Starting phenix.real_space_refine on Fri Mar 22 10:47:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbb_31877/03_2024/7vbb_31877_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbb_31877/03_2024/7vbb_31877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbb_31877/03_2024/7vbb_31877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbb_31877/03_2024/7vbb_31877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbb_31877/03_2024/7vbb_31877_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbb_31877/03_2024/7vbb_31877_neut.pdb" } resolution = 2.81 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= -0.003 sd= 0.136 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: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 45 5.49 5 Mg 1 5.21 5 S 220 5.16 5 C 20904 2.51 5 N 5784 2.21 5 O 6192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A ARG 722": "NH1" <-> "NH2" Residue "A PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 793": "NH1" <-> "NH2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A GLU 867": "OE1" <-> "OE2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A ASP 1011": "OD1" <-> "OD2" Residue "A GLU 1021": "OE1" <-> "OE2" Residue "A PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1055": "OE1" <-> "OE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A GLU 1098": "OE1" <-> "OE2" Residue "A GLU 1106": "OE1" <-> "OE2" Residue "A ARG 1110": "NH1" <-> "NH2" Residue "A ARG 1122": "NH1" <-> "NH2" Residue "A GLU 1130": "OE1" <-> "OE2" Residue "A ARG 1133": "NH1" <-> "NH2" Residue "A GLU 1164": "OE1" <-> "OE2" Residue "A GLU 1183": "OE1" <-> "OE2" Residue "A GLU 1292": "OE1" <-> "OE2" Residue "A GLU 1330": "OE1" <-> "OE2" Residue "A ARG 1340": "NH1" <-> "NH2" Residue "A GLU 1352": "OE1" <-> "OE2" Residue "A ARG 1500": "NH1" <-> "NH2" Residue "A GLU 1521": "OE1" <-> "OE2" Residue "A GLU 1575": "OE1" <-> "OE2" Residue "A GLU 1622": "OE1" <-> "OE2" Residue "A GLU 1624": "OE1" <-> "OE2" Residue "A GLU 1675": "OE1" <-> "OE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B GLU 638": "OE1" <-> "OE2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 754": "OE1" <-> "OE2" Residue "B GLU 835": "OE1" <-> "OE2" Residue "B GLU 845": "OE1" <-> "OE2" Residue "B GLU 955": "OE1" <-> "OE2" Residue "B GLU 964": "OE1" <-> "OE2" Residue "B GLU 987": "OE1" <-> "OE2" Residue "B GLU 989": "OE1" <-> "OE2" Residue "B PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1029": "NH1" <-> "NH2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C ARG 298": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 141": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "N GLU 33": "OE1" <-> "OE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N GLU 100": "OE1" <-> "OE2" Residue "N GLU 119": "OE1" <-> "OE2" Residue "N ARG 148": "NH1" <-> "NH2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "M GLU 100": "OE1" <-> "OE2" Residue "M GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33151 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1473, 11749 Classifications: {'peptide': 1473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 71, 'TRANS': 1401} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 8912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 8912 Classifications: {'peptide': 1123} Link IDs: {'PTRANS': 63, 'TRANS': 1059} Chain breaks: 1 Chain: "C" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2697 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain: "E" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1641 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 10, 'TRANS': 188} Chain breaks: 1 Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "H" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1176 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "I" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 447 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 863 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 379 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "N" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1105 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 24, 'TRANS': 126} Chain: "G" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1229 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "M" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 867 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "R" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 5} Link IDs: {'rna3p': 7} Chain: "T" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 514 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "U" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 281 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 455 SG CYS A 64 60.906 53.841 58.059 1.00 70.96 S ATOM 474 SG CYS A 67 63.491 53.402 55.902 1.00 70.13 S ATOM 529 SG CYS A 74 63.249 55.433 59.604 1.00 63.65 S ATOM 767 SG CYS A 104 63.093 106.051 47.103 1.00 76.34 S ATOM 789 SG CYS A 107 64.251 106.376 43.747 1.00 82.67 S ATOM 1491 SG CYS A 205 66.161 108.395 46.537 1.00 87.17 S ATOM 20214 SG CYS B1070 75.419 63.477 48.055 1.00 51.70 S ATOM 20236 SG CYS B1073 74.124 66.410 46.806 1.00 54.67 S ATOM 20370 SG CYS B1098 71.867 63.408 47.712 1.00 72.84 S ATOM 20391 SG CYS B1101 73.671 64.048 44.116 1.00 83.89 S ATOM 27287 SG CYS J 7 77.424 45.896 128.133 1.00 34.15 S ATOM 27311 SG CYS J 10 81.069 44.097 129.543 1.00 21.98 S ATOM 27575 SG CYS J 44 80.469 47.261 130.027 1.00 21.89 S ATOM 27581 SG CYS J 45 78.405 45.117 132.180 1.00 24.31 S ATOM 28651 SG CYS L 19 36.273 46.139 111.167 1.00 40.38 S ATOM 28787 SG CYS L 36 33.915 44.083 109.670 1.00 44.67 S ATOM 28813 SG CYS L 39 32.830 46.573 111.451 1.00 47.99 S Residues with excluded nonbonded symmetry interactions: 161 residue: pdb=" N GLY N 127 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 127 " occ=0.00 residue: pdb=" N GLY N 144 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 144 " occ=0.00 residue: pdb=" N GLY N 153 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 153 " occ=0.00 residue: pdb=" N GLY N 154 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 154 " occ=0.00 residue: pdb=" N SER G 46 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER G 46 " occ=0.00 residue: pdb=" N CYS G 47 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS G 47 " occ=0.00 residue: pdb=" N LEU G 48 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU G 48 " occ=0.00 residue: pdb=" N VAL G 49 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL G 49 " occ=0.00 residue: pdb=" N ALA G 50 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 50 " occ=0.00 residue: pdb=" N GLY G 51 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY G 51 " occ=0.00 residue: pdb=" N PRO G 52 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO G 52 " occ=0.00 residue: pdb=" N HIS G 53 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS G 53 " occ=0.00 ... (remaining 149 not shown) Time building chain proxies: 18.25, per 1000 atoms: 0.55 Number of scatterers: 33151 At special positions: 0 Unit cell: (156.6, 160.776, 176.436, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 220 16.00 P 45 15.00 Mg 1 11.99 O 6192 8.00 N 5784 7.00 C 20904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 14.58 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 64 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 205 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 107 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 104 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1101 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1073 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1070 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 44 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 7 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 39 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 36 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 19 " Number of angles added : 12 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7576 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 36 sheets defined 33.3% alpha, 12.6% beta 21 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 11.38 Creating SS restraints... Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 132 through 144 removed outlier: 4.667A pdb=" N TYR A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 removed outlier: 4.261A pdb=" N TYR A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.956A pdb=" N ALA A 179 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS A 180 " --> pdb=" O GLN A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 180' Processing helix chain 'A' and resid 184 through 199 removed outlier: 3.539A pdb=" N LYS A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.701A pdb=" N LYS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 296 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 322 through 348 Processing helix chain 'A' and resid 382 through 403 Processing helix chain 'A' and resid 404 through 407 removed outlier: 3.910A pdb=" N ASP A 407 " --> pdb=" O SER A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.642A pdb=" N LYS A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.830A pdb=" N TYR A 585 " --> pdb=" O ASN A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 611 removed outlier: 3.785A pdb=" N GLU A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 634 through 642 removed outlier: 3.567A pdb=" N GLY A 638 " --> pdb=" O HIS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 684 through 696 removed outlier: 3.810A pdb=" N ASN A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 removed outlier: 3.655A pdb=" N MET A 732 " --> pdb=" O PRO A 729 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYS A 733 " --> pdb=" O ASP A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 770 Processing helix chain 'A' and resid 770 through 792 removed outlier: 3.675A pdb=" N SER A 774 " --> pdb=" O GLY A 770 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 820 removed outlier: 3.607A pdb=" N THR A 820 " --> pdb=" O ILE A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 831 removed outlier: 3.772A pdb=" N ALA A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 851 Processing helix chain 'A' and resid 857 through 881 removed outlier: 3.846A pdb=" N ILE A 861 " --> pdb=" O ASP A 857 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 868 " --> pdb=" O LYS A 864 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 910 Processing helix chain 'A' and resid 944 through 948 Processing helix chain 'A' and resid 960 through 997 removed outlier: 3.939A pdb=" N SER A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1030 removed outlier: 3.657A pdb=" N THR