Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 10:30:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkb_11243/05_2023/6zkb_11243_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkb_11243/05_2023/6zkb_11243.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkb_11243/05_2023/6zkb_11243_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkb_11243/05_2023/6zkb_11243_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkb_11243/05_2023/6zkb_11243_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkb_11243/05_2023/6zkb_11243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkb_11243/05_2023/6zkb_11243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkb_11243/05_2023/6zkb_11243_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkb_11243/05_2023/6zkb_11243_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.012 sd= 0.052 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 P 32 5.49 5 S 280 5.16 5 C 25950 2.51 5 N 6285 2.21 5 O 7377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "4 ARG 2": "NH1" <-> "NH2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 103": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "k ARG 305": "NH1" <-> "NH2" Residue "l ARG 68": "NH1" <-> "NH2" Residue "l ARG 82": "NH1" <-> "NH2" Residue "l ARG 104": "NH1" <-> "NH2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 49": "NH1" <-> "NH2" Residue "o ARG 50": "NH1" <-> "NH2" Residue "o ARG 120": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "p ARG 56": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 51": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 19": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r ARG 37": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "s ARG 103": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 117": "NH1" <-> "NH2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 37": "NH1" <-> "NH2" Residue "t ARG 44": "NH1" <-> "NH2" Residue "t PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 64": "NH1" <-> "NH2" Residue "t ARG 92": "NH1" <-> "NH2" Residue "t ARG 121": "NH1" <-> "NH2" Residue "t ARG 128": "NH1" <-> "NH2" Residue "t ARG 134": "NH1" <-> "NH2" Residue "t ARG 149": "NH1" <-> "NH2" Residue "t ARG 176": "NH1" <-> "NH2" Residue "u ARG 19": "NH1" <-> "NH2" Residue "v ARG 70": "NH1" <-> "NH2" Residue "v TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 25": "NH1" <-> "NH2" Residue "w ARG 84": "NH1" <-> "NH2" Residue "z ARG 37": "NH1" <-> "NH2" Residue "z TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "J PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 39924 Number of models: 1 Model: "" Number of chains: 72 Chain: "4" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 334 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 7, 'TRANS': 32} Chain: "L" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4807 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 967 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "A" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 922 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2528 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Chain: "J" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 3, 'TRANS': 171} Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 236 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "M" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 288 Unusual residues: {'3PE': 1, 'CDL': 2, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "N" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 166 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "V" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 216 Unusual residues: {'3PE': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Chain: "o" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "p" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 23 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "4" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "M" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "N" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "V" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "W" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "X" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "Y" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "Z" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "l" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "m" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "n" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "o" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "p" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "q" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "r" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "s" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "u" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "v" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "w" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "x" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "y" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "z" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 21.15, per 1000 atoms: 0.53 Number of scatterers: 39924 At special positions: 0 Unit cell: (154.5, 145.5, 223.5, 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 280 16.00 P 32 15.00 O 7377 8.00 N 6285 7.00 C 25950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.04 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.03 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.03 Simple disulfide: pdb=" SG CYS s 58 " - pdb=" SG CYS s 89 " distance=2.02 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.55 Conformation dependent library (CDL) restraints added in 5.5 seconds 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 199 helices and 4 sheets defined 60.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain '4' and resid 8 through 14 removed outlier: 4.210A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 26 No H-bonds generated for 'chain '4' and resid 24 through 26' Processing helix chain 'L' and resid 3 through 23 removed outlier: 3.716A pdb=" N LEU L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.933A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.956A pdb=" N THR L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.803A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 157 removed outlier: 4.048A pdb=" N TRP L 157 " --> pdb=" O LEU L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.974A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 4.078A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.228A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.644A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.643A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.384A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 392 through 400 Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.585A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.781A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 508 removed outlier: 3.610A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 532 removed outlier: 3.891A pdb=" N TYR L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix No H-bonds generated for 'chain 'L' and resid 526 through 532' Processing helix chain 'L' and resid 536 through 546 removed outlier: 3.775A pdb=" N MET L 544 " --> pdb=" O MET L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.111A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 3.615A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 80 removed outlier: 3.656A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 109 removed outlier: 3.650A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.776A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 170 removed outlier: 3.710A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN M 144 " --> pdb=" O GLU M 141 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 176 through 179 No H-bonds generated for 'chain 'M' and resid 176 through 179' Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.829A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 219 Proline residue: M 217 - end of helix Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 248 removed outlier: 4.777A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 257 No H-bonds generated for 'chain 'M' and resid 254 through 257' Processing helix chain 'M' and resid 259 through 277 removed outlier: 4.075A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.008A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.039A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.818A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU M 398 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR M 409 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 4.119A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'M' and resid 456 through 458 No H-bonds generated for 'chain 'M' and resid 456 through 458' Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 121 Processing helix chain 'N' and resid 124 through 135 removed outlier: 3.799A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 144 Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.892A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 235 removed outlier: 4.246A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.586A pdb=" N ILE N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 270 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.690A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 removed outlier: 3.668A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.674A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 9 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 80 Processing helix chain 'V' and resid 86 through 104 Processing helix chain 'V' and resid 107 through 130 Processing helix chain 'W' and resid 16 through 45 removed outlier: 4.593A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 63 through 66 removed outlier: 3.935A pdb=" N TYR W 66 " --> pdb=" O HIS W 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 63 through 66' Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'X' and resid 8 through 21 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 69 removed outlier: 4.519A pdb=" N LYS X 69 " --> pdb=" O ILE X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 56 through 74 removed outlier: 4.333A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU Y 68 " --> pdb=" O GLN Y 64 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 56 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 116 removed outlier: 4.325A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 123 No H-bonds generated for 'chain 'Z' and resid 120 through 123' Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 171 Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 35 through 44 removed outlier: 4.816A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 118 Processing helix chain 'k' and resid 131 through 140 Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.335A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 186 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 210 through 214 Processing helix chain 'k' and resid 231 through 239 Processing helix chain 'k' and resid 253 through 263 Processing helix chain 'k' and resid 266 through 271 Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 8 No H-bonds generated for 'chain 'l' and resid 5 through 8' Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 42 Processing helix chain 'l' and resid 47 through 54 removed outlier: 4.127A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 66 Processing helix chain 'l' and resid 69 through 88 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 5 through 14 Processing helix chain 'm' and resid 16 through 34 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 38 through 47 removed outlier: 3.624A pdb=" N LEU m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 38 removed outlier: 4.040A pdb=" N ARG n 38 " --> pdb=" O LYS n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 45 through 52 removed outlier: 4.729A pdb=" N TRP n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ARG n 51 " --> pdb=" O ASN n 47 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR n 52 " --> pdb=" O GLU n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 88 Processing helix chain 'o' and resid 2 through 7 removed outlier: 3.753A pdb=" N GLN o 6 " --> pdb=" O THR o 3 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA o 7 " --> pdb=" O GLY o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 17 through 19 No H-bonds generated for 'chain 'o' and resid 17 through 19' Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 removed outlier: 3.866A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 50 removed outlier: 3.963A pdb=" N ALA p 31 " --> pdb=" O GLU p 27 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN p 32 " --> pdb=" O THR p 28 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 71 Processing helix chain 'p' and resid 83 through 93 removed outlier: 3.746A pdb=" N LEU p 91 " --> pdb=" O LEU p 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 91 Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 93 through 96 No H-bonds generated for 'chain 'q' and resid 93 through 96' Processing helix chain 'q' and resid 120 through 123 No H-bonds generated for 'chain 'q' and resid 120 through 123' Processing helix chain 'q' and resid 129 through 136 Processing helix chain 'q' and resid 138 through 141 No H-bonds generated for 'chain 'q' and resid 138 through 141' Processing helix chain 'r' and resid 5 through 24 Processing helix chain 'r' and resid 69 through 72 No H-bonds generated for 'chain 'r' and resid 69 through 72' Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 2 through 8 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 50 removed outlier: 4.225A pdb=" N HIS t 50 " --> pdb=" O ARG t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 93 through 95 No H-bonds generated for 'chain 't' and resid 93 through 95' Processing helix chain 't' and resid 100 through 105 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 140 removed outlier: 4.006A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'u' and resid 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' Processing helix chain 'u' and resid 61 through 64 No H-bonds generated for 'chain 'u' and resid 61 through 64' Processing helix chain 'v' and resid 6 through 8 No H-bonds generated for 'chain 'v' and resid 6 through 8' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 51 through 65 Processing helix chain 'w' and resid 70 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 3.781A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP w 88 " --> pdb=" O MET w 85 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA w 89 " --> pdb=" O GLN w 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA w 102 " --> pdb=" O TYR w 99 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 45 Processing helix chain 'y' and resid 16 through 31 Processing helix chain 'z' and resid 2 through 29 removed outlier: 3.506A pdb=" N VAL z 5 " --> pdb=" O TRP z 2 " (cutoff:3.500A) Proline residue: z 7 - end of helix removed outlier: 4.108A pdb=" N ILE z 18 " --> pdb=" O CYS z 15 " (cutoff:3.500A) Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 55 Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 19 through 22 No H-bonds generated for 'chain 'A' and resid 19 through 22' Processing helix chain 'A' and resid 56 through 71 removed outlier: 3.560A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 Proline residue: A 76 - end of helix removed outlier: 4.111A pdb=" N SER A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 2 through 31 removed outlier: 3.599A pdb=" N LEU H 9 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) Proline residue: H 12 - end of helix removed outlier: 3.871A pdb=" N VAL H 17 " --> pdb=" O ILE H 13 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA H 18 " --> pdb=" O LEU H 14 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 54 Processing helix chain 'H' and resid 68 through 83 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 111 Processing helix chain 'H' and resid 113 through 122 Processing helix chain 'H' and resid 126 through 154 removed outlier: 3.947A pdb=" N ALA H 135 " --> pdb=" O GLY H 131 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU H 154 " --> pdb=" O LEU H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 167 No H-bonds generated for 'chain 'H' and resid 164 through 167' Processing helix chain 'H' and resid 179 through 192 removed outlier: 4.142A pdb=" N ILE H 187 " --> pdb=" O MET H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 221 through 242 removed outlier: 3.898A pdb=" N ALA H 226 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR H 228 " --> pdb=" O PHE H 224 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA H 229 " --> pdb=" O MET H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 286 through 289 No H-bonds generated for 'chain 'H' and resid 286 through 289' Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.656A pdb=" N CYS J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU J 45 " --> pdb=" O CYS J 41 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 73 removed outlier: 4.215A pdb=" N VAL J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 108 removed outlier: 3.544A pdb=" N THR J 92 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL J 107 " --> pdb=" O MET J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 127 removed outlier: 3.845A pdb=" N ILE J 127 " --> pdb=" O ASP J 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 127' Processing helix chain 'J' and resid 138 through 148 removed outlier: 3.901A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 19 removed outlier: 3.906A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 51 removed outlier: 3.931A pdb=" N CYS K 32 " --> pdb=" O SER K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 84 removed outlier: 3.830A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 4.989A pdb=" N ALA K 72 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL K 79 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET K 80 " --> pdb=" O LEU K 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN K 83 " --> pdb=" O MET K 80 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR K 84 " --> pdb=" O VAL K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing sheet with id= A, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= B, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.538A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'k' and resid 123 through 125 removed outlier: 6.492A pdb=" N ILE k 25 " --> pdb=" O LEU k 124 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'J' and resid 112 through 115 1866 hydrogen bonds defined for protein. 5262 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: 11.28 Time building geometry restraints manager: 17.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6399 1.32 - 1.45: 10823 1.45 - 1.58: 22704 1.58 - 1.70: 65 1.70 - 1.83: 506 Bond restraints: 40497 Sorted by residual: bond pdb=" C13 ZMP X 101 " pdb=" N1 ZMP X 101 " ideal model delta sigma weight residual 1.487 1.339 0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" C10 ZMP X 101 " pdb=" S1 ZMP X 101 " ideal model delta sigma weight residual 1.852 1.715 0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.00e-02 1.00e+04 3.88e+01 bond pdb=" C16 ZMP X 101 " pdb=" N2 ZMP X 101 " ideal model delta sigma weight residual 1.474 1.349 0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" OA3 CDL W 201 " pdb=" PA1 CDL W 201 " ideal model delta sigma weight residual 1.529 1.471 0.058 1.00e-02 1.00e+04 3.34e+01 ... (remaining 40492 not shown) Histogram of bond angle deviations from ideal: 96.39 - 105.36: 1170 105.36 - 114.33: 23848 114.33 - 123.29: 27879 123.29 - 132.26: 1637 132.26 - 141.23: 138 Bond angle restraints: 54672 Sorted by residual: angle pdb=" CA3 CDL M 504 " pdb=" OA5 CDL M 504 " pdb=" PA1 CDL M 504 " ideal model delta sigma weight residual 121.27 128.12 -6.85 1.00e+00 1.00e+00 4.69e+01 angle pdb=" C MET H 91 " pdb=" N PRO H 92 " pdb=" CA PRO H 92 " ideal model delta sigma weight residual 127.00 141.23 -14.23 2.40e+00 1.74e-01 3.51e+01 angle pdb=" CA3 CDL L1003 " pdb=" OA5 CDL L1003 " pdb=" PA1 CDL L1003 " ideal model delta sigma weight residual 121.27 126.96 -5.69 1.00e+00 1.00e+00 3.24e+01 angle pdb=" C MET H 91 " pdb=" N PRO H 92 " pdb=" CD PRO H 92 " ideal model delta sigma weight residual 120.60 108.74 11.86 2.20e+00 2.07e-01 2.91e+01 angle pdb=" CB3 CDL W 201 " pdb=" OB5 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 121.27 115.91 5.36 1.00e+00 1.00e+00 2.88e+01 ... (remaining 54667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.72: 22953 18.72 - 37.43: 962 37.43 - 56.15: 311 56.15 - 74.86: 72 74.86 - 93.57: 8 Dihedral angle restraints: 24306 sinusoidal: 10515 harmonic: 13791 Sorted by residual: dihedral pdb=" CA ILE J 115 " pdb=" C ILE J 115 " pdb=" N VAL J 116 " pdb=" CA VAL J 116 " ideal model delta harmonic sigma weight residual -180.00 -116.00 -64.00 0 5.00e+00 4.00e-02 1.64e+02 dihedral pdb=" CA ILE H 13 " pdb=" C ILE H 13 " pdb=" N LEU H 14 " pdb=" CA LEU H 14 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CB CYS s 58 " pdb=" SG CYS s 58 " pdb=" SG CYS s 89 " pdb=" CB CYS s 89 " ideal model delta sinusoidal sigma weight residual -86.00 -127.65 41.65 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 24303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.033: 5918 1.033 - 2.067: 0 2.067 - 3.100: 0 3.100 - 4.134: 0 4.134 - 5.167: 5 Chirality restraints: 5923 Sorted by residual: chirality pdb=" CB4 CDL L1003 " pdb=" CB3 CDL L1003 " pdb=" CB6 CDL L1003 " pdb=" OB6 CDL L1003 " both_signs ideal model delta sigma weight residual False -2.57 2.59 -5.17 2.00e-01 2.50e+01 6.67e+02 chirality pdb=" CA4 CDL N 403 " pdb=" CA3 CDL N 403 " pdb=" CA6 CDL N 403 " pdb=" OA6 CDL N 403 " both_signs ideal model delta sigma weight residual False -2.57 2.58 -5.15 2.00e-01 2.50e+01 6.63e+02 chirality pdb=" CB4 CDL M 503 " pdb=" CB3 CDL M 503 " pdb=" CB6 CDL M 503 " pdb=" OB6 CDL M 503 " both_signs ideal model delta sigma weight residual False -2.57 2.57 -5.14 2.00e-01 2.50e+01 6.61e+02 ... (remaining 5920 not shown) Planarity restraints: 6677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE J 115 " -0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C ILE J 115 " 0.065 2.00e-02 2.50e+03 pdb=" O ILE J 115 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL J 116 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 106 " -0.023 2.00e-02 2.50e+03 2.23e-02 1.25e+01 pdb=" CG TRP A 106 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP A 106 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 106 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 106 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 106 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 106 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 106 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 106 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 106 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 53 " -0.017 2.00e-02 2.50e+03 2.49e-02 1.08e+01 pdb=" CG PHE K 53 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE K 53 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE K 53 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE K 53 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE K 53 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE K 53 " 0.001 2.00e-02 2.50e+03 ... (remaining 6674 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5785 2.76 - 3.29: 38326 3.29 - 3.83: 71683 3.83 - 4.36: 88673 4.36 - 4.90: 147264 Nonbonded interactions: 351731 Sorted by model distance: nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR H 114 " pdb=" O LEU J 61 " model vdw 2.223 2.440 nonbonded pdb=" O TYR W 28 " pdb=" OG SER w 67 " model vdw 2.257 2.440 nonbonded pdb=" O PHE u 40 " pdb=" OG SER u 44 " model vdw 2.273 2.440 nonbonded pdb=" O LEU N 337 " pdb=" OG1 THR N 340 " model vdw 2.274 2.440 ... (remaining 351726 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 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: 0.050 Extract box with map and model: 13.630 Check model and map are aligned: 0.580 Set scattering table: 0.320 Process input model: 95.420 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.008 0.148 40497 Z= 0.506 Angle : 0.988 14.229 54672 Z= 0.504 Chirality : 0.158 5.167 5923 Planarity : 0.008 0.072 6677 Dihedral : 12.406 93.575 15376 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.43 % Favored : 96.55 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.03 (0.10), residues: 4636 helix: -1.91 (0.07), residues: 2916 sheet: -1.85 (1.26), residues: 17 loop : -1.91 (0.13), residues: 1703 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 4153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1134 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 3 residues processed: 1136 average time/residue: 1.3015 time to fit residues: 1763.6386 Evaluate side-chains 762 residues out of total 4153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 759 time to evaluate : 2.856 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 2 average time/residue: 0.2947 time to fit residues: 4.8415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 385 optimal weight: 8.9990 chunk 346 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 358 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 217 optimal weight: 8.9990 chunk 266 optimal weight: 20.0000 chunk 415 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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: