Starting phenix.real_space_refine on Fri Aug 9 10:21:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5c_27208/08_2024/8d5c_27208.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5c_27208/08_2024/8d5c_27208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5c_27208/08_2024/8d5c_27208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5c_27208/08_2024/8d5c_27208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5c_27208/08_2024/8d5c_27208.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5c_27208/08_2024/8d5c_27208.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 135 5.16 5 C 13464 2.51 5 N 3669 2.21 5 O 4102 1.98 5 H 4739 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X ASP 612": "OD1" <-> "OD2" Residue "Y PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 584": "OE1" <-> "OE2" Residue "Y TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 634": "OE1" <-> "OE2" Residue "Z TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "P PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 26109 Number of models: 1 Model: "" Number of chains: 15 Chain: "X" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "Y" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "Z" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "A" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2952 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 356} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "B" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2952 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 356} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "C" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2952 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 356} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "H" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1790 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1646 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 105} Chain: "I" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1766 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 Chain: "J" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1646 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 105} Chain: "P" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1523 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 3 Chain: "Q" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1646 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 105} Time building chain proxies: 13.71, per 1000 atoms: 0.53 Number of scatterers: 26109 At special positions: 0 Unit cell: (145.41, 180.93, 198.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 O 4102 8.00 N 3669 7.00 C 13464 6.00 H 4739 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS X 598 " - pdb=" SG CYS X 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 605 " - pdb=" SG CYS C 501 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 84 " distance=2.03 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 84 " distance=2.03 Simple disulfide: pdb=" SG CYS F 130 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 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: 12.17 Conformation dependent library (CDL) restraints added in 4.5 seconds 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5050 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 44 sheets defined 19.0% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'X' and resid 529 through 547 removed outlier: 4.109A pdb=" N THR X 538 " --> pdb=" O SER X 534 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL X 539 " --> pdb=" O MET X 535 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY X 547 " --> pdb=" O LEU X 543 " (cutoff:3.500A) Processing helix chain 'X' and resid 568 through 593 removed outlier: 3.782A pdb=" N GLY X 572 " --> pdb=" O LEU X 568 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE X 573 " --> pdb=" O THR X 569 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA X 578 " --> pdb=" O LYS X 574 " (cutoff:3.500A) Processing helix chain 'X' and resid 618 through 625 removed outlier: 3.565A pdb=" N ILE X 622 " --> pdb=" O THR X 618 " (cutoff:3.500A) Processing helix chain 'X' and resid 627 through 635 Processing helix chain 'X' and resid 640 through 664 removed outlier: 3.918A pdb=" N THR X 644 " --> pdb=" O GLN X 640 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU X 663 " --> pdb=" O GLU X 659 " (cutoff:3.500A) Processing helix chain 'Y' and resid 529 through 546 removed outlier: 3.603A pdb=" N THR Y 538 " --> pdb=" O SER Y 534 " (cutoff:3.500A) Processing helix chain 'Y' and resid 565 through 567 No H-bonds generated for 'chain 'Y' and resid 565 through 567' Processing helix chain 'Y' and resid 568 through 593 removed outlier: 3.582A pdb=" N GLY Y 572 " --> pdb=" O LEU Y 568 " (cutoff:3.500A) Processing helix chain 'Y' and resid 618 through 625 removed outlier: 3.731A pdb=" N TRP Y 623 " --> pdb=" O ILE Y 619 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN Y 625 " --> pdb=" O GLU Y 621 " (cutoff:3.500A) Processing helix chain 'Y' and resid 627 through 635 Processing helix chain 'Y' and resid 638 through 664 removed outlier: 3.658A pdb=" N TYR Y 643 " --> pdb=" O THR Y 639 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR Y 644 " --> pdb=" O GLN Y 640 " (cutoff:3.500A) Processing helix chain 'Z' and resid 529 through 546 removed outlier: 3.695A pdb=" N VAL Z 539 " --> pdb=" O MET Z 535 " (cutoff:3.500A) Processing helix chain 'Z' and resid 567 through 593 removed outlier: 4.671A pdb=" N TRP Z 571 " --> pdb=" O GLN Z 567 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA Z 578 " --> pdb=" O LYS Z 574 " (cutoff:3.500A) Processing helix chain 'Z' and resid 618 through 625 Processing helix chain 'Z' and resid 627 through 635 Processing helix chain 'Z' and resid 638 through 664 removed outlier: 3.841A pdb=" N ILE Z 642 " --> pdb=" O TYR Z 638 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR Z 643 " --> pdb=" O THR Z 639 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR Z 644 " --> pdb=" O GLN Z 640 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU Z 662 " --> pdb=" O GLN Z 658 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU Z 663 " --> pdb=" O GLU Z 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 73 Processing helix chain 'A' and resid 100 through 113 removed outlier: 4.101A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 removed outlier: 4.185A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.798A pdb=" N THR A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 4.002A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 65 removed outlier: 3.977A pdb=" N ASP D 63 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 65 " --> pdb=" O TRP D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 79 Processing helix chain 'D' and resid 150 through 154 Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 99 through 116 removed outlier: 4.141A pdb=" N GLN B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 351 removed outlier: 4.508A pdb=" N GLU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 480 Processing helix chain 'E' and resid 75 through 79 removed outlier: 3.656A pdb=" N SER E 79 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 154 Processing helix chain 'C' and resid 64 through 73 Processing helix chain 'C' and resid 100 through 116 removed outlier: 3.667A pdb=" N MET C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 353 removed outlier: 4.616A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU C 351 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 4.007A pdb=" N THR C 373 " --> pdb=" O PRO C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.526A pdb=" N LEU C 390 " --> pdb=" O THR C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 480 removed outlier: 3.787A pdb=" N ASN C 478 " --> pdb=" O ASN C 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 65 removed outlier: 4.593A pdb=" N ASP F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 150 through 154 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.041A pdb=" N ALA L 83 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.738A pdb=" N ASP J 82 " --> pdb=" O GLY J 79 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA J 83 " --> pdb=" O GLU J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'P' and resid 61 through 64 removed outlier: 4.255A pdb=" N MET P 64 " --> pdb=" O GLU P 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 64' Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'Q' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'Z' and resid 604 through 609 removed outlier: 3.766A pdb=" N CYS Z 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR Z 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL C 36 " --> pdb=" O THR Z 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 39 removed outlier: 4.261A pdb=" N GLY A 495 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.519A pdb=" N LYS A 490 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.539A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.795A pdb=" N VAL A 120 " --> pdb=" O MET A 434 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 434 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 123 through 126 Processing sheet with id=AA7, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.592A pdb=" N THR A 257 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 384 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.592A pdb=" N THR A 257 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 384 " --> pdb=" O ARG A 419 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.466A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 361 Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.310A pdb=" N VAL D 4 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 40 removed outlier: 3.850A pdb=" N GLN D 40 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 99 through 102 Processing sheet with id=AB4, first strand: chain 'D' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'B' and resid 35 through 39 removed outlier: 3.611A pdb=" N GLY B 495 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 53 through 55 removed outlier: 3.527A pdb=" N PHE B 53 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS B 218 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.775A pdb=" N ILE B 84 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS B 487 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 196 through 202 removed outlier: 3.994A pdb=" N VAL B 120 " --> pdb=" O MET B 434 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 434 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 122 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 432 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 271 through 273 removed outlier: 9.978A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 11.738A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 469 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE B 468 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 359 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.539A pdb=" N ILE B 333 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 414 " --> pdb=" O ILE B 333 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 419 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR B 384 " --> pdb=" O ARG B 419 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 2 through 5 removed outlier: 4.126A pdb=" N LYS E 2 " --> pdb=" O GLU E 92 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS E 29 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TRP E 28 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU E 37 " --> pdb=" O TRP E 28 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 39 through 40 removed outlier: 3.709A pdb=" N GLN E 40 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 99 through 102 removed outlier: 6.523A pdb=" N GLN E 112 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN E 148 " --> pdb=" O GLN E 112 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 139 through 140 Processing sheet with id=AC6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.574A pdb=" N ILE C 84 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 125 through 126 Processing sheet with id=AC8, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.848A pdb=" N THR C 455 " --> pdb=" O ARG C 469 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG C 469 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.127A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 2 through 6 removed outlier: 3.961A pdb=" N LYS F 2 " --> pdb=" O GLU F 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS F 29 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 12 through 14 Processing sheet with id=AD3, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AD4, first strand: chain 'F' and resid 99 through 102 removed outlier: 6.226A pdb=" N GLN F 112 " --> pdb=" O GLN F 148 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN F 148 " --> pdb=" O GLN F 112 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 139 through 140 Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.515A pdb=" N ILE H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU H 46 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 14 removed outlier: 7.065A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR L 49 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.578A pdb=" N LEU I 82 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET I 20 " --> pdb=" O MET I 80 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA I 78 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR I 79 " --> pdb=" O THR I 70 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR I 70 " --> pdb=" O TYR I 79 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.102A pdb=" N ILE I 34 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE4, first strand: chain 'J' and resid 12 through 14 removed outlier: 6.147A pdb=" N VAL J 13 " --> pdb=" O LYS J 107 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.523A pdb=" N ALA P 78 " --> pdb=" O CYS P 22 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.522A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG P 40 " --> pdb=" O GLY P 44 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'Q' and resid 10 through 14 removed outlier: 3.619A pdb=" N ALA Q 84 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR Q 49 " --> pdb=" O MET Q 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR Q 49 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN Q 53 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 1815 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: 10.80 Time building geometry restraints manager: 13.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4739 1.04 - 1.23: 1539 1.23 - 1.43: 7737 1.43 - 1.63: 12356 1.63 - 1.83: 183 Bond restraints: 26554 Sorted by residual: bond pdb=" C TYR P 52 " pdb=" O TYR P 52 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.69e+00 bond pdb=" CA GLY I 44 " pdb=" C GLY I 44 " ideal model delta sigma weight residual 1.514 1.530 -0.015 1.41e-02 5.03e+03 1.19e+00 bond pdb=" CB PRO I 14 " pdb=" CG PRO I 14 " ideal model delta sigma weight residual 1.492 1.545 -0.053 5.00e-02 4.00e+02 1.11e+00 bond pdb=" N GLY I 44 " pdb=" CA GLY I 44 " ideal model delta sigma weight residual 1.449 1.463 -0.014 1.45e-02 4.76e+03 8.94e-01 bond pdb=" C GLN A 428 " pdb=" N GLY A 429 " ideal model delta sigma weight residual 1.331 1.317 0.013 1.46e-02 4.69e+03 8.55e-01 ... (remaining 26549 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.73: 625 106.73 - 113.56: 20564 113.56 - 120.40: 8828 120.40 - 127.24: 9997 127.24 - 134.08: 293 Bond angle restraints: 40307 Sorted by residual: angle pdb=" C ALA A 73 " pdb=" N CYS A 74 " pdb=" CA CYS A 74 " ideal model delta sigma weight residual 122.19 129.88 -7.69 2.30e+00 1.89e-01 1.12e+01 angle pdb=" C ALA C 73 " pdb=" N CYS C 74 " pdb=" CA CYS C 74 " ideal model delta sigma weight residual 121.54 127.77 -6.23 1.91e+00 2.74e-01 1.06e+01 angle pdb=" N GLU D 150 " pdb=" CA GLU D 150 " pdb=" C GLU D 150 " ideal model delta sigma weight residual 108.34 111.59 -3.25 1.31e+00 5.83e-01 6.17e+00 angle pdb=" N PHE H 51 " pdb=" CA PHE H 51 " pdb=" CB PHE H 51 " ideal model delta sigma weight