb="ZN ZN B 801 " model vdw 2.104 2.230 nonbonded pdb=" OD2 ASP J 338 " pdb="ZN ZN J 801 " model vdw 2.104 2.230 nonbonded pdb=" OD2 ASP N 338 " pdb="ZN ZN N 801 " model vdw 2.105 2.230 nonbonded pdb=" OD2 ASP F 338 " pdb="ZN ZN F 801 " model vdw 2.105 2.230 nonbonded pdb=" OD2 ASP E 245 " pdb="ZN ZN E 801 " model vdw 2.184 2.230 ... (remaining 616130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 445 or resid 447 through 515 or (resid 516 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ NE or name CZ )) or resid 517 through 656 or resid 667 through 678 or resid 680 \ through 700 or resid 801)) selection = (chain 'B' and (resid 40 through 445 or resid 447 through 700 or resid 801)) selection = (chain 'E' and (resid 40 through 445 or resid 447 through 515 or (resid 516 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ NE or name CZ )) or resid 517 through 656 or resid 667 through 678 or resid 680 \ through 700 or resid 801)) selection = (chain 'F' and (resid 40 through 445 or resid 447 through 700 or resid 801)) selection = (chain 'I' and (resid 40 through 445 or resid 447 through 515 or (resid 516 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ NE or name CZ )) or resid 517 through 656 or resid 667 through 678 or resid 680 \ through 700 or resid 801)) selection = (chain 'J' and (resid 40 through 445 or resid 447 through 700 or resid 801)) selection = (chain 'M' and (resid 40 through 445 or resid 447 through 515 or (resid 516 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ NE or name CZ )) or resid 517 through 656 or resid 667 through 678 or resid 680 \ through 700 or resid 801)) selection = (chain 'N' and (resid 40 through 445 or resid 447 through 700 or resid 801)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.94 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: 190.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 2.510 Check model and map are aligned: 0.440 Set scattering table: 0.530 Process input model: 149.820 Find NCS groups from input model: 3.540 Set up NCS constraints: 0.490 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: 0.030 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 350.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 79084 Z= 0.373 Angle : 0.924 14.546 106940 Z= 0.502 Chirality : 0.055 0.355 11928 Planarity : 0.007 0.096 13768 Dihedral : 15.433 88.858 29916 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.96 % Allowed : 8.25 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.09 % Twisted Proline : 1.92 % Twisted General : 0.26 % 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: -3.37 (0.07), residues: 9516 helix: -1.56 (0.06), residues: 4504 sheet: -1.22 (0.15), residues: 1084 loop : -3.34 (0.08), residues: 3928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 244 HIS 0.008 0.002 HIS D 452 PHE 0.020 0.002 PHE B 688 TYR 0.025 0.002 TYR I 575 ARG 0.004 0.001 ARG M 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 534 time to evaluate : 6.794 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: A 240 MET cc_start: 0.9506 (ttt) cc_final: 0.9277 (tpt) REVERT: A 320 MET cc_start: 0.8838 (mmm) cc_final: 0.8594 (mmm) REVERT: A 566 MET cc_start: 0.9516 (mtt) cc_final: 0.9289 (mtt) REVERT: A 599 TYR cc_start: 0.8843 (t80) cc_final: 0.8625 (t80) REVERT: B 40 ARG cc_start: 0.7353 (mtp85) cc_final: 0.7110 (mtp180) REVERT: B 358 MET cc_start: 0.8593 (ptp) cc_final: 0.8266 (ptm) REVERT: B 563 TYR cc_start: 0.7403 (t80) cc_final: 0.7038 (t80) REVERT: C 267 MET cc_start: 0.9013 (ptp) cc_final: 0.8381 (ppp) REVERT: D 201 MET cc_start: 0.8535 (mtm) cc_final: 0.8171 (mpp) REVERT: D 320 MET cc_start: 0.9243 (mmp) cc_final: 0.8989 (mmm) REVERT: D 430 MET cc_start: 0.9015 (ttp) cc_final: 0.8719 (mtt) REVERT: D 625 MET cc_start: 0.8672 (tpt) cc_final: 0.7925 (mmt) REVERT: E 240 MET cc_start: 0.9514 (ttt) cc_final: 0.9279 (tpt) REVERT: E 320 MET cc_start: 0.8835 (mmm) cc_final: 0.8571 (mmm) REVERT: E 566 MET cc_start: 0.9535 (mtt) cc_final: 0.9319 (mtt) REVERT: E 599 TYR cc_start: 0.8861 (t80) cc_final: 0.8629 (t80) REVERT: F 40 ARG cc_start: 0.7358 (mtp85) cc_final: 0.7108 (mtp180) REVERT: F 358 MET cc_start: 0.8591 (ptp) cc_final: 0.8255 (ptm) REVERT: F 563 TYR cc_start: 0.7429 (t80) cc_final: 0.7063 (t80) REVERT: G 267 MET cc_start: 0.9060 (ptp) cc_final: 0.8425 (ppp) REVERT: H 201 MET cc_start: 0.8648 (mtm) cc_final: 0.8291 (mpp) REVERT: H 320 MET cc_start: 0.9238 (mmp) cc_final: 0.8989 (mmm) REVERT: H 430 MET cc_start: 0.9072 (ttp) cc_final: 0.8795 (mtt) REVERT: H 625 MET cc_start: 0.8703 (tpt) cc_final: 0.7956 (mmt) REVERT: H 637 ARG cc_start: 0.8027 (tmt170) cc_final: 0.7752 (ptm160) REVERT: I 240 MET cc_start: 0.9511 (ttt) cc_final: 0.9275 (tpt) REVERT: I 320 MET cc_start: 0.8812 (mmm) cc_final: 0.8558 (mmm) REVERT: I 322 MET cc_start: 0.8994 (ttm) cc_final: 0.8539 (ttm) REVERT: I 566 MET cc_start: 0.9514 (mtt) cc_final: 0.9283 (mtt) REVERT: I 599 TYR cc_start: 0.8826 (t80) cc_final: 0.8622 (t80) REVERT: J 40 ARG cc_start: 0.7432 (mtp85) cc_final: 0.6799 (mtp-110) REVERT: J 358 MET cc_start: 0.8591 (ptp) cc_final: 0.8251 (ptm) REVERT: J 563 TYR cc_start: 0.7433 (t80) cc_final: 0.7067 (t80) REVERT: K 267 MET cc_start: 0.9043 (ptp) cc_final: 0.8403 (ppp) REVERT: L 201 MET cc_start: 0.8520 (mtm) cc_final: 0.8084 (mpp) REVERT: L 516 LEU cc_start: 0.0285 (OUTLIER) cc_final: 0.0020 (mt) REVERT: M 240 MET cc_start: 0.9499 (ttt) cc_final: 0.9273 (tpt) REVERT: M 320 MET cc_start: 0.8863 (mmm) cc_final: 0.8603 (mmm) REVERT: M 322 MET cc_start: 0.9022 (ttm) cc_final: 0.8569 (ttm) REVERT: M 566 MET cc_start: 0.9516 (mtt) cc_final: 0.9279 (mtt) REVERT: M 599 TYR cc_start: 0.8860 (t80) cc_final: 0.8633 (t80) REVERT: N 40 ARG cc_start: 0.7361 (mtp85) cc_final: 0.7117 (mtp180) REVERT: N 358 MET cc_start: 0.8589 (ptp) cc_final: 0.8258 (ptm) REVERT: N 563 TYR cc_start: 0.7440 (t80) cc_final: 0.7077 (t80) REVERT: O 267 MET cc_start: 0.9057 (ptp) cc_final: 0.8436 (ppp) REVERT: P 201 MET cc_start: 0.8531 (mtm) cc_final: 0.8125 (mpp) REVERT: P 320 MET cc_start: 0.9242 (mmp) cc_final: 0.9016 (mmm) REVERT: P 430 MET cc_start: 0.9038 (ttp) cc_final: 0.8751 (mtt) REVERT: P 625 MET cc_start: 0.8657 (tpt) cc_final: 0.7908 (mmt) outliers start: 84 outliers final: 28 residues processed: 613 average time/residue: 0.6940 time to fit residues: 739.3026 Evaluate side-chains 361 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 332 time to evaluate : 6.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 325 SER Chi-restraints excluded: chain H residue 434 VAL Chi-restraints excluded: chain H residue 497 THR Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 325 SER Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain L residue 516 LEU Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 73 SER Chi-restraints excluded: chain P residue 325 SER Chi-restraints excluded: chain P residue 434 VAL Chi-restraints excluded: chain P residue 497 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 807 optimal weight: 0.7980 chunk 724 optimal weight: 3.9990 chunk 402 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 chunk 488 optimal weight: 5.9990 chunk 387 optimal weight: 0.7980 chunk 749 optimal weight: 10.0000 chunk 289 optimal weight: 9.9990 chunk 455 optimal weight: 40.0000 chunk 557 optimal weight: 0.3980 chunk 868 optimal weight: 9.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 HIS A 286 GLN A 379 ASN A 437 ASN B 104 ASN B 286 GLN B 357 HIS B 467 HIS ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN C 72 GLN C 280 ASN C 295 ASN C 368 ASN C 513 ASN C 557 ASN ** C 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 GLN D 47 GLN D 112 ASN D 156 HIS D 293 HIS D 316 GLN D 419 HIS D 449 GLN ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 512 GLN D 564 ASN D 572 ASN E 268 HIS E 286 GLN E 379 ASN E 437 ASN E 552 ASN F 104 ASN F 286 GLN F 467 HIS ** F 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 ASN G 72 GLN G 280 ASN G 295 ASN G 513 ASN G 557 ASN ** G 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 623 GLN H 47 GLN H 112 ASN H 156 HIS H 293 HIS H 316 GLN H 449 GLN ** H 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 488 ASN H 512 GLN H 564 ASN H 572 ASN I 268 HIS I 286 GLN I 379 ASN I 500 ASN I 552 ASN J 104 ASN J 286 GLN J 467 HIS ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 681 ASN K 72 GLN K 280 ASN K 295 ASN K 505 ASN K 513 ASN K 557 ASN ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 623 GLN L 47 GLN L 112 ASN L 156 HIS L 293 HIS L 316 GLN L 449 GLN L 488 ASN L 512 GLN L 564 ASN L 572 ASN M 268 HIS M 286 GLN M 379 ASN M 437 ASN M 552 ASN N 104 ASN N 286 GLN N 467 HIS ** N 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 681 ASN O 72 GLN O 280 ASN O 295 ASN O 513 ASN O 557 ASN ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 623 GLN P 47 GLN P 112 ASN P 156 HIS P 293 HIS P 316 GLN P 419 HIS P 449 GLN ** P 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 488 ASN P 512 GLN P 564 ASN P 572 ASN Total number of N/Q/H flips: 104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 79084 Z= 0.187 Angle : 0.629 9.675 106940 Z= 0.329 Chirality : 0.043 0.210 11928 Planarity : 0.005 0.081 13768 Dihedral : 5.558 45.006 10422 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.72 % Allowed : 12.04 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.09 % Twisted Proline : 1.92 % Twisted General : 0.09 % 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: -1.78 (0.08), residues: 9516 helix: 0.09 (0.08), residues: 4324 sheet: -0.92 (0.16), residues: 984 loop : -2.67 (0.08), residues: 4208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP J 244 HIS 0.005 0.001 HIS D 452 PHE 0.034 0.001 PHE L 586 TYR 0.023 0.001 TYR E 468 ARG 0.014 0.000 ARG L 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 396 time to evaluate : 7.533 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: A 66 MET cc_start: 0.8918 (mpp) cc_final: 0.8709 (mpp) REVERT: A 240 MET cc_start: 0.9450 (ttt) cc_final: 0.9224 (tpt) REVERT: A 322 MET cc_start: 0.9063 (ttm) cc_final: 0.8814 (ttm) REVERT: A 599 TYR cc_start: 0.8830 (t80) cc_final: 0.8585 (t80) REVERT: B 118 MET cc_start: 0.9098 (mtp) cc_final: 0.8557 (ttp) REVERT: B 358 MET cc_start: 0.8530 (ptp) cc_final: 0.8298 (ptm) REVERT: B 563 TYR cc_start: 0.7126 (t80) cc_final: 0.6848 (t80) REVERT: C 103 MET cc_start: 0.8639 (ttm) cc_final: 0.8224 (ttm) REVERT: C 507 GLN cc_start: 0.7678 (tp40) cc_final: 0.7318 (pm20) REVERT: D 201 MET cc_start: 0.8336 (mtm) cc_final: 0.8017 (mpp) REVERT: D 320 MET cc_start: 0.9086 (mmp) cc_final: 0.8826 (mmp) REVERT: D 625 MET cc_start: 0.8684 (tpt) cc_final: 0.7853 (mmt) REVERT: E 66 MET cc_start: 0.8940 (mpp) cc_final: 0.8728 (mpp) REVERT: E 240 MET cc_start: 0.9445 (ttt) cc_final: 0.9225 (tpt) REVERT: E 312 MET cc_start: 0.9050 (mmm) cc_final: 0.8700 (mmm) REVERT: E 322 MET cc_start: 0.9081 (ttm) cc_final: 0.8829 (ttm) REVERT: E 599 TYR cc_start: 0.8811 (t80) cc_final: 0.8555 (t80) REVERT: F 118 MET cc_start: 0.9070 (mtp) cc_final: 0.8751 (mtp) REVERT: F 358 MET cc_start: 0.8529 (ptp) cc_final: 0.8273 (ptm) REVERT: F 563 TYR cc_start: 0.7137 (t80) cc_final: 0.6858 (t80) REVERT: G 103 MET cc_start: 0.8534 (ttm) cc_final: 0.8089 (ttm) REVERT: H 201 MET cc_start: 0.8412 (mtm) cc_final: 0.8106 (mpp) REVERT: H 320 MET cc_start: 0.9074 (mmp) cc_final: 0.8843 (mmp) REVERT: H 625 MET cc_start: 0.8707 (tpt) cc_final: 0.7937 (mmt) REVERT: I 66 MET cc_start: 0.8831 (mpp) cc_final: 0.8612 (mpp) REVERT: I 240 MET cc_start: 0.9441 (ttt) cc_final: 0.9197 (tmm) REVERT: I 322 MET cc_start: 0.9167 (ttm) cc_final: 0.8916 (ttt) REVERT: I 599 TYR cc_start: 0.8797 (t80) cc_final: 0.8564 (t80) REVERT: J 118 MET cc_start: 0.9079 (mtp) cc_final: 0.8776 (mtp) REVERT: J 358 MET cc_start: 0.8533 (ptp) cc_final: 0.8276 (ptm) REVERT: J 563 TYR cc_start: 0.7155 (t80) cc_final: 0.6874 (t80) REVERT: K 103 MET cc_start: 0.8639 (ttm) cc_final: 0.8099 (ttm) REVERT: L 46 ASP cc_start: 0.9404 (OUTLIER) cc_final: 0.8910 (m-30) REVERT: L 201 MET cc_start: 0.8359 (mtm) cc_final: 0.8008 (mpp) REVERT: L 625 MET cc_start: 0.8605 (ptt) cc_final: 0.7862 (mmt) REVERT: M 66 MET cc_start: 0.8930 (mpp) cc_final: 0.8717 (mpp) REVERT: M 240 MET cc_start: 0.9431 (ttt) cc_final: 0.9222 (tpt) REVERT: M 322 MET cc_start: 0.9186 (ttm) cc_final: 0.8934 (ttt) REVERT: M 599 TYR cc_start: 0.8828 (t80) cc_final: 0.8570 (t80) REVERT: N 118 MET cc_start: 0.9083 (mtp) cc_final: 0.8767 (mtp) REVERT: N 358 MET cc_start: 0.8527 (ptp) cc_final: 0.8279 (ptm) REVERT: N 563 TYR cc_start: 0.7166 (t80) cc_final: 0.6882 (t80) REVERT: O 103 MET cc_start: 0.8655 (ttm) cc_final: 0.8121 (ttm) REVERT: P 201 MET cc_start: 0.8348 (mtm) cc_final: 0.8034 (mpp) REVERT: P 320 MET cc_start: 0.9085 (mmp) cc_final: 0.8836 (mmp) REVERT: P 625 MET cc_start: 0.8690 (tpt) cc_final: 0.7905 (mmt) outliers start: 63 outliers final: 28 residues processed: 445 average time/residue: 0.7253 time to fit residues: 566.0701 Evaluate side-chains 353 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 324 time to evaluate : 6.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain J residue 417 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 505 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain N residue 417 ILE Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 441 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 482 optimal weight: 7.9990 chunk 269 optimal weight: 0.8980 chunk 722 optimal weight: 10.0000 chunk 591 optimal weight: 9.9990 chunk 239 optimal weight: 30.0000 chunk 869 optimal weight: 0.4980 chunk 939 optimal weight: 5.9990 chunk 774 optimal weight: 10.0000 chunk 862 optimal weight: 20.0000 chunk 296 optimal weight: 5.9990 chunk 697 optimal weight: 50.0000 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 206 HIS A 437 ASN B 139 HIS ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN ** C 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 156 HIS ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN E 206 HIS E 437 ASN E 500 ASN F 139 HIS ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN G 454 GLN ** G 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 HIS H 156 HIS H 419 HIS ** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN I 206 HIS I 437 ASN J 139 HIS ** J 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 368 ASN K 454 GLN ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 HIS M 168 ASN M 206 HIS M 500 ASN N 139 HIS ** N 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 368 ASN O 454 GLN ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 HIS P 156 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 79084 Z= 0.238 Angle : 0.625 9.995 106940 Z= 0.325 Chirality : 0.042 0.211 11928 Planarity : 0.005 0.081 13768 Dihedral : 5.286 45.949 10388 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.13 % Allowed : 14.27 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.09 % Twisted Proline : 1.92 % Twisted General : 0.09 % 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: -1.24 (0.08), residues: 9516 helix: 0.61 (0.08), residues: 4392 sheet: -0.94 (0.16), residues: 1056 loop : -2.47 (0.09), residues: 4068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 244 HIS 0.008 0.001 HIS H 452 PHE 0.025 0.001 PHE L 586 TYR 0.021 0.001 TYR E 468 ARG 0.009 0.000 ARG L 562 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 339 time to evaluate : 8.349 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: A 66 MET cc_start: 0.8938 (mpp) cc_final: 0.8660 (mpp) REVERT: A 149 MET cc_start: 0.6610 (mtt) cc_final: 0.6319 (mtt) REVERT: A 240 MET cc_start: 0.9451 (ttt) cc_final: 0.9208 (tmm) REVERT: A 312 MET cc_start: 0.9087 (mmm) cc_final: 0.8735 (mmm) REVERT: A 599 TYR cc_start: 0.8892 (t80) cc_final: 0.8610 (t80) REVERT: B 118 MET cc_start: 0.9143 (mtp) cc_final: 0.8775 (mtp) REVERT: B 322 MET cc_start: 0.8747 (ttp) cc_final: 0.8524 (tpp) REVERT: B 358 MET cc_start: 0.8522 (ptp) cc_final: 0.8252 (ptm) REVERT: B 563 TYR cc_start: 0.7139 (t80) cc_final: 0.6824 (t80) REVERT: C 103 MET cc_start: 0.8537 (ttm) cc_final: 0.8094 (ttm) REVERT: C 507 GLN cc_start: 0.7564 (tp40) cc_final: 0.7172 (pt0) REVERT: D 201 MET cc_start: 0.8337 (mtm) cc_final: 0.7871 (mpp) REVERT: D 327 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9268 (mt) REVERT: D 625 MET cc_start: 0.8655 (tpt) cc_final: 0.7840 (mmt) REVERT: E 66 MET cc_start: 0.8961 (mpp) cc_final: 0.8679 (mpp) REVERT: E 240 MET cc_start: 0.9444 (ttt) cc_final: 0.9181 (tmm) REVERT: E 312 MET cc_start: 0.9096 (mmm) cc_final: 0.8722 (mmm) REVERT: E 599 TYR cc_start: 0.8883 (t80) cc_final: 0.8591 (t80) REVERT: F 118 MET cc_start: 0.9172 (mtp) cc_final: 0.8820 (mtp) REVERT: F 322 MET cc_start: 0.8767 (ttp) cc_final: 0.8537 (tpp) REVERT: F 358 MET cc_start: 0.8562 (ptp) cc_final: 0.8255 (ptm) REVERT: F 563 TYR cc_start: 0.7158 (t80) cc_final: 0.6833 (t80) REVERT: G 103 MET cc_start: 0.8448 (ttm) cc_final: 0.7977 (ttm) REVERT: H 201 MET cc_start: 0.8323 (mtm) cc_final: 0.7793 (mpp) REVERT: H 327 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9282 (mt) REVERT: H 625 MET cc_start: 0.8686 (tpt) cc_final: 0.7874 (mmt) REVERT: I 66 MET cc_start: 0.8838 (mpp) cc_final: 0.8586 (mpp) REVERT: I 149 MET cc_start: 0.6768 (mtt) cc_final: 0.6448 (mtt) REVERT: I 240 MET cc_start: 0.9441 (ttt) cc_final: 0.9181 (tmm) REVERT: I 312 MET cc_start: 0.9097 (mmm) cc_final: 0.8750 (mmm) REVERT: I 320 MET cc_start: 0.8806 (mmm) cc_final: 0.8605 (mmt) REVERT: I 599 TYR cc_start: 0.8884 (t80) cc_final: 0.8612 (t80) REVERT: J 118 MET cc_start: 0.9153 (mtp) cc_final: 0.8776 (mtp) REVERT: J 322 MET cc_start: 0.8719 (ttp) cc_final: 0.8518 (tpp) REVERT: J 358 MET cc_start: 0.8556 (ptp) cc_final: 0.8247 (ptm) REVERT: J 563 TYR cc_start: 0.7151 (t80) cc_final: 0.6827 (t80) REVERT: K 103 MET cc_start: 0.8520 (ttm) cc_final: 0.7932 (ttm) REVERT: L 37 MET cc_start: 0.8690 (ptp) cc_final: 0.8110 (pmm) REVERT: L 201 MET cc_start: 0.8374 (mtm) cc_final: 0.7837 (mpp) REVERT: L 327 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9315 (mt) REVERT: L 625 MET cc_start: 0.8576 (ptt) cc_final: 0.7800 (mmt) REVERT: M 66 MET cc_start: 0.8951 (mpp) cc_final: 0.8673 (mpp) REVERT: M 240 MET cc_start: 0.9433 (ttt) cc_final: 0.9177 (tmm) REVERT: M 312 MET cc_start: 0.9100 (mmm) cc_final: 0.8768 (mmm) REVERT: M 320 MET cc_start: 0.8867 (mmm) cc_final: 0.8666 (mmt) REVERT: M 483 MET cc_start: 0.5121 (mpp) cc_final: 0.4862 (mpp) REVERT: M 599 TYR cc_start: 0.8908 (t80) cc_final: 0.8610 (t80) REVERT: N 118 MET cc_start: 0.9154 (mtp) cc_final: 0.8768 (mtp) REVERT: N 322 MET cc_start: 0.8735 (ttp) cc_final: 0.8518 (tpp) REVERT: N 358 MET cc_start: 0.8556 (ptp) cc_final: 0.8248 (ptm) REVERT: N 563 TYR cc_start: 0.7168 (t80) cc_final: 0.6842 (t80) REVERT: O 103 MET cc_start: 0.8454 (ttm) cc_final: 0.7822 (ttm) REVERT: P 201 MET cc_start: 0.8391 (mtm) cc_final: 0.7899 (mpp) REVERT: P 327 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9252 (mt) REVERT: P 625 MET cc_start: 0.8684 (tpt) cc_final: 0.7863 (mmt) outliers start: 99 outliers final: 54 residues processed: 428 average time/residue: 0.6812 time to fit residues: 530.6537 Evaluate side-chains 370 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 312 time to evaluate : 7.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 642 TYR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain I residue 506 VAL Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 642 TYR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 327 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 505 VAL Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain N residue 642 TYR Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 293 VAL Chi-restraints excluded: chain O residue 441 VAL Chi-restraints excluded: chain P residue 164 SER Chi-restraints excluded: chain P residue 304 VAL Chi-restraints excluded: chain P residue 327 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 859 optimal weight: 8.9990 chunk 653 optimal weight: 10.0000 chunk 451 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 415 optimal weight: 10.0000 chunk 584 optimal weight: 0.9980 chunk 872 optimal weight: 20.0000 chunk 924 optimal weight: 3.9990 chunk 456 optimal weight: 20.0000 chunk 827 optimal weight: 20.0000 chunk 249 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN A 437 ASN A 500 ASN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 474 ASN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN D 156 HIS D 449 GLN ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN ** E 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 GLN E 437 ASN ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 ASN F 474 ASN ** F 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 HIS H 449 GLN ** H 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 611 ASN I 206 HIS I 424 GLN ** J 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 437 ASN J 474 ASN ** J 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 HIS L 156 HIS L 449 GLN L 611 ASN ** M 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 424 GLN ** N 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 437 ASN N 474 ASN ** N 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 156 HIS P 449 GLN P 611 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 79084 Z= 0.302 Angle : 0.667 10.440 106940 Z= 0.348 Chirality : 0.043 0.220 11928 Planarity : 0.005 0.080 13768 Dihedral : 5.358 44.305 10388 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 1.85 % Allowed : 16.39 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.09 % Twisted Proline : 1.92 % Twisted General : 0.09 % 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: -1.14 (0.09), residues: 9516 helix: 0.68 (0.08), residues: 4408 sheet: -0.81 (0.16), residues: 1012 loop : -2.42 (0.09), residues: 4096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 244 HIS 0.006 0.001 HIS H 452 PHE 0.033 0.002 PHE P 586 TYR 0.020 0.002 TYR E 468 ARG 0.005 0.000 ARG H 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 317 time to evaluate : 6.881 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: A 66 MET cc_start: 0.8897 (mpp) cc_final: 0.8635 (mpp) REVERT: A 240 MET cc_start: 0.9448 (ttt) cc_final: 0.9211 (tpt) REVERT: A 310 GLU cc_start: 0.9091 (mp0) cc_final: 0.8818 (mp0) REVERT: A 312 MET cc_start: 0.9124 (mmm) cc_final: 0.8745 (mmm) REVERT: A 365 LEU cc_start: 0.9325 (mt) cc_final: 0.9124 (mt) REVERT: A 483 MET cc_start: 0.5355 (mpp) cc_final: 0.5027 (mpp) REVERT: A 599 TYR cc_start: 0.8942 (t80) cc_final: 0.8636 (t80) REVERT: B 118 MET cc_start: 0.9226 (mtp) cc_final: 0.8876 (mtp) REVERT: B 322 MET cc_start: 0.8800 (ttp) cc_final: 0.8553 (tpp) REVERT: B 358 MET cc_start: 0.8571 (ptp) cc_final: 0.8269 (ptm) REVERT: B 474 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8470 (t0) REVERT: B 563 TYR cc_start: 0.7130 (t80) cc_final: 0.6773 (t80) REVERT: C 103 MET cc_start: 0.8383 (ttm) cc_final: 0.7919 (ttm) REVERT: D 37 MET cc_start: 0.8866 (ptp) cc_final: 0.8261 (pmm) REVERT: D 201 MET cc_start: 0.8374 (mtm) cc_final: 0.8172 (mmp) REVERT: D 257 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7867 (mmmt) REVERT: D 327 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9239 (mt) REVERT: D 625 MET cc_start: 0.8674 (tpt) cc_final: 0.7836 (mmt) REVERT: E 66 MET cc_start: 0.8909 (mpp) cc_final: 0.8632 (mpp) REVERT: E 365 LEU cc_start: 0.9326 (mt) cc_final: 0.9118 (mt) REVERT: E 599 TYR cc_start: 0.8939 (t80) cc_final: 0.8616 (t80) REVERT: E 685 GLU cc_start: 0.8507 (pt0) cc_final: 0.8181 (pt0) REVERT: F 118 MET cc_start: 0.9223 (mtp) cc_final: 0.8874 (mtp) REVERT: F 322 MET cc_start: 0.8816 (ttp) cc_final: 0.8556 (tpp) REVERT: F 358 MET cc_start: 0.8592 (ptp) cc_final: 0.8260 (ptm) REVERT: F 474 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8432 (t0) REVERT: F 563 TYR cc_start: 0.7181 (t80) cc_final: 0.6819 (t80) REVERT: G 96 MET cc_start: 0.3993 (mmp) cc_final: 0.3789 (mmm) REVERT: G 103 MET cc_start: 0.8232 (ttm) cc_final: 0.7786 (ttm) REVERT: H 37 MET cc_start: 0.8852 (ptp) cc_final: 0.8258 (pmm) REVERT: H 257 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7825 (mmmt) REVERT: H 327 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9255 (mt) REVERT: H 625 MET cc_start: 0.8673 (tpt) cc_final: 0.7821 (mmt) REVERT: I 66 MET cc_start: 0.8860 (mpp) cc_final: 0.8600 (mpp) REVERT: I 310 GLU cc_start: 0.9090 (mp0) cc_final: 0.8818 (mp0) REVERT: I 599 TYR cc_start: 0.8935 (t80) cc_final: 0.8639 (t80) REVERT: J 118 MET cc_start: 0.9211 (mtp) cc_final: 0.8853 (mtp) REVERT: J 322 MET cc_start: 0.8794 (ttp) cc_final: 0.8555 (tpp) REVERT: J 358 MET cc_start: 0.8578 (ptp) cc_final: 0.8242 (ptm) REVERT: J 474 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8494 (t0) REVERT: J 563 TYR cc_start: 0.7179 (t80) cc_final: 0.6822 (t80) REVERT: K 103 MET cc_start: 0.8394 (ttm) cc_final: 0.7974 (ttm) REVERT: L 37 MET cc_start: 0.8625 (ptp) cc_final: 0.8288 (pmm) REVERT: L 201 MET cc_start: 0.8402 (mtm) cc_final: 0.8186 (mmp) REVERT: L 257 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7719 (mmmt) REVERT: L 327 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9289 (mt) REVERT: L 625 MET cc_start: 0.8606 (ptt) cc_final: 0.7793 (mmt) REVERT: M 66 MET cc_start: 0.8900 (mpp) cc_final: 0.8629 (mpp) REVERT: M 599 TYR cc_start: 0.8952 (t80) cc_final: 0.8635 (t80) REVERT: N 118 MET cc_start: 0.9205 (mtp) cc_final: 0.8836 (mtp) REVERT: N 322 MET cc_start: 0.8810 (ttp) cc_final: 0.8557 (tpp) REVERT: N 358 MET cc_start: 0.8572 (ptp) cc_final: 0.8235 (ptm) REVERT: N 474 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8443 (t0) REVERT: N 563 TYR cc_start: 0.7195 (t80) cc_final: 0.6837 (t80) REVERT: O 103 MET cc_start: 0.8422 (ttm) cc_final: 0.7990 (ttm) REVERT: P 37 MET cc_start: 0.8890 (ptp) cc_final: 0.8277 (pmm) REVERT: P 257 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7832 (mmmt) REVERT: P 327 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9239 (mt) REVERT: P 625 MET cc_start: 0.8684 (tpt) cc_final: 0.7852 (mmt) outliers start: 162 outliers final: 90 residues processed: 474 average time/residue: 0.6492 time to fit residues: 555.9942 Evaluate side-chains 395 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 293 time to evaluate : 6.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 417 ILE Chi-restraints excluded: chain F residue 474 ASN Chi-restraints excluded: chain F residue 530 ILE Chi-restraints excluded: chain F residue 642 TYR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 586 LYS Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 257 LYS Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 490 VAL Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain I residue 506 VAL Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain J residue 182 ILE Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 417 ILE Chi-restraints excluded: chain J residue 474 ASN Chi-restraints excluded: chain J residue 530 ILE Chi-restraints excluded: chain J residue 642 TYR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain K residue 586 LYS Chi-restraints excluded: chain L residue 257 LYS Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 327 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 505 VAL Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain N residue 331 VAL Chi-restraints excluded: chain N residue 393 VAL Chi-restraints excluded: chain N residue 413 VAL Chi-restraints excluded: chain N residue 417 ILE Chi-restraints excluded: chain N residue 474 ASN Chi-restraints excluded: chain N residue 530 ILE Chi-restraints excluded: chain N residue 642 TYR Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 232 ILE Chi-restraints excluded: chain O residue 293 VAL Chi-restraints excluded: chain O residue 441 VAL Chi-restraints excluded: chain O residue 586 LYS Chi-restraints excluded: chain P residue 164 SER Chi-restraints excluded: chain P residue 257 LYS Chi-restraints excluded: chain P residue 277 LEU Chi-restraints excluded: chain P residue 304 VAL Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain P residue 558 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 769 optimal weight: 0.8980 chunk 524 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 688 optimal weight: 7.9990 chunk 381 optimal weight: 5.9990 chunk 788 optimal weight: 5.9990 chunk 638 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 471 optimal weight: 5.9990 chunk 829 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 GLN ** F 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 HIS ** H 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 611 ASN ** J 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 GLN ** J 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 HIS L 156 HIS ** L 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 611 ASN ** M 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 424 GLN ** N 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 79084 Z= 0.243 Angle : 0.630 10.068 106940 Z= 0.327 Chirality : 0.042 0.210 11928 Planarity : 0.004 0.079 13768 Dihedral : 5.237 44.921 10388 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.06 % Allowed : 17.49 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.09 % Twisted Proline : 1.92 % Twisted General : 0.09 % 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: -0.98 (0.09), residues: 9516 helix: 0.82 (0.08), residues: 4392 sheet: -0.76 (0.16), residues: 1012 loop : -2.32 (0.09), residues: 4112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 244 HIS 0.007 0.001 HIS D 452 PHE 0.054 0.001 PHE H 586 TYR 0.019 0.001 TYR E 468 ARG 0.005 0.000 ARG H 480 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 319 time to evaluate : 6.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8901 (mpp) cc_final: 0.8633 (mpp) REVERT: A 240 MET cc_start: 0.9440 (ttt) cc_final: 0.9237 (tpt) REVERT: A 483 MET cc_start: 0.5473 (mpp) cc_final: 0.5146 (mpp) REVERT: A 599 TYR cc_start: 0.8904 (t80) cc_final: 0.8588 (t80) REVERT: B 118 MET cc_start: 0.9168 (mtp) cc_final: 0.8799 (mtp) REVERT: B 322 MET cc_start: 0.8715 (ttp) cc_final: 0.8433 (tpp) REVERT: B 358 MET cc_start: 0.8542 (ptp) cc_final: 0.8262 (ptm) REVERT: B 563 TYR cc_start: 0.7131 (t80) cc_final: 0.6762 (t80) REVERT: C 103 MET cc_start: 0.8306 (ttm) cc_final: 0.7835 (ttm) REVERT: D 37 MET cc_start: 0.8836 (ptp) cc_final: 0.8236 (pmm) REVERT: D 257 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7873 (mmmt) REVERT: D 327 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9241 (mt) REVERT: D 625 MET cc_start: 0.8659 (tpt) cc_final: 0.7821 (mmt) REVERT: E 66 MET cc_start: 0.8918 (mpp) cc_final: 0.8639 (mpp) REVERT: E 365 LEU cc_start: 0.9356 (mt) cc_final: 0.9130 (mt) REVERT: E 599 TYR cc_start: 0.8908 (t80) cc_final: 0.8578 (t80) REVERT: E 685 GLU cc_start: 0.8473 (pt0) cc_final: 0.8154 (pt0) REVERT: F 118 MET cc_start: 0.9187 (mtp) cc_final: 0.8819 (mtp) REVERT: F 322 MET cc_start: 0.8736 (ttp) cc_final: 0.8495 (tpp) REVERT: F 358 MET cc_start: 0.8570 (ptp) cc_final: 0.8247 (ptm) REVERT: F 563 TYR cc_start: 0.7159 (t80) cc_final: 0.6786 (t80) REVERT: G 103 MET cc_start: 0.8236 (ttm) cc_final: 0.7803 (ttm) REVERT: H 37 MET cc_start: 0.8819 (ptp) cc_final: 0.8226 (pmm) REVERT: H 257 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7838 (tptt) REVERT: H 327 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9237 (mt) REVERT: H 625 MET cc_start: 0.8655 (tpt) cc_final: 0.7801 (mmt) REVERT: I 66 MET cc_start: 0.8851 (mpp) cc_final: 0.8577 (mpp) REVERT: I 599 TYR cc_start: 0.8900 (t80) cc_final: 0.8591 (t80) REVERT: J 118 MET cc_start: 0.9206 (mtp) cc_final: 0.8799 (mtp) REVERT: J 322 MET cc_start: 0.8719 (ttp) cc_final: 0.8443 (tpp) REVERT: J 358 MET cc_start: 0.8551 (ptp) cc_final: 0.8230 (ptm) REVERT: J 563 TYR cc_start: 0.7147 (t80) cc_final: 0.6778 (t80) REVERT: K 96 MET cc_start: 0.4049 (mmt) cc_final: 0.3839 (mmm) REVERT: K 103 MET cc_start: 0.8290 (ttm) cc_final: 0.7869 (ttm) REVERT: L 37 MET cc_start: 0.8660 (ptp) cc_final: 0.8178 (pmm) REVERT: L 201 MET cc_start: 0.8402 (mtm) cc_final: 0.8187 (mmp) REVERT: L 257 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7739 (mmmt) REVERT: L 625 MET cc_start: 0.8622 (ptt) cc_final: 0.7791 (mmt) REVERT: M 66 MET cc_start: 0.8915 (mpp) cc_final: 0.8638 (mpp) REVERT: M 599 TYR cc_start: 0.8915 (t80) cc_final: 0.8560 (t80) REVERT: M 685 GLU cc_start: 0.8479 (pt0) cc_final: 0.8161 (pt0) REVERT: N 118 MET cc_start: 0.9196 (mtp) cc_final: 0.8781 (mtp) REVERT: N 322 MET cc_start: 0.8701 (ttp) cc_final: 0.8433 (tpp) REVERT: N 358 MET cc_start: 0.8553 (ptp) cc_final: 0.8231 (ptm) REVERT: N 563 TYR cc_start: 0.7164 (t80) cc_final: 0.6794 (t80) REVERT: O 103 MET cc_start: 0.8319 (ttm) cc_final: 0.7888 (ttm) REVERT: P 37 MET cc_start: 0.8843 (ptp) cc_final: 0.8233 (pmm) REVERT: P 257 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7843 (mmmt) REVERT: P 327 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9242 (mt) REVERT: P 625 MET cc_start: 0.8669 (tpt) cc_final: 0.7833 (mmt) outliers start: 180 outliers final: 111 residues processed: 488 average time/residue: 0.6420 time to fit residues: 568.1338 Evaluate side-chains 419 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 301 time to evaluate : 6.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 437 ASN Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 417 ILE Chi-restraints excluded: chain F residue 642 TYR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 478 ILE Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 257 LYS Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain I residue 506 VAL Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 587 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 417 ILE Chi-restraints excluded: chain J residue 642 TYR Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain K residue 478 ILE Chi-restraints excluded: chain L residue 156 HIS Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 257 LYS Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 505 VAL Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain M residue 587 VAL Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain N residue 393 VAL Chi-restraints excluded: chain N residue 413 VAL Chi-restraints excluded: chain N residue 417 ILE Chi-restraints excluded: chain N residue 642 TYR Chi-restraints excluded: chain O residue 84 ILE Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 232 ILE Chi-restraints excluded: chain O residue 293 VAL Chi-restraints excluded: chain O residue 441 VAL Chi-restraints excluded: chain O residue 478 ILE Chi-restraints excluded: chain P residue 164 SER Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 257 LYS Chi-restraints excluded: chain P residue 277 LEU Chi-restraints excluded: chain P residue 304 VAL Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain P residue 558 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 310 optimal weight: 10.0000 chunk 832 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 542 optimal weight: 0.9980 chunk 228 optimal weight: 40.0000 chunk 924 optimal weight: 4.9990 chunk 767 optimal weight: 2.9990 chunk 428 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 305 optimal weight: 0.0670 chunk 485 optimal weight: 20.0000 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 HIS B 206 HIS ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 ASN ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 GLN ** D 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN F 205 HIS F 206 HIS ** F 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 GLN ** H 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 HIS J 206 HIS ** J 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 512 GLN ** L 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 205 HIS N 206 HIS ** N 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 512 GLN ** P 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 611 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 79084 Z= 0.157 Angle : 0.586 12.047 106940 Z= 0.299 Chirality : 0.042 0.231 11928 Planarity : 0.004 0.074 13768 Dihedral : 4.894 41.413 10388 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.71 % Allowed : 17.97 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.09 % Twisted Proline : 1.92 % Twisted General : 0.09 % 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: -0.55 (0.09), residues: 9516 helix: 1.20 (0.08), residues: 4392 sheet: -0.52 (0.17), residues: 1004 loop : -2.15 (0.10), residues: 4120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 244 HIS 0.030 0.001 HIS L 156 PHE 0.045 0.001 PHE H 586 TYR 0.020 0.001 TYR A 468 ARG 0.006 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 359 time to evaluate : 6.964 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: A 66 MET cc_start: 0.8897 (mpp) cc_final: 0.8605 (mpp) REVERT: A 240 MET cc_start: 0.9433 (ttt) cc_final: 0.9214 (tpt) REVERT: A 320 MET cc_start: 0.8976 (mmp) cc_final: 0.8746 (mmm) REVERT: A 322 MET cc_start: 0.9130 (mmm) cc_final: 0.8917 (mmm) REVERT: A 599 TYR cc_start: 0.8802 (t80) cc_final: 0.8574 (t80) REVERT: B 114 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8929 (mp) REVERT: B 118 MET cc_start: 0.9155 (mtp) cc_final: 0.8531 (ttp) REVERT: B 130 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8059 (pt0) REVERT: B 183 GLU cc_start: 0.8579 (tt0) cc_final: 0.8265 (tt0) REVERT: B 358 MET cc_start: 0.8468 (ptp) cc_final: 0.8246 (ptm) REVERT: B 483 MET cc_start: 0.3098 (mtt) cc_final: 0.2785 (mtt) REVERT: B 563 TYR cc_start: 0.7004 (t80) cc_final: 0.6620 (t80) REVERT: C 103 MET cc_start: 0.8271 (ttm) cc_final: 0.7794 (ttm) REVERT: D 37 MET cc_start: 0.8789 (ptp) cc_final: 0.8198 (pmm) REVERT: D 96 MET cc_start: 0.9119 (tmm) cc_final: 0.8639 (tmm) REVERT: D 257 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7830 (tptt) REVERT: D 430 MET cc_start: 0.8950 (tpp) cc_final: 0.8612 (mpp) REVERT: D 625 MET cc_start: 0.8640 (tpt) cc_final: 0.7806 (mmt) REVERT: E 66 MET cc_start: 0.8941 (mpp) cc_final: 0.8640 (mpp) REVERT: E 322 MET cc_start: 0.9137 (mmm) cc_final: 0.8916 (mmm) REVERT: E 365 LEU cc_start: 0.9354 (mt) cc_final: 0.9139 (mt) REVERT: E 599 TYR cc_start: 0.8799 (t80) cc_final: 0.8566 (t80) REVERT: E 685 GLU cc_start: 0.8418 (pt0) cc_final: 0.8097 (pt0) REVERT: F 118 MET cc_start: 0.9158 (mtp) cc_final: 0.8460 (ttp) REVERT: F 130 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8139 (pt0) REVERT: F 183 GLU cc_start: 0.8594 (tt0) cc_final: 0.8241 (tt0) REVERT: F 243 ASP cc_start: 0.7656 (t0) cc_final: 0.6692 (p0) REVERT: F 358 MET cc_start: 0.8490 (ptp) cc_final: 0.8221 (ptm) REVERT: F 483 MET cc_start: 0.3111 (mtt) cc_final: 0.2842 (mtt) REVERT: F 563 TYR cc_start: 0.7067 (t80) cc_final: 0.6696 (t80) REVERT: G 103 MET cc_start: 0.8159 (ttm) cc_final: 0.7596 (ttm) REVERT: H 37 MET cc_start: 0.8784 (ptp) cc_final: 0.8161 (pmm) REVERT: H 257 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7860 (tptt) REVERT: H 327 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9262 (mt) REVERT: H 430 MET cc_start: 0.8964 (tpp) cc_final: 0.8688 (mpp) REVERT: H 625 MET cc_start: 0.8653 (tpt) cc_final: 0.7811 (mmt) REVERT: I 66 MET cc_start: 0.8858 (mpp) cc_final: 0.8564 (mpp) REVERT: I 315 PHE cc_start: 0.8983 (m-80) cc_final: 0.8734 (m-80) REVERT: I 322 MET cc_start: 0.9108 (mmm) cc_final: 0.8871 (mmm) REVERT: I 599 TYR cc_start: 0.8795 (t80) cc_final: 0.8577 (t80) REVERT: J 114 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8937 (mp) REVERT: J 118 MET cc_start: 0.9189 (mtp) cc_final: 0.8577 (ttp) REVERT: J 183 GLU cc_start: 0.8606 (tt0) cc_final: 0.8246 (tt0) REVERT: J 358 MET cc_start: 0.8477 (ptp) cc_final: 0.8197 (ptm) REVERT: J 483 MET cc_start: 0.3172 (mtt) cc_final: 0.2861 (mtt) REVERT: J 563 TYR cc_start: 0.7032 (t80) cc_final: 0.6654 (t80) REVERT: K 103 MET cc_start: 0.8239 (ttm) cc_final: 0.7710 (ttm) REVERT: L 37 MET cc_start: 0.8672 (ptp) cc_final: 0.8345 (pmm) REVERT: L 201 MET cc_start: 0.8388 (mtm) cc_final: 0.7747 (mpp) REVERT: L 257 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7721 (tptt) REVERT: L 625 MET cc_start: 0.8611 (ptt) cc_final: 0.7802 (mmt) REVERT: M 66 MET cc_start: 0.8933 (mpp) cc_final: 0.8638 (mpp) REVERT: M 315 PHE cc_start: 0.8968 (m-80) cc_final: 0.8712 (m-80) REVERT: M 322 MET cc_start: 0.9114 (mmm) cc_final: 0.8878 (mmm) REVERT: M 332 ILE cc_start: 0.9661 (mt) cc_final: 0.9460 (mp) REVERT: M 365 LEU cc_start: 0.9330 (mt) cc_final: 0.9107 (mt) REVERT: M 599 TYR cc_start: 0.8838 (t80) cc_final: 0.8627 (t80) REVERT: M 685 GLU cc_start: 0.8443 (pt0) cc_final: 0.8106 (pt0) REVERT: N 118 MET cc_start: 0.9179 (mtp) cc_final: 0.8510 (ttp) REVERT: N 130 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: N 183 GLU cc_start: 0.8606 (tt0) cc_final: 0.8254 (tt0) REVERT: N 358 MET cc_start: 0.8473 (ptp) cc_final: 0.8199 (ptm) REVERT: N 483 MET cc_start: 0.3146 (mtt) cc_final: 0.2834 (mtt) REVERT: N 563 TYR cc_start: 0.7084 (t80) cc_final: 0.6704 (t80) REVERT: O 103 MET cc_start: 0.8263 (ttm) cc_final: 0.7719 (ttm) REVERT: P 37 MET cc_start: 0.8801 (ptp) cc_final: 0.8198 (pmm) REVERT: P 257 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7865 (tptt) REVERT: P 430 MET cc_start: 0.8919 (tpp) cc_final: 0.8628 (mpp) REVERT: P 625 MET cc_start: 0.8686 (tpt) cc_final: 0.7860 (mmt) outliers start: 150 outliers final: 104 residues processed: 498 average time/residue: 0.6888 time to fit residues: 620.1717 Evaluate side-chains 443 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 329 time to evaluate : 7.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 437 ASN Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 417 ILE Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 642 TYR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 478 ILE Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 257 LYS Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 484 LEU Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain I residue 506 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 587 VAL Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 272 MET Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 417 ILE Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 642 TYR Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain K residue 478 ILE Chi-restraints excluded: chain L residue 257 LYS Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 429 TYR Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 505 VAL Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain M residue 587 VAL Chi-restraints excluded: chain N residue 130 GLU Chi-restraints excluded: chain N residue 272 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain N residue 413 VAL Chi-restraints excluded: chain N residue 417 ILE Chi-restraints excluded: chain N residue 555 LEU Chi-restraints excluded: chain N residue 642 TYR Chi-restraints excluded: chain O residue 84 ILE Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 232 ILE Chi-restraints excluded: chain O residue 293 VAL Chi-restraints excluded: chain O residue 441 VAL Chi-restraints excluded: chain O residue 478 ILE Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 164 SER Chi-restraints excluded: chain P residue 257 LYS Chi-restraints excluded: chain P residue 277 LEU Chi-restraints excluded: chain P residue 304 VAL Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 558 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 891 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 527 optimal weight: 0.0010 chunk 675 optimal weight: 7.9990 chunk 523 optimal weight: 9.9990 chunk 778 optimal weight: 6.9990 chunk 516 optimal weight: 4.9990 chunk 921 optimal weight: 7.9990 chunk 576 optimal weight: 4.9990 chunk 561 optimal weight: 6.9990 chunk 425 optimal weight: 8.9990 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN E 206 HIS ** F 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 HIS L 156 HIS ** L 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 HIS ** N 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 611 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 79084 Z= 0.243 Angle : 0.627 11.773 106940 Z= 0.323 Chirality : 0.043 0.255 11928 Planarity : 0.004 0.077 13768 Dihedral : 4.967 43.226 10388 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.10 % Allowed : 18.53 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.09 % Twisted Proline : 1.92 % Twisted General : 0.09 % 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: -0.55 (0.09), residues: 9516 helix: 1.20 (0.08), residues: 4372 sheet: -0.54 (0.17), residues: 1000 loop : -2.12 (0.10), residues: 4144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 244 HIS 0.009 0.001 HIS P 452 PHE 0.045 0.001 PHE D 586 TYR 0.019 0.001 TYR I 468 ARG 0.004 0.000 ARG H 480 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 316 time to evaluate : 6.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8917 (mpp) cc_final: 0.8626 (mpp) REVERT: A 240 MET cc_start: 0.9428 (ttt) cc_final: 0.9214 (tpt) REVERT: A 322 MET cc_start: 0.9112 (mmm) cc_final: 0.8881 (mmm) REVERT: A 566 MET cc_start: 0.9491 (mtt) cc_final: 0.9215 (mtm) REVERT: A 599 TYR cc_start: 0.8930 (t80) cc_final: 0.8575 (t80) REVERT: B 118 MET cc_start: 0.9220 (mtp) cc_final: 0.8788 (mtp) REVERT: B 358 MET cc_start: 0.8538 (ptp) cc_final: 0.8261 (ptm) REVERT: B 563 TYR cc_start: 0.7102 (t80) cc_final: 0.6705 (t80) REVERT: B 617 THR cc_start: 0.7708 (OUTLIER) cc_final: 0.7171 (t) REVERT: C 103 MET cc_start: 0.8249 (ttm) cc_final: 0.7763 (ttm) REVERT: C 267 MET cc_start: 0.9060 (ptp) cc_final: 0.8374 (ppp) REVERT: D 37 MET cc_start: 0.8820 (ptp) cc_final: 0.8148 (pmm) REVERT: D 257 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7843 (mmmt) REVERT: D 430 MET cc_start: 0.8969 (tpp) cc_final: 0.8667 (mpp) REVERT: D 625 MET cc_start: 0.8617 (tpt) cc_final: 0.7752 (mmt) REVERT: E 66 MET cc_start: 0.8935 (mpp) cc_final: 0.8661 (mpp) REVERT: E 322 MET cc_start: 0.9103 (mmm) cc_final: 0.8863 (mmm) REVERT: E 365 LEU cc_start: 0.9372 (mt) cc_final: 0.9165 (mt) REVERT: E 599 TYR cc_start: 0.8922 (t80) cc_final: 0.8577 (t80) REVERT: E 685 GLU cc_start: 0.8429 (pt0) cc_final: 0.8119 (pt0) REVERT: F 118 MET cc_start: 0.9225 (mtp) cc_final: 0.8814 (mtp) REVERT: F 358 MET cc_start: 0.8573 (ptp) cc_final: 0.8245 (ptm) REVERT: F 563 TYR cc_start: 0.7155 (t80) cc_final: 0.6761 (t80) REVERT: F 617 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7172 (t) REVERT: G 103 MET cc_start: 0.8126 (ttm) cc_final: 0.7663 (ttm) REVERT: G 267 MET cc_start: 0.9102 (ptp) cc_final: 0.8419 (ppp) REVERT: H 37 MET cc_start: 0.8805 (ptp) cc_final: 0.8279 (pmm) REVERT: H 257 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7864 (tptt) REVERT: H 327 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9259 (mt) REVERT: H 430 MET cc_start: 0.8994 (tpp) cc_final: 0.8697 (mpp) REVERT: H 625 MET cc_start: 0.8669 (tpt) cc_final: 0.7818 (mmt) REVERT: I 66 MET cc_start: 0.8869 (mpp) cc_final: 0.8601 (mpp) REVERT: I 322 MET cc_start: 0.9070 (mmm) cc_final: 0.8828 (mmm) REVERT: I 566 MET cc_start: 0.9485 (mtt) cc_final: 0.9208 (mtm) REVERT: I 599 TYR cc_start: 0.8921 (t80) cc_final: 0.8577 (t80) REVERT: J 118 MET cc_start: 0.9239 (mtp) cc_final: 0.8810 (mtp) REVERT: J 358 MET cc_start: 0.8557 (ptp) cc_final: 0.8224 (ptm) REVERT: J 617 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.7210 (t) REVERT: K 103 MET cc_start: 0.8230 (ttm) cc_final: 0.7786 (ttm) REVERT: K 267 MET cc_start: 0.9070 (ptp) cc_final: 0.8389 (ppp) REVERT: L 37 MET cc_start: 0.8702 (ptp) cc_final: 0.8225 (pmm) REVERT: L 201 MET cc_start: 0.8426 (mtm) cc_final: 0.7830 (mpp) REVERT: L 257 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7755 (mmmt) REVERT: L 625 MET cc_start: 0.8615 (ptt) cc_final: 0.7792 (mmt) REVERT: M 66 MET cc_start: 0.8903 (mpp) cc_final: 0.8628 (mpp) REVERT: M 322 MET cc_start: 0.9090 (mmm) cc_final: 0.8848 (mmm) REVERT: M 365 LEU cc_start: 0.9361 (mt) cc_final: 0.9152 (mt) REVERT: M 566 MET cc_start: 0.9492 (mtt) cc_final: 0.9214 (mtm) REVERT: M 599 TYR cc_start: 0.8961 (t80) cc_final: 0.8643 (t80) REVERT: M 685 GLU cc_start: 0.8438 (pt0) cc_final: 0.8138 (pt0) REVERT: N 118 MET cc_start: 0.9200 (mtp) cc_final: 0.8732 (mtp) REVERT: N 358 MET cc_start: 0.8553 (ptp) cc_final: 0.8228 (ptm) REVERT: N 617 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7168 (t) REVERT: O 103 MET cc_start: 0.8208 (ttm) cc_final: 0.7746 (ttm) REVERT: O 267 MET cc_start: 0.9082 (ptp) cc_final: 0.8414 (ppp) REVERT: P 37 MET cc_start: 0.8835 (ptp) cc_final: 0.8177 (pmm) REVERT: P 257 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7840 (tptt) REVERT: P 430 MET cc_start: 0.8959 (tpp) cc_final: 0.8666 (mpp) REVERT: P 625 MET cc_start: 0.8677 (tpt) cc_final: 0.7848 (mmt) outliers start: 184 outliers final: 130 residues processed: 496 average time/residue: 0.6562 time to fit residues: 594.4817 Evaluate side-chains 444 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 305 time to evaluate : 6.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 530 ILE Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 634 VAL Chi-restraints excluded: chain F residue 642 TYR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 478 ILE Chi-restraints excluded: chain G residue 586 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 257 LYS Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 429 TYR Chi-restraints excluded: chain H residue 484 LEU Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 490 VAL Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain I residue 506 VAL Chi-restraints excluded: chain I residue 519 ILE Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 587 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 530 ILE Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 634 VAL Chi-restraints excluded: chain J residue 642 TYR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain K residue 478 ILE Chi-restraints excluded: chain K residue 586 LYS Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 257 LYS Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 429 TYR Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 417 ILE Chi-restraints excluded: chain M residue 505 VAL Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain M residue 587 VAL Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain N residue 393 VAL Chi-restraints excluded: chain N residue 413 VAL Chi-restraints excluded: chain N residue 530 ILE Chi-restraints excluded: chain N residue 555 LEU Chi-restraints excluded: chain N residue 617 THR Chi-restraints excluded: chain N residue 634 VAL Chi-restraints excluded: chain N residue 642 TYR Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 232 ILE Chi-restraints excluded: chain O residue 293 VAL Chi-restraints excluded: chain O residue 441 VAL Chi-restraints excluded: chain O residue 478 ILE Chi-restraints excluded: chain O residue 586 LYS Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 164 SER Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 257 LYS Chi-restraints excluded: chain P residue 304 VAL Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 558 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 570 optimal weight: 4.9990 chunk 367 optimal weight: 30.0000 chunk 550 optimal weight: 4.9990 chunk 277 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 585 optimal weight: 9.9990 chunk 627 optimal weight: 20.0000 chunk 455 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 724 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN ** F 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 GLN ** F 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 GLN ** J 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 424 GLN ** N 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 611 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 79084 Z= 0.198 Angle : 0.610 12.027 106940 Z= 0.310 Chirality : 0.042 0.197 11928 Planarity : 0.004 0.072 13768 Dihedral : 4.884 41.597 10388 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.06 % Allowed : 18.88 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.09 % Twisted Proline : 1.92 % Twisted General : 0.09 % 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: -0.40 (0.09), residues: 9516 helix: 1.29 (0.08), residues: 4392 sheet: -0.48 (0.17), residues: 1000 loop : -2.00 (0.10), residues: 4124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 244 HIS 0.010 0.001 HIS L 452 PHE 0.041 0.001 PHE H 586 TYR 0.019 0.001 TYR M 468 ARG 0.004 0.000 ARG H 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 321 time to evaluate : 6.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8922 (mpp) cc_final: 0.8632 (mpp) REVERT: A 312 MET cc_start: 0.8907 (mmm) cc_final: 0.8620 (tpt) REVERT: A 320 MET cc_start: 0.9002 (mmp) cc_final: 0.8775 (mmm) REVERT: A 322 MET cc_start: 0.9135 (mmm) cc_final: 0.8894 (mmm) REVERT: A 599 TYR cc_start: 0.8876 (t80) cc_final: 0.8607 (t80) REVERT: A 685 GLU cc_start: 0.8460 (pt0) cc_final: 0.8089 (pt0) REVERT: B 114 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8705 (tp) REVERT: B 118 MET cc_start: 0.9177 (mtp) cc_final: 0.8339 (ttp) REVERT: B 358 MET cc_start: 0.8516 (ptp) cc_final: 0.8268 (ptm) REVERT: B 563 TYR cc_start: 0.7090 (t80) cc_final: 0.6692 (t80) REVERT: B 617 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7156 (t) REVERT: C 103 MET cc_start: 0.8205 (ttm) cc_final: 0.7712 (ttm) REVERT: C 267 MET cc_start: 0.9047 (ptp) cc_final: 0.8371 (ppp) REVERT: D 37 MET cc_start: 0.8827 (ptp) cc_final: 0.8438 (pmm) REVERT: D 96 MET cc_start: 0.9141 (tmm) cc_final: 0.8730 (tmm) REVERT: D 257 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7820 (tptt) REVERT: D 625 MET cc_start: 0.8616 (tpt) cc_final: 0.7748 (mmt) REVERT: E 66 MET cc_start: 0.8933 (mpp) cc_final: 0.8658 (mpp) REVERT: E 312 MET cc_start: 0.8912 (mmm) cc_final: 0.8676 (tpt) REVERT: E 322 MET cc_start: 0.9141 (mmm) cc_final: 0.8897 (mmm) REVERT: E 365 LEU cc_start: 0.9376 (mt) cc_final: 0.9067 (mt) REVERT: E 566 MET cc_start: 0.9435 (mtt) cc_final: 0.9172 (mtm) REVERT: E 599 TYR cc_start: 0.8864 (t80) cc_final: 0.8597 (t80) REVERT: E 685 GLU cc_start: 0.8419 (pt0) cc_final: 0.8103 (pt0) REVERT: F 118 MET cc_start: 0.9185 (mtp) cc_final: 0.8723 (mtp) REVERT: F 358 MET cc_start: 0.8542 (ptp) cc_final: 0.8234 (ptm) REVERT: F 563 TYR cc_start: 0.7153 (t80) cc_final: 0.6755 (t80) REVERT: F 617 THR cc_start: 0.7649 (OUTLIER) cc_final: 0.7106 (t) REVERT: G 103 MET cc_start: 0.8166 (ttm) cc_final: 0.7716 (ttm) REVERT: G 267 MET cc_start: 0.9094 (ptp) cc_final: 0.8406 (ppp) REVERT: H 37 MET cc_start: 0.8787 (ptp) cc_final: 0.8130 (pmm) REVERT: H 257 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7852 (tptt) REVERT: H 327 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9276 (mt) REVERT: H 625 MET cc_start: 0.8651 (tpt) cc_final: 0.7791 (mmt) REVERT: I 66 MET cc_start: 0.8868 (mpp) cc_final: 0.8600 (mpp) REVERT: I 322 MET cc_start: 0.9120 (mmm) cc_final: 0.8876 (mmm) REVERT: I 599 TYR cc_start: 0.8856 (t80) cc_final: 0.8600 (t80) REVERT: I 685 GLU cc_start: 0.8456 (pt0) cc_final: 0.8087 (pt0) REVERT: J 114 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8694 (tp) REVERT: J 118 MET cc_start: 0.9203 (mtp) cc_final: 0.8368 (ttp) REVERT: J 358 MET cc_start: 0.8527 (ptp) cc_final: 0.8213 (ptm) REVERT: J 563 TYR cc_start: 0.7372 (t80) cc_final: 0.7106 (t80) REVERT: J 617 THR cc_start: 0.7695 (OUTLIER) cc_final: 0.7168 (t) REVERT: K 103 MET cc_start: 0.8170 (ttm) cc_final: 0.7730 (ttm) REVERT: K 267 MET cc_start: 0.9062 (ptp) cc_final: 0.8375 (ppp) REVERT: L 37 MET cc_start: 0.8694 (ptp) cc_final: 0.8259 (pmm) REVERT: L 201 MET cc_start: 0.8457 (mtm) cc_final: 0.7881 (mpp) REVERT: L 257 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7759 (tptt) REVERT: L 625 MET cc_start: 0.8641 (ptt) cc_final: 0.7800 (mmt) REVERT: M 66 MET cc_start: 0.8931 (mpp) cc_final: 0.8655 (mpp) REVERT: M 312 MET cc_start: 0.8949 (mmm) cc_final: 0.8555 (tpt) REVERT: M 320 MET cc_start: 0.8986 (mmm) cc_final: 0.8683 (mmm) REVERT: M 322 MET cc_start: 0.9122 (mmm) cc_final: 0.8868 (mmm) REVERT: M 599 TYR cc_start: 0.8895 (t80) cc_final: 0.8609 (t80) REVERT: M 685 GLU cc_start: 0.8419 (pt0) cc_final: 0.8119 (pt0) REVERT: N 114 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8800 (tp) REVERT: N 118 MET cc_start: 0.9189 (mtp) cc_final: 0.8347 (ttp) REVERT: N 358 MET cc_start: 0.8529 (ptp) cc_final: 0.8220 (ptm) REVERT: N 563 TYR cc_start: 0.7484 (t80) cc_final: 0.7179 (t80) REVERT: N 617 THR cc_start: 0.7649 (OUTLIER) cc_final: 0.7133 (t) REVERT: O 103 MET cc_start: 0.8199 (ttm) cc_final: 0.7747 (ttm) REVERT: O 267 MET cc_start: 0.9074 (ptp) cc_final: 0.8398 (ppp) REVERT: P 37 MET cc_start: 0.8826 (ptp) cc_final: 0.8428 (pmm) REVERT: P 257 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7830 (tptt) REVERT: P 625 MET cc_start: 0.8647 (tpt) cc_final: 0.7783 (mmt) outliers start: 180 outliers final: 140 residues processed: 492 average time/residue: 0.6559 time to fit residues: 587.8786 Evaluate side-chains 456 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 304 time to evaluate : 6.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 417 ILE Chi-restraints excluded: chain F residue 530 ILE Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 634 VAL Chi-restraints excluded: chain F residue 642 TYR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 478 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 257 LYS Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 429 TYR Chi-restraints excluded: chain H residue 484 LEU Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain I residue 506 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 587 VAL Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 272 MET Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 417 ILE Chi-restraints excluded: chain J residue 530 ILE Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 634 VAL Chi-restraints excluded: chain J residue 642 TYR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain K residue 478 ILE Chi-restraints excluded: chain K residue 586 LYS Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 257 LYS Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 429 TYR Chi-restraints excluded: chain L residue 484 LEU Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 417 ILE Chi-restraints excluded: chain M residue 505 VAL Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain M residue 587 VAL Chi-restraints excluded: chain N residue 114 LEU Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 272 MET Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 413 VAL Chi-restraints excluded: chain N residue 417 ILE Chi-restraints excluded: chain N residue 530 ILE Chi-restraints excluded: chain N residue 555 LEU Chi-restraints excluded: chain N residue 617 THR Chi-restraints excluded: chain N residue 634 VAL Chi-restraints excluded: chain N residue 642 TYR Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 232 ILE Chi-restraints excluded: chain O residue 293 VAL Chi-restraints excluded: chain O residue 441 VAL Chi-restraints excluded: chain O residue 478 ILE Chi-restraints excluded: chain O residue 586 LYS Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 164 SER Chi-restraints excluded: chain P residue 257 LYS Chi-restraints excluded: chain P residue 304 VAL Chi-restraints excluded: chain P residue 429 TYR Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 558 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 838 optimal weight: 10.0000 chunk 882 optimal weight: 5.9990 chunk 805 optimal weight: 9.9990 chunk 858 optimal weight: 3.9990 chunk 516 optimal weight: 5.9990 chunk 374 optimal weight: 9.9990 chunk 674 optimal weight: 0.8980 chunk 263 optimal weight: 0.9990 chunk 775 optimal weight: 1.9990 chunk 812 optimal weight: 7.9990 chunk 855 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 500 ASN ** G 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 564 ASN ** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 466 GLN ** J 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 500 ASN ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 466 GLN ** N 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 500 ASN ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 79084 Z= 0.185 Angle : 0.613 12.401 106940 Z= 0.309 Chirality : 0.042 0.185 11928 Planarity : 0.004 0.074 13768 Dihedral : 4.819 42.065 10388 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.99 % Allowed : 19.10 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.09 % Twisted Proline : 1.92 % Twisted General : 0.05 % 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: -0.30 (0.09), residues: 9516 helix: 1.39 (0.08), residues: 4368 sheet: -0.35 (0.17), residues: 976 loop : -1.96 (0.10), residues: 4172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 244 HIS 0.010 0.001 HIS H 452 PHE 0.050 0.001 PHE L 586 TYR 0.020 0.001 TYR I 468 ARG 0.004 0.000 ARG N 324 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 330 time to evaluate : 6.914 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: A 66 MET cc_start: 0.8907 (mpp) cc_final: 0.8643 (mpp) REVERT: A 322 MET cc_start: 0.9137 (mmm) cc_final: 0.8888 (mmm) REVERT: A 566 MET cc_start: 0.9395 (mtt) cc_final: 0.9085 (mtm) REVERT: A 599 TYR cc_start: 0.8900 (t80) cc_final: 0.8599 (t80) REVERT: A 685 GLU cc_start: 0.8449 (pt0) cc_final: 0.8084 (pt0) REVERT: B 114 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8340 (mt) REVERT: B 118 MET cc_start: 0.9174 (mtp) cc_final: 0.8519 (ttp) REVERT: B 322 MET cc_start: 0.9011 (tpt) cc_final: 0.8587 (tpt) REVERT: B 358 MET cc_start: 0.8528 (ptp) cc_final: 0.8278 (ptm) REVERT: B 563 TYR cc_start: 0.7134 (t80) cc_final: 0.6743 (t80) REVERT: B 617 THR cc_start: 0.7614 (OUTLIER) cc_final: 0.7090 (t) REVERT: C 103 MET cc_start: 0.8141 (ttm) cc_final: 0.7637 (ttm) REVERT: D 37 MET cc_start: 0.8828 (ptp) cc_final: 0.8284 (pmm) REVERT: D 257 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7859 (tptt) REVERT: D 430 MET cc_start: 0.8949 (tpp) cc_final: 0.8593 (mpp) REVERT: D 625 MET cc_start: 0.8604 (tpt) cc_final: 0.7733 (mmt) REVERT: E 66 MET cc_start: 0.8934 (mpp) cc_final: 0.8659 (mpp) REVERT: E 94 TYR cc_start: 0.9330 (t80) cc_final: 0.9027 (t80) REVERT: E 320 MET cc_start: 0.9035 (mmp) cc_final: 0.8820 (mmm) REVERT: E 322 MET cc_start: 0.9141 (mmm) cc_final: 0.8885 (mmm) REVERT: E 365 LEU cc_start: 0.9407 (mt) cc_final: 0.9193 (mt) REVERT: E 599 TYR cc_start: 0.8898 (t80) cc_final: 0.8597 (t80) REVERT: E 685 GLU cc_start: 0.8433 (pt0) cc_final: 0.8121 (pt0) REVERT: F 118 MET cc_start: 0.9178 (mtp) cc_final: 0.8400 (ttp) REVERT: F 358 MET cc_start: 0.8525 (ptp) cc_final: 0.8216 (ptm) REVERT: F 563 TYR cc_start: 0.7128 (t80) cc_final: 0.6721 (t80) REVERT: F 617 THR cc_start: 0.7611 (OUTLIER) cc_final: 0.7084 (t) REVERT: G 103 MET cc_start: 0.8108 (ttm) cc_final: 0.7656 (ttm) REVERT: G 267 MET cc_start: 0.9097 (ptp) cc_final: 0.8408 (ppp) REVERT: H 37 MET cc_start: 0.8812 (ptp) cc_final: 0.8445 (pmm) REVERT: H 257 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7810 (tptt) REVERT: H 327 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9274 (mt) REVERT: H 430 MET cc_start: 0.8970 (tpp) cc_final: 0.8670 (mpp) REVERT: H 625 MET cc_start: 0.8639 (tpt) cc_final: 0.7781 (mmt) REVERT: I 66 MET cc_start: 0.8859 (mpp) cc_final: 0.8599 (mpp) REVERT: I 322 MET cc_start: 0.9117 (mmm) cc_final: 0.8879 (mmm) REVERT: I 566 MET cc_start: 0.9388 (mtt) cc_final: 0.9077 (mtm) REVERT: I 599 TYR cc_start: 0.8868 (t80) cc_final: 0.8535 (t80) REVERT: I 685 GLU cc_start: 0.8445 (pt0) cc_final: 0.8078 (pt0) REVERT: J 114 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8326 (mt) REVERT: J 118 MET cc_start: 0.9189 (mtp) cc_final: 0.8534 (ttp) REVERT: J 243 ASP cc_start: 0.7645 (t0) cc_final: 0.6785 (p0) REVERT: J 358 MET cc_start: 0.8520 (ptp) cc_final: 0.8204 (ptm) REVERT: J 563 TYR cc_start: 0.7423 (t80) cc_final: 0.7146 (t80) REVERT: J 617 THR cc_start: 0.7643 (OUTLIER) cc_final: 0.7127 (t) REVERT: K 103 MET cc_start: 0.8172 (ttm) cc_final: 0.7726 (ttm) REVERT: K 267 MET cc_start: 0.9058 (ptp) cc_final: 0.8378 (ppp) REVERT: L 37 MET cc_start: 0.8704 (ptp) cc_final: 0.8191 (pmm) REVERT: L 201 MET cc_start: 0.8511 (mtm) cc_final: 0.7927 (mpp) REVERT: L 257 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7772 (mmmt) REVERT: L 625 MET cc_start: 0.8644 (ptt) cc_final: 0.7803 (mmt) REVERT: M 66 MET cc_start: 0.8918 (mpp) cc_final: 0.8644 (mpp) REVERT: M 312 MET cc_start: 0.8888 (mmm) cc_final: 0.8536 (tpt) REVERT: M 320 MET cc_start: 0.8949 (mmm) cc_final: 0.8721 (mmm) REVERT: M 322 MET cc_start: 0.9101 (mmm) cc_final: 0.8858 (mmm) REVERT: M 566 MET cc_start: 0.9393 (mtt) cc_final: 0.9078 (mtm) REVERT: M 599 TYR cc_start: 0.8874 (t80) cc_final: 0.8633 (t80) REVERT: M 685 GLU cc_start: 0.8411 (pt0) cc_final: 0.8109 (pt0) REVERT: N 114 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8716 (tp) REVERT: N 118 MET cc_start: 0.9182 (mtp) cc_final: 0.8353 (ttp) REVERT: N 358 MET cc_start: 0.8510 (ptp) cc_final: 0.8199 (ptm) REVERT: N 563 TYR cc_start: 0.7406 (t80) cc_final: 0.7102 (t80) REVERT: N 617 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7081 (t) REVERT: O 103 MET cc_start: 0.8200 (ttm) cc_final: 0.7743 (ttm) REVERT: O 267 MET cc_start: 0.9068 (ptp) cc_final: 0.8399 (ppp) REVERT: P 37 MET cc_start: 0.8816 (ptp) cc_final: 0.8237 (pmm) REVERT: P 257 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7836 (tptt) REVERT: P 430 MET cc_start: 0.8909 (tpp) cc_final: 0.8644 (mpp) REVERT: P 625 MET cc_start: 0.8637 (tpt) cc_final: 0.7775 (mmt) outliers start: 174 outliers final: 143 residues processed: 499 average time/residue: 0.6613 time to fit residues: 594.7274 Evaluate side-chains 473 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 318 time to evaluate : 6.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 530 ILE Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 634 VAL Chi-restraints excluded: chain F residue 642 TYR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 478 ILE Chi-restraints excluded: chain G residue 586 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 257 LYS Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 429 TYR Chi-restraints excluded: chain H residue 484 LEU Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain I residue 506 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 587 VAL Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 466 GLN Chi-restraints excluded: chain J residue 530 ILE Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 634 VAL Chi-restraints excluded: chain J residue 642 TYR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain K residue 478 ILE Chi-restraints excluded: chain K residue 586 LYS Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 257 LYS Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 429 TYR Chi-restraints excluded: chain L residue 484 LEU Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 417 ILE Chi-restraints excluded: chain M residue 505 VAL Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain M residue 587 VAL Chi-restraints excluded: chain N residue 114 LEU Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 413 VAL Chi-restraints excluded: chain N residue 466 GLN Chi-restraints excluded: chain N residue 530 ILE Chi-restraints excluded: chain N residue 555 LEU Chi-restraints excluded: chain N residue 617 THR Chi-restraints excluded: chain N residue 634 VAL Chi-restraints excluded: chain N residue 642 TYR Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 232 ILE Chi-restraints excluded: chain O residue 293 VAL Chi-restraints excluded: chain O residue 441 VAL Chi-restraints excluded: chain O residue 478 ILE Chi-restraints excluded: chain O residue 586 LYS Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 164 SER Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 257 LYS Chi-restraints excluded: chain P residue 304 VAL Chi-restraints excluded: chain P residue 429 TYR Chi-restraints excluded: chain P residue 482 HIS Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 558 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 563 optimal weight: 3.9990 chunk 907 optimal weight: 7.9990 chunk 554 optimal weight: 7.9990 chunk 430 optimal weight: 3.9990 chunk 631 optimal weight: 30.0000 chunk 952 optimal weight: 8.9990 chunk 876 optimal weight: 8.9990 chunk 758 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 585 optimal weight: 5.9990 chunk 465 optimal weight: 9.