Starting phenix.real_space_refine on Mon Mar 18 22:04:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpa_9868/03_2024/6jpa_9868_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpa_9868/03_2024/6jpa_9868.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpa_9868/03_2024/6jpa_9868_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpa_9868/03_2024/6jpa_9868_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpa_9868/03_2024/6jpa_9868_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpa_9868/03_2024/6jpa_9868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpa_9868/03_2024/6jpa_9868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpa_9868/03_2024/6jpa_9868_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpa_9868/03_2024/6jpa_9868_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 10 5.49 5 S 126 5.16 5 C 14414 2.51 5 N 3598 2.21 5 O 4081 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 41": "NH1" <-> "NH2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A ARG 794": "NH1" <-> "NH2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A GLU 967": "OE1" <-> "OE2" Residue "A ARG 1022": "NH1" <-> "NH2" Residue "A GLU 1201": "OE1" <-> "OE2" Residue "A ARG 1236": "NH1" <-> "NH2" Residue "A GLU 1323": "OE1" <-> "OE2" Residue "A GLU 1327": "OE1" <-> "OE2" Residue "A ARG 1389": "NH1" <-> "NH2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1428": "NH1" <-> "NH2" Residue "A ARG 1442": "NH1" <-> "NH2" Residue "A ARG 1447": "NH1" <-> "NH2" Residue "A ARG 1472": "NH1" <-> "NH2" Residue "E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F ARG 230": "NH1" <-> "NH2" Residue "F ARG 241": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 544": "NH1" <-> "NH2" Residue "F ARG 546": "NH1" <-> "NH2" Residue "F GLU 567": "OE1" <-> "OE2" Residue "F ARG 591": "NH1" <-> "NH2" Residue "F ARG 607": "NH1" <-> "NH2" Residue "F GLU 658": "OE1" <-> "OE2" Residue "F ARG 692": "NH1" <-> "NH2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 745": "NH1" <-> "NH2" Residue "F ARG 846": "NH1" <-> "NH2" Residue "F ARG 1004": "NH1" <-> "NH2" Residue "F GLU 1022": "OE1" <-> "OE2" Residue "F GLU 1069": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22232 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 10219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1274, 10219 Classifications: {'peptide': 1274} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 38, 'TRANS': 1235} Chain breaks: 6 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "B" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 710 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 91} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1367 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 472 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 16, 439 Unusual residues: {' CA': 3, '3PE': 8, '4YH': 1, '9Z9': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1, '3PE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 16, 439 Unusual residues: {' CA': 3, '3PE': 8, '4YH': 1, '9Z9': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1, '3PE:plan-2': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 398 Chain: "F" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 102 Unusual residues: {'ETA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 15.97, per 1000 atoms: 0.72 Number of scatterers: 22232 At special positions: 0 Unit cell: (168.014, 183.288, 165.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 126 16.00 P 10 15.00 O 4081 8.00 N 3598 7.00 C 14414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=1.74 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=1.88 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=1.78 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.95 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.05 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.77 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.27 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.02 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=1.57 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM22146 O5 NAG F1104 .*. O " rejected from bonding due to valence issues. Atom "HETATM22174 O5 NAG F1114 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-3 " NAG D 1 " - " NAG D 2 " " NAG K 1 " - " NAG K 2 " " NAG L 2 " - " NAG L 3 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG F1104 " - " ASN F 326 " " NAG F1107 " - " ASN F 891 " " NAG F1114 " - " ASN F 92 " " NAG F1115 " - " ASN F 606 " " NAG F1120 " - " ASN F 784 " " NAG F1121 " - " ASN F1001 " " NAG F1122 " - " ASN F 988 " " NAG G 1 " - " ASN F 615 " " NAG H 1 " - " ASN F 186 " " NAG I 1 " - " ASN F 470 " " NAG J 1 " - " ASN F 898 " " NAG K 1 " - " ASN F 678 " " NAG L 1 " - " ASN F 827 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.57 Conformation dependent library (CDL) restraints added in 5.6 seconds 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5110 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 15 sheets defined 48.6% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.22 Creating SS restraints... Processing helix chain 'A' and resid 45 through 48 No H-bonds generated for 'chain 'A' and resid 45 through 48' Processing helix chain 'A' and resid 53 through 68 removed outlier: 3.686A pdb=" N LEU A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 81 through 103 removed outlier: 3.513A pdb=" N GLY A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 121 through 143 removed outlier: 3.539A pdb=" N LEU A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 178 removed outlier: 3.716A pdb=" N ARG A 168 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Proline residue: A 172 - end of helix removed outlier: 4.280A pdb=" N GLY A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 192 removed outlier: 4.106A pdb=" N VAL A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 218 removed outlier: 3.653A pdb=" N PHE A 197 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N HIS A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 201 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 207 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 208 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 216 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 294 through 305 Processing helix chain 'A' and resid 310 through 319 removed outlier: 3.570A pdb=" N PHE A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 345 Processing helix chain 'A' and resid 350 through 375 removed outlier: 3.933A pdb=" N LYS A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY A 373 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 429 removed outlier: 4.042A pdb=" N HIS A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 429 " --> pdb=" O CYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 451 removed outlier: 3.919A pdb=" N ILE A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 483 removed outlier: 3.521A pdb=" N SER A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 4.002A pdb=" N PHE A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 493' Processing helix chain 'A' and resid 495 through 516 removed outlier: 3.847A pdb=" N PHE A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS A 505 " --> pdb=" O CYS A 501 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 541 removed outlier: 3.827A pdb=" N ARG A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 530 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR A 541 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 558 removed outlier: 3.690A pdb=" N ALA A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 581 removed outlier: 3.557A pdb=" N LEU A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 Processing helix chain 'A' and resid 616 through 627 removed outlier: 3.790A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 676 removed outlier: 3.579A pdb=" N LEU A 636 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N CYS A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 removed outlier: 3.545A pdb=" N LYS A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 removed outlier: 3.787A pdb=" N HIS A 793 " --> pdb=" O ARG A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 809 through 815 removed outlier: 3.894A pdb=" N ALA A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 831 Processing helix chain 'A' and resid 833 through 853 removed outlier: 3.665A pdb=" N PHE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 882 removed outlier: 3.556A pdb=" N LEU A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 900 removed outlier: 3.849A pdb=" N VAL A 898 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 899 " --> pdb=" O ILE A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 912 through 924 removed outlier: 3.745A pdb=" N VAL A 917 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 950 Processing helix chain 'A' and resid 1000 through 1011 removed outlier: 3.611A pdb=" N MET A1004 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1025 Processing helix chain 'A' and resid 1039 through 1070 removed outlier: 3.625A pdb=" N TYR A1048 " --> pdb=" O PHE A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1094 removed outlier: 3.764A pdb=" N CYS A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A1090 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR A1091 " --> pdb=" O GLN A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1116 removed outlier: 3.564A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A1115 " --> pdb=" O VAL A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1135 Processing helix chain 'A' and resid 1144 through 1170 removed outlier: 3.565A pdb=" N ILE A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP A1151 " --> pdb=" O ASN A1147 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A1167 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1205 removed outlier: 3.713A pdb=" N PHE A1185 " --> pdb=" O PRO A1181 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A1204 " --> pdb=" O SER A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1237 No H-bonds generated for 'chain 'A' and resid 1235 through 1237' Processing helix chain 'A' and resid 1240 through 1248 Processing helix chain 'A' and resid 1251 through 1261 Processing helix chain 'A' and resid 1268 through 1289 Processing helix chain 'A' and resid 1309 through 1320 Processing helix chain 'A' and resid 1325 through 1331 Processing helix chain 'A' and resid 1349 through 1351 No H-bonds generated for 'chain 'A' and resid 1349 through 1351' Processing helix chain 'A' and resid 1355 through 1387 removed outlier: 3.610A pdb=" N TYR A1358 " --> pdb=" O ASN A1355 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR A1360 " --> pdb=" O ALA A1357 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A1361 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A1362 " --> pdb=" O TYR A1359 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A1363 " --> pdb=" O TYR A1360 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A1367 " --> pdb=" O PHE A1364 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A1376 " --> pdb=" O ILE A1373 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A1377 " --> pdb=" O ASN A1374 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A1378 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASP A1385 " --> pdb=" O ASP A1382 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A1387 " --> pdb=" O PHE A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1408 removed outlier: 3.926A pdb=" N GLU A1401 " --> pdb=" O HIS A1397 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A1403 " --> pdb=" O LEU A1399 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU A1408 " --> pdb=" O ALA A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1428 removed outlier: 3.558A pdb=" N ARG A1427 " --> pdb=" O VAL A1423 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1450 removed outlier: 4.021A pdb=" N LEU A1448 " --> pdb=" O ALA A1444 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A1449 " --> pdb=" O CYS A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1474 removed outlier: 3.673A pdb=" N LEU A1467 " --> pdb=" O PHE A1463 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE A1468 " --> pdb=" O ASN A1464 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A1469 " --> pdb=" O ALA A1465 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A1474 " --> pdb=" O LEU A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1483 through 1492 removed outlier: 3.935A pdb=" N ASN A1487 " --> pdb=" O PHE A1483 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A1492 " --> pdb=" O GLU A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1500 through 1505 removed outlier: 3.764A pdb=" N MET A1503 " --> pdb=" O ARG A1500 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU A1505 " --> pdb=" O SER A1502 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 28 removed outlier: 4.437A pdb=" N VAL E 11 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR E 12 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE E 14 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE E 20 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU E 22 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA E 23 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA E 26 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 27 " --> pdb=" O MET E 24 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 28 " --> pdb=" O THR E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 127 removed outlier: 3.960A pdb=" N PHE E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 164 Proline residue: E 139 - end of helix removed outlier: 3.518A pdb=" N PHE E 143 " --> pdb=" O PRO E 139 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER E 154 " --> pdb=" O CYS E 150 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER E 161 " --> pdb=" O VAL E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 201 removed outlier: 4.082A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE E 197 " --> pdb=" O PHE E 193 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 96 removed outlier: 3.625A pdb=" N LYS B 83 " --> pdb=" O MET B 79 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.991A pdb=" N ARG B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 303 removed outlier: 3.703A pdb=" N MET C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU C 297 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 300 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 356 removed outlier: 3.891A pdb=" N GLU C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'C' and resid 394 through 401 removed outlier: 4.052A pdb=" N GLN C 398 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 412 through 424 removed outlier: 3.928A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing helix chain 'C' and resid 439 through 457 removed outlier: 3.868A pdb=" N HIS C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 37 Processing helix chain 'F' and resid 42 through 52 Processing helix chain 'F' and resid 54 through 64 removed outlier: 3.651A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 109 removed outlier: 3.726A pdb=" N SER F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 201 removed outlier: 3.919A pdb=" N GLU F 184 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALA F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU F 191 " --> pdb=" O TRP F 187 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 199 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU F 201 " --> pdb=" O LYS F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 250 removed outlier: 3.863A pdb=" N GLY F 249 " --> pdb=" O TRP F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 269 through 283 removed outlier: 3.618A pdb=" N ARG F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER F 279 " --> pdb=" O ARG F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 323 Processing helix chain 'F' and resid 337 through 346 Processing helix chain 'F' and resid 372 through 378 removed outlier: 3.941A pdb=" N LYS F 377 " --> pdb=" O GLU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 407 Processing helix chain 'F' and resid 427 through 432 removed outlier: 3.836A pdb=" N LEU F 432 " --> pdb=" O LEU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 437 No H-bonds generated for 'chain 'F' and resid 434 through 437' Processing helix chain 'F' and resid 440 through 443 Processing helix chain 'F' and resid 496 through 499 No H-bonds generated for 'chain 'F' and resid 496 through 499' Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 563 through 566 No H-bonds generated for 'chain 'F' and resid 563 through 566' Processing helix chain 'F' and resid 574 through 581 Processing helix chain 'F' and resid 641 through 646 Processing helix chain 'F' and resid 679 through 692 removed outlier: 3.686A pdb=" N PHE F 689 " --> pdb=" O ASN F 685 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE F 690 " --> pdb=" O PHE F 686 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP F 691 " --> pdb=" O ASN F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 721 removed outlier: 3.838A pdb=" N GLU F 717 " --> pdb=" O GLY F 713 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 718 " --> pdb=" O PHE F 714 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL F 719 " --> pdb=" O THR F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 753 removed outlier: 3.533A pdb=" N GLU F 753 " --> pdb=" O LYS F 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 749 through 753' Processing helix chain 'F' and resid 765 through 772 removed outlier: 3.560A pdb=" N LEU F 771 " --> pdb=" O TYR F 767 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) Processing helix chain 'F' and resid 821 through 829 removed outlier: 3.507A pdb=" N GLU F 826 " --> pdb=" O ASN F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 880 No H-bonds generated for 'chain 'F' and resid 878 through 880' Processing helix chain 'F' and resid 883 through 891 removed outlier: 3.561A pdb=" N ASN F 891 " --> pdb=" O ARG F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 1024 through 1026 No H-bonds generated for 'chain 'F' and resid 1024 through 1026' Processing helix chain 'F' and resid 1046 through 1052 removed outlier: 4.333A pdb=" N LYS F1051 " --> pdb=" O CYS F1047 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN F1052 " --> pdb=" O ASP F1048 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 226 through 228 Processing sheet with id= B, first strand: chain 'A' and resid 955 through 957 Processing sheet with id= C, first strand: chain 'A' and resid 971 through 975 Processing sheet with id= D, first strand: chain 'E' and resid 48 through 50 removed outlier: 3.683A pdb=" N CYS E 57 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN E 79 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.704A pdb=" N PHE B 103 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 146 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS B 139 " --> pdb=" O TRP B 144 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N TRP B 144 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 277 through 279 removed outlier: 5.206A pdb=" N ILE C 385 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE C 432 " --> pdb=" O TYR C 388 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 309 through 313 removed outlier: 6.652A pdb=" N LEU C 363 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N THR C 312 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA C 365 " --> pdb=" O THR C 312 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'F' and resid 68 through 72 Processing sheet with id= I, first strand: chain 'F' and resid 167 through 170 removed outlier: 4.290A pdb=" N LEU F 216 " --> pdb=" O SER F 212 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 411 through 415 removed outlier: 3.641A pdb=" N TYR F 411 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 359 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE F 290 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE F 258 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN F 292 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N VAL F 260 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ALA F 294 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 513 through 517 Processing sheet with id= L, first strand: chain 'F' and resid 777 through 779 Processing sheet with id= M, first strand: chain 'F' and resid 992 through 994 removed outlier: 3.617A pdb=" N MET F 864 " --> pdb=" O ILE F 855 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 896 through 902 removed outlier: 3.620A pdb=" N GLN F 983 " --> pdb=" O ASN F 898 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 905 through 907 removed outlier: 3.574A pdb=" N SER F 905 " --> pdb=" O CYS F 977 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN F 975 " --> pdb=" O CYS F 907 " (cutoff:3.500A) 817 hydrogen bonds defined for protein. 2144 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: 7.38 Time building geometry restraints manager: 10.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 3515 1.27 - 1.41: 5751 1.41 - 1.55: 13211 1.55 - 1.69: 38 1.69 - 1.84: 194 Bond restraints: 22709 Sorted by residual: bond pdb=" C21 3PE A1907 " pdb=" O21 3PE A1907 " ideal model delta sigma weight residual 1.316 1.459 -0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" C2 A4YH A1915 " pdb=" C5 A4YH A1915 " ideal model delta sigma weight residual 1.385 1.527 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C11A4YH A1915 " pdb=" C13A4YH A1915 " ideal model delta sigma weight residual 1.384 1.525 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C21 3PE A1904 " pdb=" O21 3PE A1904 " ideal model delta sigma weight residual 1.316 1.456 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C21 3PE A1913 " pdb=" O21 3PE A1913 " ideal model delta sigma weight residual 1.316 1.456 -0.140 2.00e-02 2.50e+03 4.90e+01 ... (remaining 22704 not shown) Histogram of bond angle deviations from ideal: 97.46 - 113.93: 13346 113.93 - 130.39: 17254 130.39 - 146.85: 129 146.85 - 163.32: 0 163.32 - 179.78: 2 Bond angle restraints: 30731 Sorted by residual: angle pdb=" N ILE A 106 " pdb=" CA ILE A 106 " pdb=" C ILE A 106 " ideal model delta sigma weight residual 111.56 100.82 10.74 8.60e-01 1.35e+00 1.56e+02 angle pdb=" N HIS F 867 " pdb=" CA HIS F 867 " pdb=" C HIS F 867 " ideal model delta sigma weight residual 111.28 122.21 -10.93 1.09e+00 8.42e-01 1.01e+02 angle pdb=" N LYS F 478 " pdb=" CA LYS F 478 " pdb=" C LYS F 478 " ideal model delta sigma weight residual 111.28 121.86 -10.58 1.09e+00 8.42e-01 9.43e+01 angle pdb=" N LYS F 991 " pdb=" CA LYS F 991 " pdb=" C LYS F 991 " ideal model delta sigma weight residual 111.28 119.94 -8.66 1.09e+00 8.42e-01 6.31e+01 angle pdb=" N ASN F 325 " pdb=" CA ASN F 325 " pdb=" C ASN F 325 " ideal model delta sigma weight residual 111.71 120.82 -9.11 1.15e+00 7.56e-01 6.28e+01 ... (remaining 30726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.38: 12959 27.38 - 54.76: 883 54.76 - 82.15: 163 82.15 - 109.53: 36 109.53 - 136.91: 17 Dihedral angle restraints: 14058 sinusoidal: 6159 harmonic: 7899 Sorted by residual: dihedral pdb=" CB CYS F 406 " pdb=" SG CYS F 406 " pdb=" SG CYS F1074 " pdb=" CB CYS F1074 " ideal model delta sinusoidal sigma weight residual -86.00 0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS F 907 " pdb=" SG CYS F 907 " pdb=" SG CYS F 977 " pdb=" CB CYS F 977 " ideal model delta sinusoidal sigma weight residual 93.00 174.05 -81.05 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CB CYS F 844 " pdb=" SG CYS F 844 " pdb=" SG CYS F 853 " pdb=" CB CYS F 853 " ideal model delta sinusoidal sigma weight residual -86.00 -162.01 76.01 1 1.00e+01 1.00e-02 7.28e+01 ... (remaining 14055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.766: 3496 0.766 - 1.531: 2 1.531 - 2.297: 0 2.297 - 3.063: 1 3.063 - 3.828: 1 Chirality restraints: 3500 Sorted by residual: chirality pdb=" C1 NAG L 3 " pdb=" O3 NAG L 2 " pdb=" C2 NAG L 3 " pdb=" O5 NAG L 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-02 2.50e+03 1.03e+03 chirality pdb=" C1 NAG F1120 " pdb=" ND2 ASN F 784 " pdb=" C2 NAG F1120 " pdb=" O5 NAG F1120 " both_signs ideal model delta sigma weight residual False -2.40 1.43 -3.83 2.00e-01 2.50e+01 3.66e+02 chirality pdb=" C1 NAG D 2 " pdb=" O3 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.90e+02 ... (remaining 3497 not shown) Planarity restraints: 3826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG L 1 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.345 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG D 1 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.116 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F1104 " -0.314 2.00e-02 2.50e+03 2.66e-01 8.85e+02 pdb=" C7 NAG F1104 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG F1104 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG F1104 " 0.461 2.00e-02 2.50e+03 pdb=" O7 NAG F1104 " -0.042 2.00e-02 2.50e+03 ... (remaining 3823 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 187 2.52 - 3.11: 16888 3.11 - 3.71: 33074 3.71 - 4.30: 49286 4.30 - 4.90: 79290 Nonbonded interactions: 178725 Sorted by model distance: nonbonded pdb=" O ASN F 480 " pdb=" ND2 ASN F 480 " model vdw 1.921 2.520 nonbonded pdb=" O ARG A 247 " pdb=" OG1 THR A 248 " model vdw 2.051 2.440 nonbonded pdb=" OD1 ASN F 891 " pdb=" O5 NAG F1107 " model vdw 2.082 3.040 nonbonded pdb=" O GLY A 109 " pdb=" O PHE A 110 " model vdw 2.152 3.040 nonbonded pdb=" O GLY F 521 " pdb=" OD1 ASP F 562 " model vdw 2.208 3.040 ... (remaining 178720 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.350 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 67.750 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.130 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: 0.000 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5847 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 : 0.013 0.153 22709 Z= 0.863 Angle : 1.510 15.177 30731 Z= 0.904 Chirality : 0.121 3.828 3500 Planarity : 0.013 0.300 3813 Dihedral : 19.061 136.909 8909 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 38.35 Ramachandran Plot: Outliers : 1.69 % Allowed : 8.77 % Favored : 89.54 % Rotamer: Outliers : 11.40 % Allowed : 10.92 % Favored : 77.69 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.14), residues: 2659 helix: -2.70 (0.12), residues: 1280 sheet: -1.26 (0.34), residues: 214 loop : -2.47 (0.16), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP E 32 HIS 0.017 0.002 HIS E 31 PHE 0.042 0.003 PHE F 663 TYR 0.060 0.003 TYR F 762 ARG 0.020 0.002 ARG F 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 366 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable