Starting phenix.real_space_refine on Mon Mar 18 20:50:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jp5_9866/03_2024/6jp5_9866_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jp5_9866/03_2024/6jp5_9866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jp5_9866/03_2024/6jp5_9866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jp5_9866/03_2024/6jp5_9866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jp5_9866/03_2024/6jp5_9866_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jp5_9866/03_2024/6jp5_9866_updated.pdb" } resolution = 2.9 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 9 5.49 5 S 126 5.16 5 C 14268 2.51 5 N 3596 2.21 5 O 4066 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 174": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 794": "NH1" <-> "NH2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1022": "NH1" <-> "NH2" Residue "A PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1099": "NH1" <-> "NH2" Residue "A ARG 1236": "NH1" <-> "NH2" Residue "A ARG 1242": "NH1" <-> "NH2" Residue "A TYR 1344": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22068 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: "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: "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: 73 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: "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: 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: "A" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 308 Unusual residues: {' CA': 3, '3PE': 8, 'C5U': 1, 'NAG': 1, 'PC1': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'3PE:plan-1': 1, '3PE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 116 Unusual residues: {'ETA': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 15.56, per 1000 atoms: 0.71 Number of scatterers: 22068 At special positions: 0 Unit cell: (171.287, 184.379, 164.741, 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 9 15.00 O 4066 8.00 N 3596 7.00 C 14268 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=2.23 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=1.78 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.02 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.36 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=1.50 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.04 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 "HETATM21968 O5 NAG F1104 .*. O " rejected from bonding due to valence issues. Atom "HETATM21996 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 1 " - " NAG L 2 " 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 F1125 " NAG-ASN " NAG A1901 " - " ASN A 257 " " 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 F1125 " - " ASN F 827 " " 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 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.52 Conformation dependent library (CDL) restraints added in 5.3 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: 112 helices and 14 sheets defined 47.3% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.32 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 56 No H-bonds generated for 'chain 'A' and resid 53 through 56' Processing helix chain 'A' and resid 59 through 69 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 84 No H-bonds generated for 'chain 'A' and resid 81 through 84' Processing helix chain 'A' and resid 89 through 103 removed outlier: 3.641A pdb=" N VAL A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 121 through 143 removed outlier: 3.873A pdb=" N VAL A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 180 through 191 removed outlier: 4.395A pdb=" N VAL A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 218 removed outlier: 3.998A pdb=" N HIS A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 201 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 203 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 204 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 205 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE A 208 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 209 " --> pdb=" O MET A 206 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 210 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 211 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 213 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 removed outlier: 3.884A pdb=" N CYS A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.557A pdb=" N LEU A 298 " --> pdb=" O TRP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 323 through 345 Processing helix chain 'A' and resid 350 through 371 removed outlier: 3.935A 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) Processing helix chain 'A' and resid 420 through 430 Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.502A pdb=" N ALA A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 485 removed outlier: 3.531A pdb=" N HIS A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 4.015A pdb=" N PHE A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.858A 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 497 through 516 removed outlier: 3.522A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 3.922A 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: 3.714A pdb=" N GLU A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 No H-bonds generated for 'chain 'A' and resid 523 through 526' Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 534 through 541 removed outlier: 4.102A pdb=" N ILE A 538 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 540 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 557 removed outlier: 3.542A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 581 removed outlier: 3.792A pdb=" N LEU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 611 Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.744A pdb=" N ASN A 622 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 646 removed outlier: 3.554A pdb=" N ILE A 639 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 644 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 654 removed outlier: 3.614A pdb=" N LEU A 652 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 