residual 111.20 115.18 -3.98 1.62e+00 3.81e-01 6.03e+00 angle pdb=" N GLY I 106 " pdb=" CA GLY I 106 " pdb=" C GLY I 106 " ideal model delta sigma weight residual 111.85 114.38 -2.53 1.06e+00 8.90e-01 5.70e+00 ... (remaining 40302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13663 17.96 - 35.93: 983 35.93 - 53.89: 210 53.89 - 71.86: 63 71.86 - 89.82: 25 Dihedral angle restraints: 14944 sinusoidal: 6650 harmonic: 8294 Sorted by residual: dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -170.62 84.62 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -169.42 83.42 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 170.19 -77.19 1 1.00e+01 1.00e-02 7.47e+01 ... (remaining 14941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2247 0.032 - 0.065: 728 0.065 - 0.097: 167 0.097 - 0.130: 159 0.130 - 0.162: 9 Chirality restraints: 3310 Sorted by residual: chirality pdb=" CA ILE I 48 " pdb=" N ILE I 48 " pdb=" C ILE I 48 " pdb=" CB ILE I 48 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CG LEU I 45 " pdb=" CB LEU I 45 " pdb=" CD1 LEU I 45 " pdb=" CD2 LEU I 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA VAL I 37 " pdb=" N VAL I 37 " pdb=" C VAL I 37 " pdb=" CB VAL I 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 3307 not shown) Planarity restraints: 4424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 51 " -0.024 2.00e-02 2.50e+03 1.67e-02 8.34e+00 pdb=" CG PHE H 51 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE H 51 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE H 51 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 51 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 51 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE H 51 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE H 51 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE H 51 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE H 51 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE H 51 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE H 51 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 33 " -0.018 2.00e-02 2.50e+03 1.12e-02 5.02e+00 pdb=" CG TRP H 33 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP H 33 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP H 33 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 33 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 33 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 33 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 33 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP H 33 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP H 33 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP H 33 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 33 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 33 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP H 33 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 497 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 498 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 498 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 498 " -0.024 5.00e-02 4.00e+02 ... (remaining 4421 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 466 2.17 - 2.78: 22158 2.78 - 3.39: 44282 3.39 - 3.99: 62846 3.99 - 4.60: 89864 Nonbonded interactions: 219616 Sorted by model distance: nonbonded pdb=" OG1 THR I 70 " pdb="HE22 GLN I 81 " model vdw 1.567 2.450 nonbonded pdb=" OD1 ASP Q 27C" pdb=" HG SER Q 31 " model vdw 1.612 2.450 nonbonded pdb=" OE1 GLN I 39 " pdb=" HH TYR I 91 " model vdw 1.639 2.450 nonbonded pdb=" HG1 THR L 20 " pdb=" OD1 ASN L 74 " model vdw 1.643 2.450 nonbonded pdb=" HZ1 LYS J 39 " pdb=" OE1 GLN J 42 " model vdw 1.667 2.450 ... (remaining 219611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'H' and (resid 1 through 71 or resid 76 through 114)) selection = (chain 'I' and (resid 1 through 25 or resid 27 through 93 or (resid 94 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 95 \ through 114)) } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'Q' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.530 Extract box with map and model: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 75.290 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 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 : 0.002 0.053 21815 Z= 0.131 Angle : 0.476 7.689 29603 Z= 0.268 Chirality : 0.040 0.162 3310 Planarity : 0.003 0.043 3790 Dihedral : 13.149 89.821 7924 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 32.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.61 (0.16), residues: 2666 helix: 1.65 (0.28), residues: 405 sheet: -0.85 (0.19), residues: 708 loop : -2.02 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP H 33 HIS 0.005 0.001 HIS A 374 PHE 0.049 0.001 PHE H 51 TYR 0.015 0.001 TYR H 97 ARG 0.002 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 2.786 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7944 (mmm) cc_final: 0.7698 (mmp) REVERT: E 78 ASP cc_start: 0.6339 (t70) cc_final: 0.6095 (t70) REVERT: E 87 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6135 (tm-30) REVERT: F 14 LEU cc_start: 0.5947 (mm) cc_final: 0.5557 (mm) REVERT: F 70 ILE cc_start: 0.6836 (mm) cc_final: 0.6529 (mm) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.4031 time to fit residues: 196.4431 Evaluate side-chains 237 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 239 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: