Starting phenix.real_space_refine on Mon Mar 18 16:56:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjw_9515/03_2024/5gjw_9515_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjw_9515/03_2024/5gjw_9515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjw_9515/03_2024/5gjw_9515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjw_9515/03_2024/5gjw_9515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjw_9515/03_2024/5gjw_9515_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjw_9515/03_2024/5gjw_9515_updated.pdb" } resolution = 3.9 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 124 5.16 5 C 13944 2.51 5 N 3558 2.21 5 O 3932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1040": "OE1" <-> "OE2" Residue "A ARG 1175": "NH1" <-> "NH2" Residue "A ARG 1389": "NH1" <-> "NH2" Residue "A ARG 1416": "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 ARG 164": "NH1" <-> "NH2" Residue "F TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 546": "NH1" <-> "NH2" Residue "F TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 21561 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 10261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1291, 10261 Classifications: {'peptide': 1291} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 1250} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 94 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: "E" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1304 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain breaks: 4 Chain: "F" Number of atoms: 7572 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 942, 7556 Unusual residues: {'ETA': 1} Classifications: {'peptide': 941, 'undetermined': 1} Link IDs: {'LINK_CpN': 1, 'PTRANS': 40, 'TRANS': 900} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 942, 7556 Unusual residues: {'ETA': 1} Classifications: {'peptide': 941, 'undetermined': 1} Link IDs: {'LINK_CpN': 1, 'PTRANS': 40, 'TRANS': 900} Chain breaks: 6 bond proxies already assigned to first conformer: 7696 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {' CA': 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 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG F 315 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 315 " occ=0.50 Time building chain proxies: 15.13, per 1000 atoms: 0.70 Number of scatterers: 21561 At special positions: 0 Unit cell: (188.76, 171.6, 158.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 124 16.00 O 3932 8.00 N 3558 7.00 C 13944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.10 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.01 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.04 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.04 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.04 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.04 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.04 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.01 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " NAG L 3 " NAG-ASN " NAG A1901 " - " ASN A 257 " " NAG D 1 " - " ASN F 350 " " NAG F1204 " - " ASN F 326 " " NAG F1207 " - " ASN F 891 " " NAG F1214 " - " ASN F 94 " " NAG F1215 " - " ASN F 606 " " NAG F1220 " - " ASN F 784 " " NAG F1221 " - " ASN F1001 " " NAG F1222 " - " 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 " Time building additional restraints: 8.69 Conformation dependent library (CDL) restraints added in 5.2 seconds 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 17 sheets defined 49.8% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.24 Creating SS restraints... Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 51 through 69 removed outlier: 3.916A pdb=" N ILE A 56 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE A 57 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU A 58 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 62 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 63 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS A 65 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 107 removed outlier: 3.708A pdb=" N LYS A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 138 removed outlier: 3.666A pdb=" N GLY A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 167 through 178 removed outlier: 3.539A pdb=" N LEU A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.602A pdb=" N ASN A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 200 through 217 removed outlier: 3.503A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 removed outlier: 4.495A pdb=" N LEU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 311 through 318 Processing helix chain 'A' and resid 323 through 342 removed outlier: 4.010A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 347 No H-bonds generated for 'chain 'A' and resid 344 through 347' Processing helix chain 'A' and resid 349 through 375 removed outlier: 3.768A pdb=" N SER A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 432 through 436 removed outlier: 3.522A pdb=" N TRP A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 436' Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 459 through 486 removed