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 466 GLN ** F 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 611 ASN ** I 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 466 GLN ** J 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 611 ASN ** M 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 466 GLN ** N 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 611 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 79084 Z= 0.232 Angle : 0.648 11.915 106940 Z= 0.328 Chirality : 0.042 0.270 11928 Planarity : 0.004 0.073 13768 Dihedral : 4.898 41.751 10388 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.01 % Allowed : 19.22 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.09 % Twisted Proline : 1.92 % Twisted General : 0.09 % 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: -0.38 (0.09), residues: 9516 helix: 1.25 (0.08), residues: 4388 sheet: -0.44 (0.17), residues: 976 loop : -1.94 (0.10), residues: 4152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 428 HIS 0.010 0.001 HIS D 452 PHE 0.056 0.001 PHE L 586 TYR 0.020 0.001 TYR M 468 ARG 0.006 0.000 ARG J 324 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19032 Ramachandran restraints generated. 9516 Oldfield, 0 Emsley, 9516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 316 time to evaluate : 6.913 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: A 66 MET cc_start: 0.8903 (mpp) cc_final: 0.8644 (mpp) REVERT: A 322 MET cc_start: 0.9124 (mmm) cc_final: 0.8877 (mmm) REVERT: A 599 TYR cc_start: 0.8938 (t80) cc_final: 0.8633 (t80) REVERT: A 685 GLU cc_start: 0.8454 (pt0) cc_final: 0.8108 (pt0) REVERT: B 114 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8716 (tp) REVERT: B 118 MET cc_start: 0.9190 (mtp) cc_final: 0.8334 (ttp) REVERT: B 322 MET cc_start: 0.9084 (tpt) cc_final: 0.8672 (tpt) REVERT: B 358 MET cc_start: 0.8554 (ptp) cc_final: 0.8293 (ptm) REVERT: B 563 TYR cc_start: 0.7155 (t80) cc_final: 0.6760 (t80) REVERT: B 617 THR cc_start: 0.7643 (OUTLIER) cc_final: 0.7139 (t) REVERT: C 103 MET cc_start: 0.8087 (ttm) cc_final: 0.7708 (ttm) REVERT: D 37 MET cc_start: 0.8763 (ptp) cc_final: 0.8446 (pmm) REVERT: D 430 MET cc_start: 0.8934 (tpp) cc_final: 0.8647 (mpp) REVERT: D 625 MET cc_start: 0.8590 (tpt) cc_final: 0.7734 (mmt) REVERT: E 66 MET cc_start: 0.8933 (mpp) cc_final: 0.8662 (mpp) REVERT: E 312 MET cc_start: 0.9203 (ttm) cc_final: 0.8663 (tpt) REVERT: E 322 MET cc_start: 0.9126 (mmm) cc_final: 0.8881 (mmm) REVERT: E 599 TYR cc_start: 0.8934 (t80) cc_final: 0.8623 (t80) REVERT: E 685 GLU cc_start: 0.8424 (pt0) cc_final: 0.8080 (pt0) REVERT: F 118 MET cc_start: 0.9219 (mtp) cc_final: 0.8208 (mtp) REVERT: F 243 ASP cc_start: 0.7704 (t0) cc_final: 0.6894 (p0) REVERT: F 358 MET cc_start: 0.8576 (ptp) cc_final: 0.8259 (ptm) REVERT: F 563 TYR cc_start: 0.7229 (t80) cc_final: 0.6847 (t80) REVERT: F 617 THR cc_start: 0.7646 (OUTLIER) cc_final: 0.7138 (t) REVERT: G 103 MET cc_start: 0.8113 (ttm) cc_final: 0.7643 (ttm) REVERT: G 267 MET cc_start: 0.9095 (ptp) cc_final: 0.8415 (ppp) REVERT: H 37 MET cc_start: 0.8749 (ptp) cc_final: 0.8107 (pmm) REVERT: H 327 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9284 (mt) REVERT: H 430 MET cc_start: 0.8934 (tpp) cc_final: 0.8580 (mtt) REVERT: H 625 MET cc_start: 0.8643 (tpt) cc_final: 0.7780 (mmt) REVERT: I 66 MET cc_start: 0.8882 (mpp) cc_final: 0.8618 (mpp) REVERT: I 322 MET cc_start: 0.9081 (mmm) cc_final: 0.8834 (mmm) REVERT: I 566 MET cc_start: 0.9419 (mtt) cc_final: 0.9163 (mtm) REVERT: I 599 TYR cc_start: 0.8905 (t80) cc_final: 0.8514 (t80) REVERT: I 685 GLU cc_start: 0.8451 (pt0) cc_final: 0.8103 (pt0) REVERT: J 114 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8697 (tp) REVERT: J 118 MET cc_start: 0.9213 (mtp) cc_final: 0.8350 (ttp) REVERT: J 243 ASP cc_start: 0.7651 (t0) cc_final: 0.6913 (p0) REVERT: J 358 MET cc_start: 0.8580 (ptp) cc_final: 0.8234 (ptm) REVERT: J 563 TYR cc_start: 0.7425 (t80) cc_final: 0.7146 (t80) REVERT: J 617 THR cc_start: 0.7640 (OUTLIER) cc_final: 0.7127 (t) REVERT: K 103 MET cc_start: 0.8151 (ttm) cc_final: 0.7702 (ttm) REVERT: K 267 MET cc_start: 0.9091 (ptp) cc_final: 0.8400 (ppp) REVERT: K 592 MET cc_start: 0.9170 (ppp) cc_final: 0.8912 (ppp) REVERT: L 37 MET cc_start: 0.8616 (ptp) cc_final: 0.8210 (pmm) REVERT: L 201 MET cc_start: 0.8544 (mtm) cc_final: 0.7963 (mpp) REVERT: L 257 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7732 (mmmt) REVERT: L 430 MET cc_start: 0.9230 (tpp) cc_final: 0.8655 (mtt) REVERT: L 625 MET cc_start: 0.8657 (ptt) cc_final: 0.7827 (mmt) REVERT: M 66 MET cc_start: 0.8956 (mpp) cc_final: 0.8687 (mpp) REVERT: M 312 MET cc_start: 0.8934 (mmm) cc_final: 0.8552 (tpt) REVERT: M 320 MET cc_start: 0.8989 (mmm) cc_final: 0.8736 (mmm) REVERT: M 322 MET cc_start: 0.9087 (mmm) cc_final: 0.8835 (mmm) REVERT: M 599 TYR cc_start: 0.8929 (t80) cc_final: 0.8581 (t80) REVERT: M 685 GLU cc_start: 0.8426 (pt0) cc_final: 0.8097 (pt0) REVERT: N 114 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8804 (tp) REVERT: N 118 MET cc_start: 0.9194 (mtp) cc_final: 0.8334 (ttp) REVERT: N 243 ASP cc_start: 0.7685 (t0) cc_final: 0.6887 (p0) REVERT: N 358 MET cc_start: 0.8563 (ptp) cc_final: 0.8244 (ptm) REVERT: N 563 TYR cc_start: 0.7363 (t80) cc_final: 0.7063 (t80) REVERT: N 617 THR cc_start: 0.7592 (OUTLIER) cc_final: 0.7077 (t) REVERT: O 103 MET cc_start: 0.8175 (ttm) cc_final: 0.7715 (ttm) REVERT: O 267 MET cc_start: 0.9094 (ptp) cc_final: 0.8411 (ppp) REVERT: O 592 MET cc_start: 0.9152 (ppp) cc_final: 0.8909 (ppp) REVERT: P 37 MET cc_start: 0.8716 (ptp) cc_final: 0.8388 (pmm) REVERT: P 430 MET cc_start: 0.8925 (tpp) cc_final: 0.8661 (mpp) REVERT: P 625 MET cc_start: 0.8638 (tpt) cc_final: 0.7768 (mmt) outliers start: 176 outliers final: 153 residues processed: 484 average time/residue: 0.6392 time to fit residues: 563.7221 Evaluate side-chains 472 residues out of total 8748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 310 time to evaluate : 6.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 466 GLN Chi-restraints excluded: chain F residue 530 ILE Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 634 VAL Chi-restraints excluded: chain F residue 642 TYR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 478 ILE Chi-restraints excluded: chain G residue 586 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 429 TYR Chi-restraints excluded: chain H residue 484 LEU Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain I residue 506 VAL Chi-restraints excluded: chain I residue 519 ILE Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 587 VAL Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 272 MET Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 466 GLN Chi-restraints excluded: chain J residue 530 ILE Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 634 VAL Chi-restraints excluded: chain J residue 642 TYR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain K residue 478 ILE Chi-restraints excluded: chain K residue 586 LYS Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 257 LYS Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 429 TYR Chi-restraints excluded: chain L residue 484 LEU Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 417 ILE Chi-restraints excluded: chain M residue 505 VAL Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain M residue 587 VAL Chi-restraints excluded: chain N residue 114 LEU Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 393 VAL Chi-restraints excluded: chain N residue 413 VAL Chi-restraints excluded: chain N residue 466 GLN Chi-restraints excluded: chain N residue 530 ILE Chi-restraints excluded: chain N residue 555 LEU Chi-restraints excluded: chain N residue 617 THR Chi-restraints excluded: chain N residue 634 VAL Chi-restraints excluded: chain N residue 642 TYR Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 232 ILE Chi-restraints excluded: chain O residue 293 VAL Chi-restraints excluded: chain O residue 441 VAL Chi-restraints excluded: chain O residue 478 ILE Chi-restraints excluded: chain O residue 586 LYS Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 164 SER Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 304 VAL Chi-restraints excluded: chain P residue 429 TYR Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 558 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 956 random chunks: chunk 602 optimal weight: 0.6980 chunk 807 optimal weight: 0.0370 chunk 232 optimal weight: 5.9990 chunk 699 optimal weight: 7.9990 chunk 111 optimal weight: 0.0970 chunk 210 optimal weight: 10.0000 chunk 759 optimal weight: 6.9990 chunk 317 optimal weight: 3.9990 chunk 780 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 overall best weight: 2.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 466 GLN ** F 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 HIS ** G 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 611 ASN ** I 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 466 GLN ** J 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 611 ASN ** M 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 466 GLN ** N 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 611 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.068638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.049962 restraints weight = 600126.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.050964 restraints weight = 315890.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.051517 restraints weight = 211716.336| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 79084 Z= 0.174 Angle : 0.625 11.379 106940 Z= 0.312 Chirality : 0.042 0.212 11928 Planarity : 0.004 0.073 13768 Dihedral : 4.784 41.548 10388 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.79 % Allowed : 19.64 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.09 % Twisted Proline : 1.92 % Twisted General : 0.05 % 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: -0.20 (0.09), residues: 9516 helix: 1.44 (0.08), residues: 4360 sheet: -0.37 (0.17), residues: 976 loop : -1.86 (0.10), residues: 4180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 244 HIS 0.008 0.001 HIS H 452 PHE 0.054 0.001 PHE L 586 TYR 0.020 0.001 TYR A 468 ARG 0.007 0.000 ARG J 324 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14190.19 seconds wall clock time: 250 minutes 23.84 seconds (15023.84 seconds total)