Starting phenix.real_space_refine on Mon Mar 18 18:27:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jp8_9867/03_2024/6jp8_9867_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jp8_9867/03_2024/6jp8_9867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jp8_9867/03_2024/6jp8_9867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jp8_9867/03_2024/6jp8_9867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jp8_9867/03_2024/6jp8_9867_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jp8_9867/03_2024/6jp8_9867_updated.pdb" } resolution = 2.7 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 S 126 5.16 5 C 14087 2.51 5 N 3587 2.21 5 O 3996 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 213": "OE1" <-> "OE2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 498": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 794": "NH1" <-> "NH2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A GLU 1014": "OE1" <-> "OE2" Residue "A ARG 1022": "NH1" <-> "NH2" Residue "A ARG 1099": "NH1" <-> "NH2" Residue "A TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1236": "NH1" <-> "NH2" Residue "A ARG 1242": "NH1" <-> "NH2" Residue "A TYR 1365": "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 "F TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F ARG 230": "NH1" <-> "NH2" Residue "F ARG 241": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 544": "NH1" <-> "NH2" Residue "F ARG 546": "NH1" <-> "NH2" Residue "F GLU 567": "OE1" <-> "OE2" Residue "F ARG 591": "NH1" <-> "NH2" Residue "F ARG 607": "NH1" <-> "NH2" Residue "F GLU 658": "OE1" <-> "OE2" Residue "F ARG 692": "NH1" <-> "NH2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 745": "NH1" <-> "NH2" Residue "F ARG 846": "NH1" <-> "NH2" Residue "F ARG 1004": "NH1" <-> "NH2" Residue "F GLU 1022": "OE1" <-> "OE2" Residue "F GLU 1069": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21801 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "B" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 710 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 91} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1367 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "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: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' CA': 2, 'C8U': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 102 Unusual residues: {'ETA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.22, per 1000 atoms: 0.65 Number of scatterers: 21801 At special positions: 0 Unit cell: (170.196, 182.197, 165.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 126 16.00 F 3 9.00 O 3996 8.00 N 3587 7.00 C 14087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.05 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.91 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.40 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.75 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.77 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.27 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.02 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=1.57 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM21715 O5 NAG F1104 .*. O " rejected from bonding due to valence issues. Atom "HETATM21743 O5 NAG F1114 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-3 " NAG D 1 " - " NAG D 2 " " NAG K 1 " - " NAG K 2 " " NAG L 2 " - " NAG L 3 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG F1104 " - " ASN F 326 " " NAG F1107 " - " ASN F 891 " " NAG F1114 " - " ASN F 92 " " NAG F1115 " - " ASN F 606 " " NAG F1120 " - " ASN F 784 " " NAG F1121 " - " ASN F1001 " " NAG F1122 " - " ASN F 988 " " NAG G 1 " - " ASN F 615 " " NAG H 1 " - " ASN F 186 " " NAG I 1 " - " ASN F 470 " " NAG J 1 " - " ASN F 898 " " NAG K 1 " - " ASN F 678 " " NAG L 1 " - " ASN F 827 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.62 Conformation dependent library (CDL) restraints added in 5.1 seconds 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5110 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 14 sheets defined 46.5% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.22 Creating SS restraints... 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: 4.088A 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: 3.895A pdb=" N LEU E 22 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA E 23 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 3.793A 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: 3.961A pdb=" N PHE E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE E 123 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 164 Proline residue: E 139 - end of helix removed outlier: 4.014A pdb=" N MET E 142 " --> pdb=" O ARG E 138 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE E 143 " --> pdb=" O PRO E 139 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER E 154 " --> pdb=" O CYS E 150 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER E 161 " --> pdb=" O VAL E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 201 removed outlier: 4.081A 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: 3.644A pdb=" N ILE E 197 " --> pdb=" O PHE E 193 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 96 removed outlier: 3.624A pdb=" N LYS B 83 " --> pdb=" O MET B 79 " (cutoff:3.500A) removed outlier: 4.196A 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: 3.684A pdb=" N ARG B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.991A pdb=" N ARG B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 303 removed outlier: 3.703A pdb=" N MET C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 297 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.911A pdb=" N HIS C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 356 removed outlier: 3.891A pdb=" N GLU C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'C' and resid 394 through 403 removed outlier: 4.052A pdb=" N GLN C 398 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 3.518A 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: 4.469A pdb=" N ALA C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 457 removed outlier: 3.867A pdb=" N HIS C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 52 through 70 removed outlier: 3.578A pdb=" N ILE A 57 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 88 Processing helix chain 'A' and resid 90 through 103 removed outlier: 3.718A pdb=" N SER A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 114 No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'A' and resid 121 through 142 removed outlier: 3.586A pdb=" N LEU A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.718A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 180 through 193 removed outlier: 3.725A pdb=" N VAL A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 218 Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 294 through 305 Processing helix chain 'A' and resid 311 through 320 removed outlier: 3.605A pdb=" N THR A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 346 removed outlier: 4.437A pdb=" N ARG A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 371 removed outlier: 3.607A pdb=" N ARG A 354 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TRP A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 429 removed outlier: 4.037A pdb=" N HIS A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP A 427 " --> pdb=" O TRP A 423 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 429 " --> pdb=" O CYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 439 through 450 removed outlier: 3.794A pdb=" N LEU A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 485 removed outlier: 3.752A pdb=" N ASN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 484 " --> pdb=" O LEU A 480 " (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 496 through 514 removed outlier: 4.535A pdb=" N CYS A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 503 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 541 removed outlier: 3.907A pdb=" N LEU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N THR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LYS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR A 541 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 581 removed outlier: 3.726A pdb=" N ASN A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 611 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 634 through 662 removed outlier: 3.526A pdb=" N VAL A 637 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 639 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 642 " --> pdb=" O ILE A 639 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 643 " --> pdb=" O TYR A 640 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 644 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 646 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS A 647 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 648 " --> pdb=" O PHE A 645 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A 649 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 650 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 652 " --> pdb=" O ASN A 649 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 653 " --> pdb=" O TYR A 650 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE A 656 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU A 657 " --> pdb=" O ASN A 654 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE A 659 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 660 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A 661 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 678 removed outlier: 3.728A pdb=" N ALA A 678 " --> pdb=" O GLN A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 685 No H-bonds generated for 'chain 'A' and resid 682 through 685' Processing helix chain 'A' and resid 791 through 794 No H-bonds generated for 'chain 'A' and resid 791 through 794' Processing helix chain 'A' and resid 802 through 817 removed outlier: 3.643A pdb=" N LEU A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 833 removed outlier: 3.542A pdb=" N ILE A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 833 " --> pdb=" O ASN A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 851 removed outlier: 3.826A pdb=" N THR A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 882 Processing helix chain 'A' and resid 893 through 896 No H-bonds generated for 'chain 'A' and resid 893 through 896' Processing helix chain 'A' and resid 898 through 905 removed outlier: 3.733A pdb=" N LEU A 902 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG A 903 " --> pdb=" O ARG A 900 " (cutoff:3.500A) Proline residue: A 904 - end of helix Processing helix chain 'A' and resid 907 through 910 No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 912 through 927 removed outlier: 3.727A pdb=" N HIS A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 917 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 950 removed outlier: 3.546A pdb=" N PHE A 940 " --> pdb=" O THR A 936 " (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: 3.589A pdb=" N ILE A1046 " --> pdb=" O ILE A1043 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A1047 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A1048 " --> pdb=" O PHE A1045 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A1051 " --> pdb=" O TYR A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1072 removed outlier: 4.239A pdb=" N PHE A1063 " --> pdb=" O ILE A1059 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A1064 " --> pdb=" O PHE A1060 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN A1071 " --> pdb=" O THR A1067 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A1072 " --> pdb=" O PHE A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1094 removed outlier: 3.593A pdb=" N CYS A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN A1090 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR A1091 " --> pdb=" O GLN A1087 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A1092 " --> pdb=" O CYS A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 4.054A pdb=" N VAL A1114 " --> pdb=" O GLN A1110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A1115 " --> pdb=" O VAL A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1136 removed outlier: 3.568A pdb=" N PHE A1125 " --> pdb=" O GLU A1121 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET A1129 " --> pdb=" O PHE A1125 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A1130 " --> pdb=" O ALA A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1147 No H-bonds generated for 'chain 'A' and resid 1144 through 1147' Processing helix chain 'A' and resid 1149 through 1171 removed outlier: 3.554A pdb=" N LEU A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN A1154 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1178 No H-bonds generated for 'chain 'A' and resid 1175 through 1178' Processing helix chain 'A' and resid 1181 through 1205 removed outlier: 3.567A pdb=" N ASP A1186 " --> pdb=" O TRP A1182 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A1196 " --> pdb=" O GLY A1192 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A1197 " --> pdb=" O SER A1193 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A1204 " --> pdb=" O SER A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1248 removed outlier: 3.532A pdb=" N PHE A1238 " --> pdb=" O PHE A1235 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A1242 " --> pdb=" O ARG A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1266 removed outlier: 3.589A pdb=" N SER A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1289 removed outlier: 4.050A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1321 Processing helix chain 'A' and resid 1325 through 1330 Processing helix chain 'A' and resid 1355 through 1382 removed outlier: 3.678A pdb=" N TYR A1358 " --> pdb=" O ASN A1355 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A1361 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A1362 " --> pdb=" O TYR A1359 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A1363 " --> pdb=" O TYR A1360 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS A1368 " --> pdb=" O TYR A1365 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A1369 " --> pdb=" O MET A1366 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A1372 " --> pdb=" O ALA A1369 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A1373 " --> pdb=" O PHE A1370 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A1374 " --> pdb=" O LEU A1371 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A1377 " --> pdb=" O ASN A1374 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET A1381 " --> pdb=" O ALA A1378 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A1382 " --> pdb=" O VAL A1379 " (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 1409 removed outlier: 3.753A pdb=" N ALA A1404 " --> pdb=" O ASP A1400 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1450 No H-bonds generated for 'chain 'A' and resid 1447 through 1450' Processing helix chain 'A' and resid 1463 through 1472 removed outlier: 3.611A pdb=" N LEU A1467 " --> pdb=" O PHE A1463 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N PHE A1468 " --> pdb=" O ASN A1464 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A1469 " --> pdb=" O ALA A1465 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A1471 " --> pdb=" O LEU A1467 " (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: 3.738A pdb=" N ALA F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 201 removed outlier: 3.919A pdb=" N GLU F 184 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 3.932A 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: 5.120A 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: 4.307A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 199 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.797A 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: 3.616A 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: 3.685A 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: 3.836A pdb=" N LEU F 432 " --> pdb=" O LEU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 437 No H-bonds generated for 'chain 'F' and resid 434 through 437' Processing helix chain 'F' and resid 440 through 443 Processing helix chain 'F' and resid 496 through 499 No H-bonds generated for 'chain 'F' and resid 496 through 499' Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 563 through 566 No H-bonds generated for 'chain 'F' and resid 563 through 566' Processing helix chain 'F' and resid 574 through 581 Processing helix chain 'F' and resid 641 through 646 Processing helix chain 'F' and resid 679 through 692 removed outlier: 3.686A pdb=" N PHE F 689 " --> pdb=" O ASN F 685 " (cutoff:3.500A) removed outlier: 3.635A 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: 3.532A 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: 3.507A pdb=" N GLU F 826 " --> pdb=" O ASN F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 880 No H-bonds generated for 'chain 'F' and resid 878 through 880' Processing helix chain 'F' and resid 883 through 891 removed outlier: 3.561A pdb=" N ASN F 891 " --> pdb=" O ARG F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 1024 through 1026 No H-bonds generated for 'chain 'F' and resid 1024 through 1026' Processing helix chain 'F' and resid 1046 through 1052 removed outlier: 4.335A 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 sheet with id= A, first strand: chain 'E' and resid 48 through 50 removed outlier: 3.681A pdb=" N CYS E 57 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN E 79 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.704A pdb=" N PHE B 103 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 146 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS B 139 " --> pdb=" O TRP B 144 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TRP B 144 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 432 through 434 removed outlier: 6.846A pdb=" N VAL C 364 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N LEU C 279 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LEU C 366 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 225 through 228 removed outlier: 3.969A pdb=" N THR A 225 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 262 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 260 " --> pdb=" O TYR A 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 955 through 957 Processing sheet with id= F, first strand: chain 'A' and resid 971 through 975 Processing sheet with id= G, first strand: chain 'F' and resid 68 through 72 Processing sheet with id= H, first strand: chain 'F' and resid 167 through 170 removed outlier: 4.288A 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: 4.756A 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: 4.636A 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= I, 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: 3.514A 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: 7.870A pdb=" N ILE F 258 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 6.888A 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= J, first strand: chain 'F' and resid 513 through 517 Processing sheet with id= K, first strand: chain 'F' and resid 777 through 779 Processing sheet with id= L, first strand: chain 'F' and resid 992 through 994 removed outlier: 3.618A pdb=" N MET F 864 " --> pdb=" O ILE F 855 " (cutoff:3.500A) Processing sheet with id= M, 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= N, 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) 760 hydrogen bonds defined for protein. 2075 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: 7.15 Time building geometry restraints manager: 9.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3540 1.30 - 1.44: 6130 1.44 - 1.57: 12415 1.57 - 1.70: 4 1.70 - 1.84: 194 Bond restraints: 22283 Sorted by residual: bond pdb=" N09 C8U A1901 " pdb=" O11 C8U A1901 " ideal model delta sigma weight residual 1.220 1.400 -0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" C02 C8U A1901 " pdb=" C03 C8U A1901 " ideal model delta sigma weight residual 1.351 1.521 -0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" C05 C8U A1901 " pdb=" C06 C8U A1901 " ideal model delta sigma weight residual 1.364 1.524 -0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" C ALA F 665 " pdb=" N PRO F 666 " ideal model delta sigma weight residual 1.334 1.206 0.128 2.34e-02 1.83e+03 2.99e+01 bond pdb=" C ALA F 780 " pdb=" N PRO F 781 " ideal model delta sigma weight residual 1.330 1.389 -0.059 1.22e-02 6.72e+03 2.32e+01 ... (remaining 22278 not shown) Histogram of bond angle deviations from ideal: 97.46 - 105.69: 515 105.69 - 113.92: 12315 113.92 - 122.15: 13387 122.15 - 130.38: 3881 130.38 - 138.61: 119 Bond angle restraints: 30217 Sorted by residual: angle pdb=" N HIS F 867 " pdb=" CA HIS F 867 " pdb=" C HIS F 867 " ideal model delta sigma weight residual 111.28 122.21 -10.93 1.09e+00 8.42e-01 1.01e+02 angle pdb=" N LYS F 478 " pdb=" CA LYS F 478 " pdb=" C LYS F 478 " ideal model delta sigma weight residual 111.28 121.91 -10.63 1.09e+00 8.42e-01 9.51e+01 angle pdb=" N ALA A 450 " pdb=" CA ALA A 450 " pdb=" C ALA A 450 " ideal model delta sigma weight residual 111.28 121.84 -10.56 1.09e+00 8.42e-01 9.39e+01 angle pdb=" N LEU A 217 " pdb=" CA LEU A 217 " pdb=" C LEU A 217 " ideal model delta sigma weight residual 111.36 120.71 -9.35 1.09e+00 8.42e-01 7.36e+01 angle pdb=" N ARG A 41 " pdb=" CA ARG A 41 " pdb=" C ARG A 41 " ideal model delta sigma weight residual 111.07 120.11 -9.04 1.07e+00 8.73e-01 7.15e+01 ... (remaining 30212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.39: 12979 27.39 - 54.78: 531 54.78 - 82.18: 89 82.18 - 109.57: 25 109.57 - 136.96: 14 Dihedral angle restraints: 13638 sinusoidal: 5739 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 0.03 -86.03 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS F 907 " pdb=" SG CYS F 907 " pdb=" SG CYS F 977 " pdb=" CB CYS F 977 " ideal model delta sinusoidal sigma weight residual 93.00 174.04 -81.04 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CB CYS F 844 " pdb=" SG CYS F 844 " pdb=" SG CYS F 853 " pdb=" CB CYS F 853 " ideal model delta sinusoidal sigma weight residual -86.00 -161.98 75.98 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 13635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.765: 3474 0.765 - 1.531: 2 1.531 - 2.296: 0 2.296 - 3.062: 1 3.062 - 3.827: 1 Chirality restraints: 3478 Sorted by residual: chirality pdb=" C1 NAG L 3 " pdb=" O3 NAG L 2 " pdb=" C2 NAG L 3 " pdb=" O5 NAG L 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-02 2.50e+03 1.04e+03 chirality pdb=" C1 NAG F1120 " pdb=" ND2 ASN F 784 " pdb=" C2 NAG F1120 " pdb=" O5 NAG F1120 " both_signs ideal model delta sigma weight residual False -2.40 1.43 -3.83 2.00e-01 2.50e+01 3.66e+02 chirality pdb=" C1 NAG D 2 " pdb=" O3 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.94e+02 ... (remaining 3475 not shown) Planarity restraints: 3807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.346 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG L 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.344 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 3804 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 114 2.48 - 3.09: 14288 3.09 - 3.69: 32901 3.69 - 4.30: 48578 4.30 - 4.90: 78052 Nonbonded interactions: 173933 Sorted by model distance: nonbonded pdb=" O ARG F 846 " pdb=" ND2 ASN F 847 " model vdw 1.877 2.520 nonbonded pdb=" O ASN F 480 " pdb=" ND2 ASN F 480 " model vdw 1.920 2.520 nonbonded pdb=" O LYS F 845 " pdb=" OG SER F 848 " model vdw 1.973 2.440 nonbonded pdb=" OD1 ASN F 891 " pdb=" O5 NAG F1107 " model vdw 2.082 3.040 nonbonded pdb=" CB PHE A 656 " pdb=" ND2 ASN A1058 " model vdw 2.134 3.520 ... (remaining 173928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 8.070 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 61.940 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.150 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5020 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.180 22283 Z= 0.853 Angle : 1.476 15.280 30217 Z= 0.871 Chirality : 0.124 3.827 3478 Planarity : 0.014 0.300 3794 Dihedral : 16.092 136.960 8489 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 25.96 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.22 % Favored : 92.33 % Rotamer: Outliers : 6.07 % Allowed : 7.50 % Favored : 86.44 % Cbeta Deviations : 0.31 % 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: -4.05 (0.14), residues: 2659 helix: -2.98 (0.11), residues: 1295 sheet: -1.24 (0.35), residues: 212 loop : -2.46 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.005 TRP E 32 HIS 0.027 0.003 HIS A 992 PHE 0.047 0.005 PHE A1289 TYR 0.071 0.005 TYR A 627 ARG 0.037 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 574 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 434 time to evaluate : 2.299 Fit side-chains 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