outlier: 4.261A pdb=" N ASP A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 495 through 516 removed outlier: 3.690A pdb=" N ASP A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 537 removed outlier: 3.586A pdb=" N CYS A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.651A pdb=" N VAL A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 553 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 580 removed outlier: 4.259A pdb=" N ILE A 559 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ALA A 560 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 563 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 564 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 570 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 572 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 574 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 575 " --> pdb=" O ILE A 572 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 576 " --> pdb=" O PHE A 573 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 580 " --> pdb=" O GLY A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 611 removed outlier: 3.578A pdb=" N VAL A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 611 " --> pdb=" O VAL A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 627 removed outlier: 3.500A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 684 removed outlier: 3.691A pdb=" N ILE A 642 " --> pdb=" O ILE A 639 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 643 " --> pdb=" O TYR A 640 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A 644 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 646 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N CYS A 647 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY A 648 " --> pdb=" O PHE A 645 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 650 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 651 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 655 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 661 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A 663 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 668 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 669 " --> pdb=" O GLU A 666 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 671 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N SER A 672 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 673 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 676 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS A 677 " --> pdb=" O GLN A 674 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 679 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 680 " --> pdb=" O LYS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 796 removed outlier: 3.583A pdb=" N HIS A 793 " --> pdb=" O ARG A 789 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 794 " --> pdb=" O VAL A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 817 removed outlier: 4.089A pdb=" N ASN A 803 " --> pdb=" O THR A 799 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE A 804 " --> pdb=" O TRP A 800 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 851 removed outlier: 3.513A pdb=" N PHE A 835 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 858 No H-bonds generated for 'chain 'A' and resid 856 through 858' Processing helix chain 'A' and resid 862 through 882 removed outlier: 3.674A pdb=" N PHE A 868 " --> pdb=" O CYS A 864 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 869 " --> pdb=" O ARG A 865 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 870 " --> pdb=" O ASN A 866 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 909 removed outlier: 4.736A pdb=" N ARG A 900 " --> pdb=" O LEU A 896 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU A 902 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARG A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) Proline residue: A 904 - end of helix removed outlier: 4.942A pdb=" N ALA A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE A 908 " --> pdb=" O PRO A 904 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASN A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 950 removed outlier: 4.899A pdb=" N ARG A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR A 927 " --> pdb=" O VAL A 923 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A 930 " --> pdb=" O ARG A 926 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 943 " --> pdb=" O GLN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1011 removed outlier: 3.720A pdb=" N MET A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR A1009 " --> pdb=" O MET A1005 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A1010 " --> pdb=" O SER A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1024 removed outlier: 3.858A pdb=" N ARG A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1074 removed outlier: 3.752A pdb=" N ILE A1046 " --> pdb=" O ILE A1043 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A1047 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A1050 " --> pdb=" O ILE A1047 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A1053 " --> pdb=" O ILE A1050 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A1056 " --> pdb=" O ALA A1053 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY A1062 " --> pdb=" O ILE A1059 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A1065 " --> pdb=" O GLY A1062 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A1068 " --> pdb=" O ILE A1065 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY A1072 " --> pdb=" O GLN A1069 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A1073 " --> pdb=" O GLU A1070 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A1074 " --> pdb=" O GLN A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1094 removed outlier: 3.636A pdb=" N LEU A1093 " --> pdb=" O VAL A1089 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A1094 " --> pdb=" O GLN A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1116 removed outlier: 3.579A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A1114 " --> pdb=" O GLN A1110 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A1116 " --> pdb=" O TRP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1133 removed outlier: 3.578A pdb=" N ILE A1133 " --> pdb=" O MET A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1171 removed outlier: 3.582A pdb=" N ILE A1152 " --> pdb=" O HIS A1148 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN A1154 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1179 No H-bonds generated for 'chain 'A' and resid 1177 through 1179' Processing helix chain 'A' and resid 1181 through 1204 removed outlier: 3.522A pdb=" N PHE A1187 " --> pdb=" O ASN A1183 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A1191 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A1196 " --> pdb=" O GLY A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1248 removed outlier: 4.899A pdb=" N ARG A1236 " --> pdb=" O SER A1232 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A1237 " --> pdb=" O ALA A1233 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE A1238 " --> pdb=" O PHE A1234 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ARG A1239 " --> pdb=" O PHE A1235 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A1240 " --> pdb=" O ARG A1236 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG A1242 " --> pdb=" O PHE A1238 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU A1243 " --> pdb=" O ARG A1239 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE A1244 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS A1245 " --> pdb=" O MET A1241 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU A1246 " --> pdb=" O ARG A1242 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU A1247 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER A1248 " --> pdb=" O ILE A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1266 removed outlier: 3.886A pdb=" N THR A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU A1256 " --> pdb=" O GLY A1252 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A1265 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A1266 " --> pdb=" O LYS A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1288 removed outlier: 3.721A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A1275 " --> pdb=" O ALA A1271 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A1283 " --> pdb=" O PHE A1279 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A1287 " --> pdb=" O VAL A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.576A pdb=" N LEU A1314 " --> pdb=" O PRO A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1329 Processing helix chain 'A' and resid 1355 through 1376 removed outlier: 3.657A pdb=" N TYR A1358 " --> pdb=" O ASN A1355 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR A1359 " --> pdb=" O PHE A1356 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A1361 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE A1362 " --> pdb=" O TYR A1359 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A1366 " --> pdb=" O SER A1363 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A1367 " --> pdb=" O PHE A1364 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N CYS A1368 " --> pdb=" O TYR A1365 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE A1370 " --> pdb=" O LEU A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1387 removed outlier: 3.987A pdb=" N ASP A1382 " --> pdb=" O ALA A1378 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP A1385 " --> pdb=" O MET A1381 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TYR A1386 " --> pdb=" O ASP A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1397 through 1409 removed outlier: 3.750A pdb=" N LYS A1403 " --> pdb=" O LEU A1399 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A1404 " --> pdb=" O ASP A1400 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP A1406 " --> pdb=" O PHE A1402 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A1407 " --> pdb=" O LYS A1403 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A1408 " --> pdb=" O ALA A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1421 through 1427 Processing helix chain 'A' and resid 1443 through 1449 removed outlier: 4.670A pdb=" N LEU A1448 " --> pdb=" O ALA A1444 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1474 removed outlier: 3.704A pdb=" N THR A1473 " --> pdb=" O ALA A1469 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A1474 " --> pdb=" O LEU A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1497 removed outlier: 3.761A pdb=" N GLU A1488 " --> pdb=" O GLU A1484 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A1496 " --> pdb=" O ALA A1492 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1514 Proline residue: A1511 - end of helix Processing helix chain 'B' and resid 81 through 94 removed outlier: 4.824A pdb=" N GLU B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.545A pdb=" N ARG B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLN B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 304 removed outlier: 3.778A pdb=" N LEU C 297 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 302 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N HIS C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 344 through 360 removed outlier: 3.952A pdb=" N ARG C 359 " --> pdb=" O PHE C 355 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR C 360 " --> pdb=" O GLU C 356 " (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 Processing helix chain 'C' and resid 406 through 424 removed outlier: 5.291A pdb=" N HIS C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN C 413 " --> pdb=" O SER C 409 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN C 415 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 457 removed outlier: 3.589A pdb=" N TYR C 449 " --> pdb=" O HIS C 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 5 No H-bonds generated for 'chain 'E' and resid 2 through 5' Processing helix chain 'E' and resid 7 through 28 removed outlier: 4.083A pdb=" N VAL E 11 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR E 12 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 13 " --> pdb=" O ARG E 10 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS E 15 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 18 " --> pdb=" O CYS E 15 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE E 20 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA E 23 " --> pdb=" O ILE E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 127 removed outlier: 3.553A pdb=" N PHE E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE E 123 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 163 Proline residue: E 139 - end of helix removed outlier: 3.769A pdb=" N PHE E 143 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA E 147 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY E 148 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET E 158 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 203 removed outlier: 3.792A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER E 198 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 53 removed outlier: 3.547A pdb=" N THR F 48 " --> pdb=" O GLU F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 63 Processing helix chain 'F' and resid 78 through 111 removed outlier: 3.527A pdb=" N ASN F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA F 106 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 201 removed outlier: 3.905A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU F 191 " --> pdb=" O TRP F 187 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASP F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASP F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG F 199 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU F 200 " --> pdb=" O LYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'F' and resid 244 through 250 removed outlier: 3.709A pdb=" N GLN F 248 " --> pdb=" O PRO F 244 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY F 249 " --> pdb=" O TRP F 245 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA F 250 " --> pdb=" O TYR F 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 244 through 250' 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 284 removed outlier: 3.678A pdb=" N ILE F 274 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER F 279 " --> pdb=" O ARG F 275 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU F 283 " --> pdb=" O SER F 279 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 3.546A pdb=" N LEU F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 322 " --> pdb=" O LYS F 318 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 345 removed outlier: 3.779A pdb=" N GLU F 344 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN F 345 " --> pdb=" O PHE F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 378 Processing helix chain 'F' and resid 399 through 407 Processing helix chain 'F' and resid 421 through 424 No H-bonds generated for 'chain 'F' and resid 421 through 424' Processing helix chain 'F' and resid 427 through 437 removed outlier: 3.744A pdb=" N VAL F 431 " --> pdb=" O TYR F 428 " (cutoff:3.500A) Proline residue: F 435 - end of helix Processing helix chain 'F' and resid 496 through 502 removed outlier: 3.727A pdb=" N LEU F 502 " --> pdb=" O ASP F 498 " (cutoff:3.500A) 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 571 through 580 removed outlier: 3.877A pdb=" N GLU F 575 " --> pdb=" O ASP F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 643 through 651 Processing helix chain 'F' and resid 653 through 655 No H-bonds generated for 'chain 'F' and resid 653 through 655' Processing helix chain 'F' and resid 679 through 693 removed outlier: 3.560A pdb=" N PHE F 689 " --> pdb=" O ASN F 685 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE F 690 " --> pdb=" O PHE F 686 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP F 691 " --> pdb=" O ASN F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 704 through 721 removed outlier: 3.867A pdb=" N LEU F 709 " --> pdb=" O ILE F 705 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY F 713 " --> pdb=" O LEU F 709 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE F 714 " --> pdb=" O LEU F 710 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU F 718 " --> pdb=" O PHE F 714 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL F 719 " --> pdb=" O THR F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 765 through 772 removed outlier: 3.505A pdb=" N ARG F 769 " --> pdb=" O SER F 765 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) Processing helix chain 'F' and resid 821 through 832 removed outlier: 3.507A pdb=" N SER F 832 " --> pdb=" O PHE F 828 " (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: 3.509A pdb=" N HIS F 888 " --> pdb=" O SER F 884 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN F 891 " --> pdb=" O ARG F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 1046 through 1049 No H-bonds generated for 'chain 'F' and resid 1046 through 1049' Processing sheet with id= A, first strand: chain 'A' and resid 955 through 957 Processing sheet with id= B, first strand: chain 'A' and resid 972 through 975 removed outlier: 3.660A pdb=" N ARG A 986 " --> pdb=" O TYR A 972 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1416 through 1418 Processing sheet with id= D, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.602A pdb=" N PHE B 103 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE B 146 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS B 139 " --> pdb=" O TRP B 144 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TRP B 144 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 147 " --> pdb=" O GLY B 157 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 277 through 280 removed outlier: 5.902A pdb=" N ILE C 385 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C 280 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL C 387 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 432 " --> pdb=" O TYR C 388 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 309 through 314 removed outlier: 6.720A pdb=" N LEU C 363 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR C 312 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA C 365 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 314 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASP C 367 " --> pdb=" O VAL C 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 33 through 36 Processing sheet with id= H, first strand: chain 'E' and resid 48 through 50 Processing sheet with id= I, first strand: chain 'F' and resid 217 through 219 removed outlier: 3.798A pdb=" N VAL F 489 " --> pdb=" O GLY F 211 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 258 through 261 Processing sheet with id= K, first strand: chain 'F' and resid 359 through 362 removed outlier: 6.715A pdb=" N ARG F 385 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU F 362 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE F 387 " --> pdb=" O LEU F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 389 through 391 removed outlier: 6.737A pdb=" N TYR F 413 " --> pdb=" O SER F 390 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'F' and resid 587 through 595 Processing sheet with id= N, first strand: chain 'F' and resid 661 through 664 removed outlier: 3.816A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA F 734 " --> pdb=" O LYS F 818 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 777 through 779 removed outlier: 3.756A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 993 through 998 removed outlier: 4.000A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET F 864 " --> pdb=" O ILE F 855 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 896 through 902 removed outlier: 3.590A pdb=" N SER F 900 " --> pdb=" O GLN F 981 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.32 Time building geometry restraints manager: 9.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6543 1.34 - 1.46: 5688 1.46 - 1.59: 9614 1.59 - 1.72: 0 1.72 - 1.84: 191 Bond restraints: 22036 Sorted by residual: bond pdb=" CA ASP F 239 " pdb=" CB ASP F 239 " ideal model delta sigma weight residual 1.529 1.440 0.088 1.34e-02 5.57e+03 4.34e+01 bond pdb=" N LEU F 102 " pdb=" CA LEU F 102 " ideal model delta sigma weight residual 1.456 1.541 -0.084 1.31e-02 5.83e+03 4.13e+01 bond pdb=" N PRO F 527 " pdb=" CD PRO F 527 " ideal model delta sigma weight residual 1.473 1.562 -0.089 1.40e-02 5.10e+03 4.05e+01 bond pdb=" C PRO A1431 " pdb=" N PRO A1432 " ideal model delta sigma weight residual 1.335 1.409 -0.074 1.19e-02 7.06e+03 3.86e+01 bond pdb=" C ALA F 780 " pdb=" N PRO F 781 " ideal model delta sigma weight residual 1.330 1.407 -0.077 1.25e-02 6.40e+03 3.77e+01 ... (remaining 22031 not shown) Histogram of bond angle deviations from ideal: 86.55 - 97.45: 19 97.45 - 108.35: 1547 108.35 - 119.26: 16947 119.26 - 130.16: 11228 130.16 - 141.07: 132 Bond angle restraints: 29873 Sorted by residual: angle pdb=" N TYR F 661 " pdb=" CA TYR F 661 " pdb=" C TYR F 661 " ideal model delta sigma weight residual 109.25 86.55 22.70 1.53e+00 4.27e-01 2.20e+02 angle pdb=" N TYR E 176 " pdb=" CA TYR E 176 " pdb=" C TYR E 176 " ideal model delta sigma weight residual 108.76 87.47 21.29 1.69e+00 3.50e-01 1.59e+02 angle pdb=" N SER F 390 " pdb=" CA SER F 390 " pdb=" C SER F 390 " ideal model delta sigma weight residual 109.24 89.60 19.64 1.67e+00 3.59e-01 1.38e+02 angle pdb=" N GLN F 447 " pdb=" CA GLN F 447 " pdb=" C GLN F 447 " ideal model delta sigma weight residual 108.52 89.51 19.01 1.63e+00 3.76e-01 1.36e+02 angle pdb=" C VAL F 550 " pdb=" N GLN F 551 " pdb=" CA GLN F 551 " ideal model delta sigma weight residual 120.63 138.57 -17.94 1.61e+00 3.86e-01 1.24e+02 ... (remaining 29868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.12: 12965 23.12 - 46.24: 386 46.24 - 69.37: 71 69.37 - 92.49: 19 92.49 - 115.61: 11 Dihedral angle restraints: 13452 sinusoidal: 5611 harmonic: 7841 Sorted by residual: dihedral pdb=" CA VAL F 894 " pdb=" C VAL F 894 " pdb=" N TYR F 895 " pdb=" CA TYR F 895 " ideal model delta harmonic sigma weight residual 180.00 85.90 94.10 0 5.00e+00 4.00e-02 3.54e+02 dihedral pdb=" CA TYR F 220 " pdb=" C TYR F 220 " pdb=" N PRO F 221 " pdb=" CA PRO F 221 " ideal model delta harmonic sigma weight residual 180.00 106.42 73.58 0 5.00e+00 4.00e-02 2.17e+02 dihedral pdb=" CA GLU F 476 " pdb=" C GLU F 476 " pdb=" N ASN F 477 " pdb=" CA ASN F 477 " ideal model delta harmonic sigma weight residual -180.00 -106.47 -73.53 0 5.00e+00 4.00e-02 2.16e+02 ... (remaining 13449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3236 0.136 - 0.273: 185 0.273 - 0.409: 20 0.409 - 0.546: 4 0.546 - 0.682: 4 Chirality restraints: 3449 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN F 827 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C1 NAG F1220 " pdb=" ND2 ASN F 784 " pdb=" C2 NAG F1220 " pdb=" O5 NAG F1220 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA PRO A1310 " pdb=" N PRO A1310 " pdb=" C PRO A1310 " pdb=" CB PRO A1310 " both_signs ideal model delta sigma weight residual False 2.72 2.12 0.60 2.00e-01 2.50e+01 8.94e+00 ... (remaining 3446 not shown) Planarity restraints: 3760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 615 " 0.209 2.00e-02 2.50e+03 2.69e-01 9.04e+02 pdb=" CG ASN F 615 " -0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN F 615 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN F 615 " -0.448 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.330 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 350 " -0.117 2.00e-02 2.50e+03 2.24e-01 6.26e+02 pdb=" CG ASN F 350 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASN F 350 " -0.092 2.00e-02 2.50e+03 pdb=" ND2 ASN F 350 " 0.399 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.254 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR F 220 " 0.109 5.00e-02 4.00e+02 1.70e-01 4.61e+01 pdb=" N PRO F 221 " -0.294 5.00e-02 4.00e+02 pdb=" CA PRO F 221 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO F 221 " 0.094 5.00e-02 4.00e+02 ... (remaining 3757 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 122 2.45 - 3.07: 14292 3.07 - 3.68: 31436 3.68 - 4.29: 46488 4.29 - 4.90: 72869 Nonbonded interactions: 165207 Sorted by model distance: nonbonded pdb=" ND2 ASN A 269 " pdb=" CE2 TYR A 621 " model vdw 1.844 3.420 nonbonded pdb=" O PRO F 531 " pdb=" CG LYS F 532 " model vdw 2.056 3.440 nonbonded pdb=" CG2 ILE A1380 " pdb=" CE2 PHE A1384 " model vdw 2.141 3.760 nonbonded pdb=" OH TYR A 71 " pdb=" NH2 ARG A 165 " model vdw 2.169 2.520 nonbonded pdb=" CG ARG A 165 " pdb=" NH2 ARG A 168 " model vdw 2.179 3.520 ... (remaining 165202 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.700 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 62.430 Find NCS groups from input model: 0.620 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: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 0.012 0.134 22036 Z= 0.750 Angle : 1.514 22.704 29873 Z= 0.865 Chirality : 0.077 0.682 3449 Planarity : 0.009 0.170 3745 Dihedral : 12.658 115.611 8347 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 1.75 % Allowed : 12.76 % Favored : 85.50 % Rotamer: Outliers : 1.50 % Allowed : 3.27 % Favored : 95.22 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 5.61 % Twisted General : 1.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.28 (0.12), residues: 2638 helix: -3.69 (0.08), residues: 1283 sheet: -1.86 (0.29), residues: 271 loop : -3.55 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP A 459 HIS 0.012 0.003 HIS A 992 PHE 0.038 0.004 PHE F 363 TYR 0.067 0.005 TYR F 609 ARG 0.022 0.002 ARG F 769 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 727 time to evaluate : 2.411 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