A1029 " --> pdb=" O ILE A1026 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A1030 " --> pdb=" O PRO A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1043 Processing helix chain 'A' and resid 1043 through 1051 Processing helix chain 'A' and resid 1053 through 1060 removed outlier: 4.049A pdb=" N LEU A1057 " --> pdb=" O LEU A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1079 Processing helix chain 'A' and resid 1087 through 1092 Processing helix chain 'A' and resid 1095 through 1103 removed outlier: 4.499A pdb=" N ALA A1102 " --> pdb=" O GLU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1126 removed outlier: 4.041A pdb=" N GLN A1118 " --> pdb=" O SER A1114 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A1119 " --> pdb=" O PRO A1115 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU A1126 " --> pdb=" O ARG A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1140 removed outlier: 3.765A pdb=" N ALA A1140 " --> pdb=" O LYS A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.530A pdb=" N VAL A1149 " --> pdb=" O PRO A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1179 removed outlier: 3.801A pdb=" N THR A1165 " --> pdb=" O GLU A1161 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A1176 " --> pdb=" O GLN A1172 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A1179 " --> pdb=" O ALA A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1202 removed outlier: 3.949A pdb=" N THR A1194 " --> pdb=" O ASP A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1226 removed outlier: 3.758A pdb=" N LEU A1214 " --> pdb=" O ALA A1210 " (cutoff:3.500A) Proline residue: A1222 - end of helix Processing helix chain 'A' and resid 1244 through 1252 Processing helix chain 'A' and resid 1271 through 1286 removed outlier: 3.924A pdb=" N LYS A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A1280 " --> pdb=" O LYS A1276 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A1286 " --> pdb=" O LYS A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1293 No H-bonds generated for 'chain 'A' and resid 1291 through 1293' Processing helix chain 'A' and resid 1323 through 1331 removed outlier: 4.029A pdb=" N TYR A1326 " --> pdb=" O PRO A1323 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A1327 " --> pdb=" O HIS A1324 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLN A1328 " --> pdb=" O ALA A1325 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A1329 " --> pdb=" O TYR A1326 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A1330 " --> pdb=" O TYR A1327 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A1331 " --> pdb=" O GLN A1328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1323 through 1331' Processing helix chain 'A' and resid 1334 through 1345 Processing helix chain 'A' and resid 1345 through 1359 removed outlier: 4.116A pdb=" N MET A1351 " --> pdb=" O PHE A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1509 removed outlier: 3.640A pdb=" N ARG A1501 " --> pdb=" O ALA A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1547 Processing helix chain 'A' and resid 1585 through 1592 removed outlier: 4.968A pdb=" N LYS A1590 " --> pdb=" O GLU A1587 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A1592 " --> pdb=" O PHE A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1612 Processing helix chain 'A' and resid 1613 through 1631 removed outlier: 4.247A pdb=" N ARG A1619 " --> pdb=" O GLU A1615 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A1620 " --> pdb=" O ALA A1616 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A1631 " --> pdb=" O ASP A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1649 removed outlier: 3.758A pdb=" N LEU A1641 " --> pdb=" O ASP A1637 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A1643 " --> pdb=" O ARG A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1687 Processing helix chain 'A' and resid 1695 through 1702 removed outlier: 3.657A pdb=" N VAL A1702 " --> pdb=" O ALA A1698 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 51 removed outlier: 3.582A pdb=" N SER B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 46 " --> pdb=" O HIS B 42 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 61 removed outlier: 4.002A pdb=" N GLY B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.664A pdb=" N GLU B 158 " --> pdb=" O GLN B 154 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 159' Processing helix chain 'B' and resid 195 through 202 removed outlier: 3.677A pdb=" N LYS B 199 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR B 200 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY B 202 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 275 through 289 removed outlier: 3.831A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 319 through 332 removed outlier: 3.552A pdb=" N ILE B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 358 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 376 through 404 removed outlier: 3.635A pdb=" N GLU B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.561A pdb=" N MET B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 423 removed outlier: 3.666A pdb=" N THR B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 removed outlier: 4.091A pdb=" N PHE B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 431 " --> pdb=" O THR B 427 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 removed outlier: 3.652A pdb=" N TYR B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 removed outlier: 3.663A pdb=" N ALA B 479 " --> pdb=" O ALA B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 538 removed outlier: 3.653A pdb=" N CYS B 535 " --> pdb=" O PRO B 531 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.610A pdb=" N ILE B 640 " --> pdb=" O MET B 637 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE B 641 " --> pdb=" O GLU B 638 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET B 642 " --> pdb=" O GLN B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 637 through 642' Processing helix chain 'B' and resid 676 through 680 removed outlier: 3.560A pdb=" N ASN B 680 " --> pdb=" O SER B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 removed outlier: 3.655A pdb=" N ASN B 685 " --> pdb=" O GLN B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 730 Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 800 through 804 removed outlier: 3.838A pdb=" N LEU B 804 " --> pdb=" O PRO B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 924 removed outlier: 3.660A pdb=" N ARG B 923 " --> pdb=" O GLY B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 942 removed outlier: 4.199A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B 933 " --> pdb=" O LEU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 968 Processing helix chain 'B' and resid 1038 through 1046 Processing helix chain 'B' and resid 1050 through 1059 removed outlier: 3.592A pdb=" N LEU B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1125 removed outlier: 3.824A pdb=" N ARG B1117 " --> pdb=" O PRO B1113 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 248 through 256 removed outlier: 3.953A pdb=" N GLU C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 317 through 341 Processing helix chain 'E' and resid 5 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.718A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.936A pdb=" N LYS E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 4.289A pdb=" N ILE E 126 " --> pdb=" O PRO E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 removed outlier: 3.845A pdb=" N THR E 157 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.755A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 48 through 60 Processing helix chain 'K' and resid 93 through 128 removed outlier: 3.658A pdb=" N ASN K 101 " --> pdb=" O GLN K 97 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG K 128 " --> pdb=" O GLN K 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 36 Processing helix chain 'N' and resid 52 through 57 Processing helix chain 'N' and resid 99 through 102 Processing helix chain 'G' and resid 60 through 64 removed outlier: 3.785A pdb=" N LEU G 64 " --> pdb=" O PRO G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 74 removed outlier: 3.800A pdb=" N ARG G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 160 removed outlier: 3.738A pdb=" N GLU G 159 " --> pdb=" O PRO G 156 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN G 160 " --> pdb=" O LYS G 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 156 through 160' Processing helix chain 'M' and resid 35 through 39 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.518A pdb=" N ASN M 82 " --> pdb=" O LEU M 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1690 through 1691 removed outlier: 4.414A pdb=" N GLY A 14 " --> pdb=" O ASP B1133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 88 removed outlier: 10.825A pdb=" N LEU A 83 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N VAL A 303 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N LEU A 85 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE A 301 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.670A pdb=" N THR A 224 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 436 through 437 removed outlier: 4.076A pdb=" N ILE B1035 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 447 removed outlier: 6.041A pdb=" N CYS A 446 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE A 456 " --> pdb=" O ARG A 567 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 471 removed outlier: 4.136A pdb=" N MET A 496 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS A 541 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA A 494 " --> pdb=" O HIS A 541 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 708 Processing sheet with id=AA9, first strand: chain 'A' and resid 917 through 918 Processing sheet with id=AB1, first strand: chain 'A' and resid 1000 through 1001 Processing sheet with id=AB2, first strand: chain 'A' and resid 1562 through 1565 removed outlier: 3.686A pdb=" N VAL A1577 " --> pdb=" O ASN A1565 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A1266 " --> pdb=" O LEU A1578 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1288 through 1289 removed outlier: 3.717A pdb=" N VAL A1288 " --> pdb=" O TYR A1554 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A1554 " --> pdb=" O VAL A1288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1526 through 1528 removed outlier: 4.043A pdb=" N GLU I 51 " --> pdb=" O VAL A1299 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1713 through 1714 Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 68 removed outlier: 3.529A pdb=" N PHE B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP B 117 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA B 80 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 115 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 82 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS B 113 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 116 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE B 133 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 118 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LYS B 131 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N TRP B 120 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE B 129 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 122 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS B 127 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.506A pdb=" N LEU B 182 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET B 181 " --> pdb=" O CYS B 471 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 190 through 193 removed outlier: 5.364A pdb=" N TYR B 208 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN B 223 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE B 239 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 519 through 520 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 632 through 635 current: chain 'B' and resid 658 through 660 Processing sheet with id=AC1, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AC2, first strand: chain 'B' and resid 594 through 598 Processing sheet with id=AC3, first strand: chain 'B' and resid 695 through 696 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 695 through 696 current: chain 'B' and resid 913 through 915 removed outlier: 7.461A pdb=" N MET B 757 " --> pdb=" O SER B 894 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 896 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 759 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS B 882 " --> pdb=" O LEU B1002 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 712 through 714 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 771 through 780 current: chain 'B' and resid 847 through 855 removed outlier: 7.965A pdb=" N CYS B 847 " --> pdb=" O PRO B 874 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL B 849 " --> pdb=" O ARG B 872 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG B 872 " --> pdb=" O VAL B 849 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN B 851 " --> pdb=" O THR B 870 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N CYS B 866 " --> pdb=" O CYS B 855 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 866 through 874 current: chain 'L' and resid 25 through 26 Processing sheet with id=AC5, first strand: chain 'B' and resid 828 through 830 removed outlier: 3.516A pdb=" N TYR B 828 " --> pdb=" O PHE B 837 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 835 " --> pdb=" O ASN B 830 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1068 through 1070 Processing sheet with id=AC7, first strand: chain 'B' and resid 1079 through 1080 Processing sheet with id=AC8, first strand: chain 'C' and resid 13 through 14 removed outlier: 4.698A pdb=" N LEU C 236 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASP C 304 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N ARG C 234 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 173 through 176 removed outlier: 4.560A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU C 207 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN C 96 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASP C 209 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL C 94 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU C 211 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL C 92 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 167 through 168 removed outlier: 3.518A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 263 through 265 Processing sheet with id=AD3, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.170A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.523A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.561A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 90 through 91 removed outlier: 5.453A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 27 through 31 Processing sheet with id=AD8, first strand: chain 'N' and resid 18 through 20 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 18 through 20 current: chain 'N' and resid 76 through 85 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 76 through 85 current: chain 'N' and resid 105 through 107 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 105 through 107 current: chain 'M' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 68 through 72 current: chain 'M' and resid 98 through 111 Processing sheet with id=AD9, first strand: chain 'G' and resid 48 through 59 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 48 through 59 current: chain 'G' and resid 112 through 123 No H-bonds generated for sheet with id=AD9 1013 hydrogen bonds defined for protein. 2811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 13.79 Time building geometry restraints manager: 15.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5407 1.29 - 1.43: 8827 1.43 - 1.57: 19274 1.57 - 1.70: 90 1.70 - 1.84: 341 Bond restraints: 33939 Sorted by residual: bond pdb=" C CYS I 20 " pdb=" N SER I 21 " ideal model delta sigma weight residual 1.332 1.689 -0.356 1.40e-02 5.10e+03 6.47e+02 bond pdb=" C ARG M 66 " pdb=" N LEU M 67 " ideal model delta sigma weight residual 1.331 1.221 0.110 1.22e-02 6.72e+03 8.13e+01 bond pdb=" C PRO B 590 " pdb=" O PRO B 590 " ideal model delta sigma weight residual 1.246 1.176 0.070 8.50e-03 1.38e+04 6.75e+01 bond pdb=" C ALA M 61 " pdb=" N ALA M 62 " ideal model delta sigma weight residual 1.331 1.227 0.103 1.34e-02 5.57e+03 5.93e+01 bond pdb=" C ASN N 155 " pdb=" N PRO N 156 " ideal model delta sigma weight residual 1.329 1.418 -0.089 1.18e-02 7.18e+03 5.68e+01 ... (remaining 33934 not shown) Histogram of bond angle deviations from ideal: 86.78 - 98.09: 15 98.09 - 109.39: 4564 109.39 - 120.70: 30510 120.70 - 132.00: 10944 132.00 - 143.31: 44 Bond angle restraints: 46077 Sorted by residual: angle pdb=" O PHE I 13 " pdb=" C PHE I 13 " pdb=" N GLN I 14 " ideal model delta sigma weight residual 122.96 143.31 -20.35 1.26e+00 6.30e-01 2.61e+02 angle pdb=" O CYS I 20 " pdb=" C CYS I 20 " pdb=" N SER I 21 " ideal model delta sigma weight residual 123.22 104.82 18.40 1.14e+00 7.69e-01 2.60e+02 angle pdb=" N VAL C 164 " pdb=" CA VAL C 164 " pdb=" C VAL C 164 " ideal model delta sigma weight residual 112.12 98.62 13.50 8.40e-01 1.42e+00 2.58e+02 angle pdb=" CA PHE I 13 " pdb=" C PHE I 13 " pdb=" N GLN I 14 " ideal model delta sigma weight residual 115.46 90.41 25.05 1.57e+00 4.06e-01 2.54e+02 angle pdb=" C CYS J 10 " pdb=" CA CYS J 10 " pdb=" CB CYS J 10 " ideal model delta sigma weight residual 110.24 86.78 23.46 1.67e+00 3.59e-01 1.97e+02 ... (remaining 46072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 18010 18.03 - 36.06: 1828 36.06 - 54.10: 539 54.10 - 72.13: 143 72.13 - 90.16: 31 Dihedral angle restraints: 20551 sinusoidal: 8805 harmonic: 11746 Sorted by residual: dihedral pdb=" N GLN A 553 " pdb=" C GLN A 553 " pdb=" CA GLN A 553 " pdb=" CB GLN A 553 " ideal model delta harmonic sigma weight residual 122.80 150.82 -28.02 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" C CYS J 10 " pdb=" N CYS J 10 " pdb=" CA CYS J 10 " pdb=" CB CYS J 10 " ideal model delta harmonic sigma weight residual -122.60 -94.72 -27.88 0 2.50e+00 1.60e-01 1.24e+02 dihedral pdb=" C GLN A 553 " pdb=" N GLN A 553 " pdb=" CA GLN A 553 " pdb=" CB GLN A 553 " ideal model delta harmonic sigma weight residual -122.60 -150.39 27.79 0 2.50e+00 1.60e-01 1.24e+02 ... (remaining 20548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 4918 0.249 - 0.499: 177 0.499 - 0.748: 12 0.748 - 0.997: 0 0.997 - 1.247: 1 Chirality restraints: 5108 Sorted by residual: chirality pdb=" CA GLN A 553 " pdb=" N GLN A 553 " pdb=" C GLN A 553 " pdb=" CB GLN A 553 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.89e+01 chirality pdb=" CA PRO C 259 " pdb=" N PRO C 259 " pdb=" C PRO C 259 " pdb=" CB PRO C 259 " both_signs ideal model delta sigma weight residual False 2.72 1.98 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CB THR K 25 " pdb=" CA THR K 25 " pdb=" OG1 THR K 25 " pdb=" CG2 THR K 25 " both_signs ideal model delta sigma weight residual False 2.55 1.89 0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 5105 not shown) Planarity restraints: 5801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE I 13 " 0.025 2.00e-02 2.50e+03 7.11e-02 5.05e+01 pdb=" C PHE I 13 " -0.122 2.00e-02 2.50e+03 pdb=" O PHE I 13 " 0.056 2.00e-02 2.50e+03 pdb=" N GLN I 14 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 8 " 0.032 2.00e-02 2.50e+03 6.39e-02 4.09e+01 pdb=" C PHE J 8 " -0.111 2.00e-02 2.50e+03 pdb=" O PHE J 8 " 0.040 2.00e-02 2.50e+03 pdb=" N THR J 9 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET M 109 " 0.029 2.00e-02 2.50e+03 5.99e-02 3.58e+01 pdb=" C MET M 109 " -0.103 2.00e-02 2.50e+03 pdb=" O MET M 109 " 0.041 2.00e-02 2.50e+03 pdb=" N GLN M 110 " 0.034 2.00e-02 2.50e+03 ... (remaining 5798 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 125 2.45 - 3.06: 22356 3.06 - 3.68: 48185 3.68 - 4.29: 76835 4.29 - 4.90: 127366 Nonbonded interactions: 274867 Sorted by model distance: nonbonded pdb=" NH2 ARG B 180 " pdb=" OP1 G R -4 " model vdw 1.842 2.520 nonbonded pdb=" NH2 ARG A 418 " pdb=" OP1 DA T 13 " model vdw 1.978 2.520 nonbonded pdb=" OD1 ASP A 590 " pdb="MG MG A2003 " model vdw 1.982 2.170 nonbonded pdb=" OE1 GLN M 12 " pdb=" NE2 GLN M 98 " model vdw 2.008 2.520 nonbonded pdb=" NZ LYS A 408 " pdb=" CD2 LEU A 409 " model vdw 2.055 3.540 ... (remaining 274862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.96 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: 1.580 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: 8.970 Check model and map are aligned: 0.510 Set scattering table: 0.290 Process input model: 102.830 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 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 : 0.010 0.356 33939 Z= 0.643 Angle : 1.488 25.045 46077 Z= 1.046 Chirality : 0.101 1.247 5108 Planarity : 0.008 0.116 5801 Dihedral : 16.578 90.160 12975 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 28.27 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.65 % Favored : 90.95 % Rotamer: Outliers : 6.12 % Allowed : 7.34 % Favored : 86.54 % Cbeta Deviations : 2.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.12), residues: 4001 helix: -1.82 (0.13), residues: 1214 sheet: -1.90 (0.19), residues: 646 loop : -2.71 (0.12), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 9 HIS 0.021 0.002 HIS C 166 PHE 0.050 0.002 PHE B 75 TYR 0.045 0.002 TYR B 826 ARG 0.010 0.001 ARG G 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 764 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 PHE cc_start: 0.4968 (OUTLIER) cc_final: 0.4204 (t80) REVERT: A 409 LEU cc_start: 0.3735 (OUTLIER) cc_final: 0.2668 (pp) REVERT: A 454 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7506 (OUTLIER) REVERT: A 550 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7784 (mp) REVERT: A 635 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7420 (mtt) REVERT: A 860 MET cc_start: 0.7023 (tpt) cc_final: 0.6786 (ttp) REVERT: A 864 LYS cc_start: 0.7794 (mttt) cc_final: 0.7130 (tmtt) REVERT: A 963 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: A 1239 MET cc_start: 0.1161 (ptt) cc_final: 0.0233 (tpt) REVERT: A 1272 LYS cc_start: 0.6584 (OUTLIER) cc_final: 0.6020 (mmpt) REVERT: A 1317 LEU cc_start: 0.4614 (OUTLIER) cc_final: 0.4202 (mt) REVERT: A 1340 ARG cc_start: 0.4170 (OUTLIER) cc_final: 0.3507 (mmp80) REVERT: A 1342 MET cc_start: 0.5898 (mmm) cc_final: 0.5383 (mmm) REVERT: B 74 SER cc_start: 0.4059 (OUTLIER) cc_final: 0.3810 (t) REVERT: B 231 ASN cc_start: 0.6930 (OUTLIER) cc_final: 0.6480 (m110) REVERT: B 285 MET cc_start: 0.6188 (mtm) cc_final: 0.5931 (mtp) REVERT: B 337 LYS cc_start: 0.5341 (OUTLIER) cc_final: 0.5019 (mmtt) REVERT: B 345 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.6097 (tpp) REVERT: B 489 LEU cc_start: 0.8314 (tt) cc_final: 0.8027 (tt) REVERT: B 659 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: B 928 MET cc_start: 0.8088 (ttt) cc_final: 0.7885 (ttp) REVERT: C 44 ARG cc_start: 0.7304 (ttp80) cc_final: 0.6304 (ptt90) REVERT: C 48 ASN cc_start: 0.7146 (m110) cc_final: 0.6849 (m-40) REVERT: C 161 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6556 (pt0) REVERT: C 288 PHE cc_start: 0.6727 (m-10) cc_final: 0.6521 (m-10) REVERT: E 8 TYR cc_start: 0.7748 (t80) cc_final: 0.7548 (t80) REVERT: E 155 GLU cc_start: 0.5497 (mt-10) cc_final: 0.5261 (mm-30) REVERT: H 16 ASP cc_start: 0.7043 (t0) cc_final: 0.6335 (m-30) REVERT: I 15 SER cc_start: 0.7483 (OUTLIER) cc_final: 0.6904 (p) REVERT: I 17 LEU cc_start: 0.5171 (OUTLIER) cc_final: 0.4675 (mt) REVERT: L 49 THR cc_start: 0.7839 (p) cc_final: 0.7571 (p) REVERT: G 95 ASN cc_start: 0.0258 (OUTLIER) cc_final: -0.0314 (m-40) REVERT: G 104 ASP cc_start: 0.1765 (p0) cc_final: 0.1232 (p0) REVERT: M 99 MET cc_start: 0.4548 (ttm) cc_final: 0.3135 (mtt) outliers start: 217 outliers final: 39 residues processed: 918 average time/residue: 1.2767 time to fit residues: 1419.3357 Evaluate side-chains 539 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 483 time to evaluate : 3.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 963 GLU Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1272 LYS Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1340 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 429 PRO Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 114 PRO Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 169 MET Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 0.9990 chunk 304 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 315 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 191 optimal weight: 0.5980 chunk 234 optimal weight: 1.9990 chunk 365 optimal weight: 40.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 271 ASN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN A 381 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN A 486 ASN A 551 ASN A 557 HIS A 564 HIS A 586 ASN A 595 ASN A 597 HIS A 600 GLN A 617 GLN A 632 GLN A 652 HIS A 728 ASN A 753 HIS ** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 GLN A 850 HIS A 859 ASN A 877 ASN A 918 GLN ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 HIS A1068 HIS A1076 GLN A1109 ASN A1118 GLN A1136 GLN A1177 GLN A1313 GLN A1329 GLN A1579 ASN A1690 HIS A1717 GLN B 9 ASN B 97 ASN B 147 ASN B 150 ASN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS B 280 ASN B 313 ASN B 330 GLN B 468 HIS B 473 HIS B 523 GLN B 625 ASN B 709 ASN B 734 ASN B 846 ASN B 857 ASN ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 GLN ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 59 ASN C 127 GLN ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN N 88 GLN ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 33939 Z= 0.261 Angle : 0.753 11.445 46077 Z= 0.389 Chirality : 0.048 0.273 5108 Planarity : 0.005 0.059 5801 Dihedral : 12.576 83.681 5081 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.77 % Favored : 93.13 % Rotamer: Outliers : 5.70 % Allowed : 15.81 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.03 % 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: -2.33 (0.12), residues: 4001 helix: -0.68 (0.14), residues: 1210 sheet: -1.36 (0.19), residues: 661 loop : -2.16 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 120 HIS 0.007 0.001 HIS A 397 PHE 0.025 0.002 PHE E 73 TYR 0.036 0.002 TYR A 754 ARG 0.012 0.001 ARG B 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 542 time to evaluate : 3.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 PHE cc_start: 0.5677 (OUTLIER) cc_final: 0.4468 (t80) REVERT: A 348 GLU cc_start: 0.3926 (OUTLIER) cc_final: 0.3677 (tm-30) REVERT: A 409 LEU cc_start: 0.3172 (OUTLIER) cc_final: 0.2572 (pp) REVERT: A 607 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.7064 (mt-10) REVERT: A 864 LYS cc_start: 0.7710 (mttt) cc_final: 0.7218 (tmtt) REVERT: A 903 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8551 (ttmm) REVERT: A 963 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: A 969 MET cc_start: 0.8928 (mtp) cc_final: 0.8547 (mtp) REVERT: A 1239 MET cc_start: 0.1830 (ptt) cc_final: 0.0748 (tpt) REVERT: A 1272 LYS cc_start: 0.6675 (OUTLIER) cc_final: 0.6255 (mmtt) REVERT: A 1318 ARG cc_start: 0.3968 (ppp80) cc_final: 0.3655 (ttt-90) REVERT: A 1340 ARG cc_start: 0.4186 (OUTLIER) cc_final: 0.3353 (mmp80) REVERT: B 6 ARG cc_start: 0.7577 (tpt170) cc_final: 0.7210 (ttm170) REVERT: B 17 LYS cc_start: 0.7174 (ptpp) cc_final: 0.6558 (mmmt) REVERT: B 158 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6904 (pt0) REVERT: B 231 ASN cc_start: 0.7160 (OUTLIER) cc_final: 0.6801 (m110) REVERT: B 261 ASP cc_start: 0.7414 (m-30) cc_final: 0.7188 (m-30) REVERT: B 296 THR cc_start: 0.5642 (OUTLIER) cc_final: 0.5090 (p) REVERT: B 442 LYS cc_start: 0.6965 (mmtm) cc_final: 0.6300 (mptt) REVERT: B 659 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: B 680 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8581 (m-40) REVERT: B 694 GLN cc_start: 0.7601 (mt0) cc_final: 0.7347 (mm110) REVERT: B 781 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6748 (tt) REVERT: B 809 ASP cc_start: 0.6700 (m-30) cc_final: 0.6375 (m-30) REVERT: B 928 MET cc_start: 0.8219 (ttt) cc_final: 0.7951 (ttp) REVERT: C 44 ARG cc_start: 0.7175 (ttp80) cc_final: 0.6805 (ttp80) REVERT: C 133 THR cc_start: 0.7828 (OUTLIER) cc_final: 0.7584 (p) REVERT: E 8 TYR cc_start: 0.7940 (t80) cc_final: 0.7729 (t80) REVERT: E 121 MET cc_start: 0.5819 (OUTLIER) cc_final: 0.4998 (mmm) REVERT: H 13 LYS cc_start: 0.7672 (mmtp) cc_final: 0.7264 (mmtp) REVERT: L 49 THR cc_start: 0.8022 (p) cc_final: 0.7678 (p) outliers start: 202 outliers final: 65 residues processed: 675 average time/residue: 1.2404 time to fit residues: 1021.9995 Evaluate side-chains 522 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 441 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 963 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1011 ASP Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1272 LYS Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1340 ARG Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1710 THR Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 766 ARG Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1011 GLN Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain M residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** 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 306, in __init__ self.caller(self.refine_xyz) 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 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.4181 > 50: distance: 96 - 101: 18.124 distance: 101 - 102: 6.637 distance: 102 - 103: 11.040 distance: 102 - 105: 12.642 distance: 103 - 104: 9.850 distance: 103 - 112: 9.261 distance: 105 - 106: 32.390 distance: 106 - 107: 14.439 distance: 107 - 108: 7.922 distance: 108 - 109: 8.338 distance: 109 - 110: 4.833 distance: 109 - 111: 14.781 distance: 112 - 113: 34.341 distance: 113 - 114: 19.678 distance: 113 - 116: 21.347 distance: 114 - 122: 20.971 distance: 116 - 117: 26.261 distance: 117 - 118: 19.479 distance: 117 - 119: 18.645 distance: 118 - 120: 44.081 distance: 119 - 121: 31.654 distance: 120 - 121: 10.931 distance: 122 - 123: 24.061 distance: 123 - 124: 46.416 distance: 123 - 126: 26.869 distance: 124 - 125: 4.228 distance: 124 - 133: 31.373 distance: 126 - 127: 42.756 distance: 127 - 128: 51.134 distance: 128 - 129: 22.602 distance: 129 - 130: 4.009 distance: 130 - 131: 24.961 distance: 133 - 134: 25.547 distance: 134 - 135: 6.164 distance: 134 - 137: 10.697 distance: 135 - 136: 27.703 distance: 135 - 145: 16.515 distance: 137 - 138: 26.264 distance: 138 - 139: 23.130 distance: 138 - 140: 10.471 distance: 139 - 141: 4.129 distance: 140 - 142: 6.943 distance: 141 - 143: 9.630 distance: 142 - 143: 24.698 distance: 143 - 144: 6.371 distance: 145 - 146: 30.118 distance: 146 - 147: 27.730 distance: 146 - 149: 17.531 distance: 147 - 148: 13.724 distance: 147 - 156: 16.171 distance: 149 - 150: 11.086 distance: 150 - 151: 13.001 distance: 151 - 152: 23.515 distance: 152 - 153: 13.907 distance: 153 - 154: 17.109 distance: 153 - 155: 13.875 distance: 156 - 157: 16.955 distance: 157 - 158: 8.251 distance: 158 - 159: 33.572 distance: 158 - 163: 21.313 distance: 160 - 161: 13.514 distance: 160 - 162: 26.487 distance: 163 - 164: 13.677 distance: 164 - 165: 21.975 distance: 164 - 167: 15.503 distance: 165 - 166: 6.460 distance: 165 - 171: 16.628 distance: 167 - 168: 36.054 distance: 168 - 169: 24.447 distance: 168 - 170: 32.853 distance: 171 - 172: 11.927 distance: 172 - 173: 32.377 distance: 172 - 175: 17.505 distance: 173 - 174: 7.576 distance: 173 - 177: 41.555 distance: 175 - 176: 19.274 distance: 177 - 178: 10.090 distance: 178 - 179: 6.886 distance: 178 - 181: 23.009 distance: 179 - 180: 6.804 distance: 179 - 183: 31.927 distance: 181 - 182: 44.446 distance: 183 - 184: 12.907 distance: 184 - 185: 20.122 distance: 184 - 187: 37.095 distance: 185 - 186: 42.175 distance: 185 - 189: 23.062 distance: 187 - 188: 48.280