653 " --> pdb=" O ASN A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 662 Processing helix chain 'A' and resid 666 through 676 removed outlier: 3.564A pdb=" N THR A 671 " --> pdb=" O ALA A 667 " (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: 4.064A pdb=" N ARG A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 removed outlier: 4.125A pdb=" N HIS A 793 " --> pdb=" O ARG A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 805 Processing helix chain 'A' and resid 809 through 815 removed outlier: 3.897A 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: 3.667A 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: 3.677A 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: 3.637A 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: 3.671A pdb=" N LEU A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 900 removed outlier: 3.848A pdb=" N VAL A 898 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 899 " --> pdb=" O ILE A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 910 removed outlier: 3.826A pdb=" N ALA A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE A 908 " --> pdb=" O PRO A 904 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 910 " --> pdb=" O ARG A 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 903 through 910' Processing helix chain 'A' and resid 912 through 925 removed outlier: 3.710A pdb=" N VAL A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 925 " --> pdb=" O VAL A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 950 removed outlier: 3.596A pdb=" N GLN A 948 " --> pdb=" O CYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 978 No H-bonds generated for 'chain 'A' and resid 976 through 978' Processing helix chain 'A' and resid 1000 through 1011 Processing helix chain 'A' and resid 1016 through 1024 Processing helix chain 'A' and resid 1039 through 1051 removed outlier: 3.742A pdb=" N ILE A1043 " --> pdb=" O GLU A1040 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A1044 " --> pdb=" O MET A1041 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A1046 " --> pdb=" O ILE A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1069 removed outlier: 3.764A pdb=" N PHE A1063 " --> pdb=" O ILE A1059 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1094 removed outlier: 3.763A pdb=" N CYS A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A1090 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR A1091 " --> pdb=" O GLN A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 3.593A pdb=" N VAL A1114 " --> pdb=" O GLN A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1124 removed outlier: 3.544A pdb=" N LEU A1123 " --> pdb=" O TYR A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1136 removed outlier: 3.678A pdb=" N ILE A1133 " --> pdb=" O MET A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1172 removed outlier: 3.566A pdb=" N ILE A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP A1151 " --> pdb=" O ASN A1147 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A1160 " --> pdb=" O ALA A1156 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A1165 " --> pdb=" O PHE A1161 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A1167 " --> pdb=" O LEU A1163 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A1171 " --> pdb=" O LEU A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1205 removed outlier: 3.650A pdb=" N ASP A1196 " --> pdb=" O GLY A1192 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A1203 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR A1204 " --> pdb=" O SER A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1238 Processing helix chain 'A' and resid 1241 through 1247 removed outlier: 3.508A pdb=" N ILE A1244 " --> pdb=" O MET A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1265 removed outlier: 3.512A pdb=" N LEU A1256 " --> pdb=" O GLY A1252 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A1260 " --> pdb=" O LEU A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1288 removed outlier: 4.035A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A1287 " --> pdb=" O VAL A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1321 Processing helix chain 'A' and resid 1325 through 1331 Processing helix chain 'A' and resid 1355 through 1382 removed outlier: 3.640A pdb=" N PHE A1361 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A1367 " --> pdb=" O PHE A1364 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS A1368 " --> pdb=" O TYR A1365 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A1369 " --> pdb=" O MET A1366 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A1370 " --> pdb=" O LEU A1367 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A1371 " --> pdb=" O CYS A1368 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A1372 " --> pdb=" O ALA A1369 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A1373 " --> pdb=" O PHE A1370 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A1374 " --> pdb=" O LEU A1371 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE A1376 " --> pdb=" O ILE A1373 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A1377 " --> pdb=" O ASN A1374 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A1380 " --> pdb=" O VAL A1377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A1381 " --> pdb=" O ALA A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1387 No H-bonds generated for 'chain 'A' and resid 1384 through 1387' Processing helix chain 'A' and resid 1396 through 1408 removed outlier: 3.927A 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: 4.387A pdb=" N GLU A1408 " --> pdb=" O ALA A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1428 removed outlier: 3.559A pdb=" N ARG A1427 " --> pdb=" O VAL A1423 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1450 removed outlier: 4.022A 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: 4.751A pdb=" N PHE A1468 " --> pdb=" O ASN A1464 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A1469 " --> pdb=" O ALA A1465 " (cutoff:3.500A) removed outlier: 3.901A 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: 4.218A pdb=" N ARG A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A1492 " --> pdb=" O GLU A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1500 through 1505 removed outlier: 3.763A pdb=" N MET A1503 " --> pdb=" O ARG A1500 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A1505 " --> pdb=" O SER A1502 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 28 removed outlier: 4.440A pdb=" N VAL E 11 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR E 12 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE E 14 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE E 20 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.896A 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: 3.794A 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: 3.525A pdb=" N LEU E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 164 Proline residue: E 139 - end of helix removed outlier: 3.608A pdb=" N PHE E 143 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR E 144 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE E 146 " --> pdb=" O PHE E 143 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA E 147 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS E 150 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE E 152 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL E 153 " --> pdb=" O CYS E 150 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 155 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN E 160 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG E 164 " --> pdb=" O SER E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 201 removed outlier: 4.083A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 3.643A 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 '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: 3.652A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 109 removed outlier: 3.725A pdb=" N SER F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.737A 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: 5.131A pdb=" N ASP F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 4.306A 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: 3.797A pdb=" N GLU F 201 " --> pdb=" O LYS F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 250 removed outlier: 3.862A 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: 3.617A pdb=" N ARG F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.686A 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 335 through 346 Processing helix chain 'F' and resid 372 through 378 removed outlier: 3.940A 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: 3.837A 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: 3.606A pdb=" N ASP F 691 " --> pdb=" O ASN F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 721 removed outlier: 3.839A 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: 4.106A 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: 3.561A 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: 3.506A 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: 4.334A pdb=" N LYS F1051 " --> pdb=" O CYS F1047 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLN F1052 " --> pdb=" O ASP F1048 " (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: 4.198A pdb=" N GLU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.992A 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: 3.619A 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: 3.702A pdb=" N MET C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 3.853A 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: 3.563A pdb=" N LEU C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.910A 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 403 removed outlier: 4.053A pdb=" N GLN C 398 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 3.517A 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: 3.926A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.511A 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: 3.866A pdb=" N HIS C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU C 450 " --> pdb=" O LEU C 446 " (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 971 through 975 Processing sheet with id= C, first strand: chain 'E' and resid 48 through 50 removed outlier: 3.680A pdb=" N CYS E 57 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN E 79 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 68 through 72 Processing sheet with id= E, first strand: chain 'F' and resid 167 through 170 removed outlier: 4.289A 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: 6.417A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.331A 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: 6.647A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 411 through 415 removed outlier: 3.643A pdb=" N TYR F 411 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE F 359 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.405A 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: 8.235A pdb=" N VAL F 260 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ALA F 294 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 513 through 517 Processing sheet with id= H, first strand: chain 'F' and resid 777 through 779 Processing sheet with id= I, first strand: chain 'F' and resid 992 through 994 removed outlier: 3.624A pdb=" N MET F 864 " --> pdb=" O ILE F 855 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 896 through 902 removed outlier: 3.619A pdb=" N GLN F 983 " --> pdb=" O ASN F 898 " (cutoff:3.500A) Processing sheet with id= K, 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: 3.594A pdb=" N GLN F 975 " --> pdb=" O CYS F 907 " (cutoff:3.500A) Processing sheet with id= L, 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: 5.700A pdb=" N LYS B 139 " --> pdb=" O TRP B 144 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TRP B 144 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 277 through 280 removed outlier: 5.654A pdb=" N ILE C 385 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL C 280 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL C 387 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE C 432 " --> pdb=" O TYR C 388 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 309 through 313 removed outlier: 6.649A pdb=" N LEU C 363 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N THR C 312 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA C 365 " --> pdb=" O THR C 312 " (cutoff:3.500A) No H-bonds generated for sheet with id= N 734 hydrogen bonds defined for protein. 1940 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: 7.87 Time building geometry restraints manager: 10.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3603 1.31 - 1.44: 6228 1.44 - 1.57: 12495 1.57 - 1.70: 20 1.70 - 1.84: 194 Bond restraints: 22540 Sorted by residual: bond pdb=" N21 C5U A1911 " pdb=" O22 C5U A1911 " ideal model delta sigma weight residual 1.205 1.397 -0.192 2.00e-02 2.50e+03 9.21e+01 bond pdb=" C05 C5U A1911 " pdb=" C06 C5U A1911 " ideal model delta sigma weight residual 1.355 1.524 -0.169 2.00e-02 2.50e+03 7.13e+01 bond pdb=" C08 C5U A1911 " pdb=" C09 C5U A1911 " ideal model delta sigma weight residual 1.357 1.523 -0.166 2.00e-02 2.50e+03 6.87e+01 bond pdb=" C21 3PE A1913 " pdb=" O21 3PE A1913 " ideal model delta sigma weight residual 1.316 1.458 -0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C21 3PE A1905 " pdb=" O21 3PE A1905 " ideal model delta sigma weight residual 1.316 1.458 -0.142 2.00e-02 2.50e+03 5.06e+01 ... (remaining 22535 not shown) Histogram of bond angle deviations from ideal: 93.51 - 102.55: 134 102.55 - 111.59: 9823 111.59 - 120.64: 12871 120.64 - 129.68: 7531 129.68 - 138.73: 157 Bond angle restraints: 30516 Sorted by residual: angle pdb=" N LYS F 478 " pdb=" CA LYS F 478 " pdb=" C LYS F 478 " ideal model delta sigma weight residual 111.28 121.89 -10.61 1.09e+00 8.42e-01 9.47e+01 angle pdb=" N MET A 493 " pdb=" CA MET A 493 " pdb=" C MET A 493 " ideal model delta sigma weight residual 111.28 121.17 -9.89 1.09e+00 8.42e-01 8.23e+01 angle pdb=" N ASP F 869 " pdb=" CA ASP F 869 " pdb=" C ASP F 869 " ideal model delta sigma weight residual 113.28 103.40 9.88 1.22e+00 6.72e-01 6.56e+01 angle pdb=" N LYS F 991 " pdb=" CA LYS F 991 " pdb=" C LYS F 991 " ideal model delta sigma weight residual 111.28 120.02 -8.74 1.09e+00 8.42e-01 6.43e+01 angle pdb=" N ASN F 325 " pdb=" CA ASN F 325 " pdb=" C ASN F 325 " ideal model delta sigma weight residual 111.71 120.85 -9.14 1.15e+00 7.56e-01 6.31e+01 ... (remaining 30511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.40: 13168 27.40 - 54.79: 598 54.79 - 82.19: 77 82.19 - 109.59: 27 109.59 - 136.98: 14 Dihedral angle restraints: 13884 sinusoidal: 5985 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 0.08 -86.08 1 1.00e+01 1.00e-02 8.94e+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 93.00 174.04 -81.04 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CB CYS A 245 " pdb=" SG CYS A 245 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual 93.00 20.47 72.53 1 1.00e+01 1.00e-02 6.72e+01 ... (remaining 13881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.765: 3482 0.765 - 1.530: 2 1.530 - 2.295: 0 2.295 - 3.060: 1 3.060 - 3.825: 1 Chirality restraints: 3486 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O3 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-02 2.50e+03 1.05e+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 1.42 -3.82 2.00e-01 2.50e+01 3.66e+02 chirality pdb=" C1 NAG L 1 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " pdb=" O4 NAG F1125 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.15e+02 ... (remaining 3483 not shown) Planarity restraints: 3825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F1125 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG F1125 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG F1125 " 0.103 2.00e-02 2.50e+03 pdb=" N2 NAG F1125 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG F1125 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.344 2.00e-02 2.50e+03 2.98e-01 1.11e+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 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F1104 " -0.315 2.00e-02 2.50e+03 2.67e-01 8.88e+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 " 0.462 2.00e-02 2.50e+03 pdb=" O7 NAG F1104 " -0.042 2.00e-02 2.50e+03 ... (remaining 3822 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 158 2.52 - 3.11: 16294 3.11 - 3.71: 32824 3.71 - 4.30: 47819 4.30 - 4.90: 78388 Nonbonded interactions: 175483 Sorted by model distance: nonbonded pdb=" O ASN F 480 " pdb=" ND2 ASN F 480 " model vdw 1.921 2.520 nonbonded pdb=" O3 NAG A1901 " pdb=" O7 NAG A1901 " model vdw 1.949 2.440 nonbonded pdb=" O GLY F 521 " pdb=" OD1 ASP F 562 " model vdw 2.209 3.040 nonbonded pdb=" N GLU F 792 " pdb=" OE1 GLU F 792 " model vdw 2.215 2.520 nonbonded pdb=" CD2 TYR A 117 " pdb=" OD1 ASN A 123 " model vdw 2.221 3.340 ... (remaining 175478 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' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'I' } 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.650 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 66.690 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.160 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: 92.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 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 : 0.016 0.192 22540 Z= 1.036 Angle : 1.544 15.262 30516 Z= 0.902 Chirality : 0.125 3.825 3486 Planarity : 0.014 0.300 3811 Dihedral : 16.263 136.983 8735 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 28.83 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.71 % Favored : 91.69 % Rotamer: Outliers : 6.11 % Allowed : 8.27 % Favored : 85.62 % Cbeta Deviations : 0.16 % 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: -3.65 (0.14), residues: 2659 helix: -2.61 (0.12), residues: 1309 sheet: -1.12 (0.35), residues: 221 loop : -2.29 (0.16), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.005 TRP E 32 HIS 0.026 0.004 HIS A 992 PHE 0.059 0.005 PHE A1289 TYR 0.093 0.005 TYR A 627 ARG 0.027 0.002 ARG A 594 *********************** 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 527 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 386 time to evaluate : 2.483 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 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