Starting phenix.real_space_refine on Thu Aug 8 21:12:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cro_30453/08_2024/7cro_30453.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cro_30453/08_2024/7cro_30453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cro_30453/08_2024/7cro_30453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cro_30453/08_2024/7cro_30453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cro_30453/08_2024/7cro_30453.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cro_30453/08_2024/7cro_30453.cif" } resolution = 3.75 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12063 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 336 5.49 5 S 30 5.16 5 C 8235 2.51 5 N 2762 2.21 5 O 3431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M GLU 59": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "I GLU 1040": "OE1" <-> "OE2" Residue "I ARG 1060": "NH1" <-> "NH2" Residue "I GLU 1101": "OE1" <-> "OE2" Residue "I ARG 1138": "NH1" <-> "NH2" Residue "I ARG 1160": "NH1" <-> "NH2" Residue "I GLU 1174": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14797 Number of models: 1 Model: "" Number of chains: 12 Chain: "M" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 833 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1, 'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 803 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1, 'NLE:plan-1': 2} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "A" Number of atoms: 3420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3420 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "K" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3468 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "I" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1731 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 13, 'TRANS': 205} Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13279 SG CYS I1016 59.525 92.667 71.375 1.00 74.39 S ATOM 13293 SG CYS I1018 62.061 90.974 69.713 1.00 91.22 S ATOM 13354 SG CYS I1026 59.637 93.550 67.996 1.00 85.87 S ATOM 13398 SG CYS I1032 58.228 89.896 69.399 1.00 68.52 S ATOM 13475 SG CYS I1041 54.903 93.115 69.256 1.00 88.65 S ATOM 13556 SG CYS I1052 56.026 94.118 66.143 1.00 84.65 S ATOM 14669 SG CYS I1191 35.820 63.419 55.974 1.00110.31 S ATOM 14686 SG CYS I1193 37.494 65.438 53.715 1.00103.59 S ATOM 14715 SG CYS I1198 38.607 61.460 51.915 1.00105.52 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N SAM I1401 " occ=0.93 ... (25 atoms not shown) pdb=" O4' SAM I1401 " occ=0.93 Time building chain proxies: 8.14, per 1000 atoms: 0.55 Number of scatterers: 14797 At special positions: 0 Unit cell: (136.08, 151.2, 173.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 30 16.00 P 336 15.00 O 3431 8.00 N 2762 7.00 C 8235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.41 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I1402 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1026 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1032 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1018 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1016 " pdb=" ZN I1403 " pdb="ZN ZN I1403 " - pdb=" SG CYS I1041 " pdb="ZN ZN I1403 " - pdb=" SG CYS I1052 " pdb=" ZN I1404 " pdb="ZN ZN I1404 " - pdb=" SG CYS I1191 " pdb="ZN ZN I1404 " - pdb=" SG CYS I1193 " pdb="ZN ZN I1404 " - pdb=" SG CYS I1198 " Number of angles added : 6 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 59.4% alpha, 0.0% beta 114 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 5.50 Creating SS restraints... Processing helix chain 'M' and resid 44 through 57 removed outlier: 4.582A pdb=" N LEU M 48 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU M 50 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE M 51 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER M 57 " --> pdb=" O ARG M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 77 removed outlier: 3.616A pdb=" N LEU M 70 " --> pdb=" O PRO M 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL M 71 " --> pdb=" O PHE M 67 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG M 72 " --> pdb=" O GLN M 68 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 removed outlier: 4.050A pdb=" N NLE M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA M 91 " --> pdb=" O SER M 87 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU M 92 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN M 93 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU M 94 " --> pdb=" O NLE M 90 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA M 95 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU M 97 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN M 108 " --> pdb=" O PHE M 104 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU M 109 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS M 110 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 132 removed outlier: 4.195A pdb=" N ILE M 124 " --> pdb=" O NLE M 120 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN M 125 " --> pdb=" O PRO M 121 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 42 removed outlier: 4.943A pdb=" N GLY B 28 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N THR B 30 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS B 31 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 3.779A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.507A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.331A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.605A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 21' Processing helix chain 'C' and resid 26 through 36 removed outlier: 4.094A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 5.367A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 61 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 66 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 97 removed outlier: 3.776A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLU C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N GLU C 92 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 5.031A pdb=" N LEU C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 116' Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.754A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.654A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 120 removed outlier: 3.842A pdb=" N THR D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Proline residue: D 100 - end of helix removed outlier: 5.878A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 4.680A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.944A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.068A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N NLE E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU E 94 " --> pdb=" O NLE E 90 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 4.112A pdb=" N ILE E 124 " --> pdb=" O NLE E 120 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 41 removed outlier: 5.673A pdb=" N GLY F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N THR F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS F 31 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Proline residue: F 32 - end of helix Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.127A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.290A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.759A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 16 through 21' Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.920A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 72 removed outlier: 5.426A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 97 removed outlier: 3.753A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU G 91 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N GLU G 92 " --> pdb=" O ARG G 88 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU G 93 " --> pdb=" O ASN G 89 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 4.610A pdb=" N LEU G 116 " --> pdb=" O GLN G 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 112 through 116' Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.905A pdb=" N TYR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.982A pdb=" N SER H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N MET H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA H 74 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 121 removed outlier: 4.324A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR H 93 " --> pdb=" O ARG H 89 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG H 96 " --> pdb=" O GLN H 92 " (cutoff:3.500A) Proline residue: H 100 - end of helix removed outlier: 6.269A pdb=" N LEU H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYR H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 1009 through 1013 removed outlier: 4.262A pdb=" N ILE I1013 " --> pdb=" O ASP I1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1009 through 1013' Processing helix chain 'I' and resid 1032 through 1037 removed outlier: 4.038A pdb=" N LEU I1037 " --> pdb=" O LEU I1033 " (cutoff:3.500A) Processing helix chain 'I' and resid 1055 through 1060 removed outlier: 3.810A pdb=" N LYS I1059 " --> pdb=" O GLN I1055 " (cutoff:3.500A) Processing helix chain 'I' and resid 1098 through 1112 removed outlier: 3.514A pdb=" N ALA I1104 " --> pdb=" O GLU I1100 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA I1109 " --> pdb=" O ARG I1105 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU I1111 " --> pdb=" O LYS I1107 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASN I1112 " --> pdb=" O HIS I1108 " (cutoff:3.500A) Processing helix chain 'I' and resid 1135 through 1140 removed outlier: 4.470A pdb=" N PHE I1139 " --> pdb=" O ASN I1135 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N MET I1140 " --> pdb=" O TYR I1136 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1135 through 1140' 246 hydrogen bonds defined for protein. 738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 300 hydrogen bonds 600 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 5.29 Time building geometry restraints manager: 7.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2912 1.33 - 1.45: 4975 1.45 - 1.57: 7155 1.57 - 1.69: 670 1.69 - 1.81: 43 Bond restraints: 15755 Sorted by residual: bond pdb=" CA LYS I 998 " pdb=" C LYS I 998 " ideal model delta sigma weight residual 1.524 1.487 0.037 1.26e-02 6.30e+03 8.73e+00 bond pdb=" C2 SAM I1401 " pdb=" N3 SAM I1401 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" C8 SAM I1401 " pdb=" N7 SAM I1401 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" C2 SAM I1401 " pdb=" N1 SAM I1401 " ideal model delta sigma weight residual 1.329 1.380 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" N LYS I 998 " pdb=" CA LYS I 998 " ideal model delta sigma weight residual 1.457 1.424 0.033 1.41e-02 5.03e+03 5.54e+00 ... (remaining 15750 not shown) Histogram of bond angle deviations from ideal: 97.46 - 104.77: 1393 104.77 - 112.08: 8639 112.08 - 119.39: 4841 119.39 - 126.70: 6865 126.70 - 134.01: 990 Bond angle restraints: 22728 Sorted by residual: angle pdb=" O3' DA A 28 " pdb=" C3' DA A 28 " pdb=" C2' DA A 28 " ideal model delta sigma weight residual 111.50 100.64 10.86 1.50e+00 4.44e-01 5.24e+01 angle pdb=" N LYS I 995 " pdb=" CA LYS I 995 " pdb=" C LYS I 995 " ideal model delta sigma weight residual 111.03 116.38 -5.35 1.11e+00 8.12e-01 2.32e+01 angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 111.67 115.92 -4.25 9.20e-01 1.18e+00 2.13e+01 angle pdb=" N LYS I1124 " pdb=" CA LYS I1124 " pdb=" C LYS I1124 " ideal model delta sigma weight residual 109.96 103.55 6.41 1.50e+00 4.44e-01 1.83e+01 angle pdb=" C4' DA A 28 " pdb=" C3' DA A 28 " pdb=" O3' DA A 28 " ideal model delta sigma weight residual 110.00 115.85 -5.85 1.50e+00 4.44e-01 1.52e+01 ... (remaining 22723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 6949 34.78 - 69.56: 1614 69.56 - 104.34: 33 104.34 - 139.11: 0 139.11 - 173.89: 1 Dihedral angle restraints: 8597 sinusoidal: 5709 harmonic: 2888 Sorted by residual: dihedral pdb=" CA HIS E 39 " pdb=" C HIS E 39 " pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta harmonic sigma weight residual 180.00 155.32 24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" N ASP I1125 " pdb=" C ASP I1125 " pdb=" CA ASP I1125 " pdb=" CB ASP I1125 " ideal model delta harmonic sigma weight residual 122.80 133.29 -10.49 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" CA TYR I1062 " pdb=" C TYR I1062 " pdb=" N PRO I1063 " pdb=" CA PRO I1063 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 8594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2408 0.074 - 0.149: 153 0.149 - 0.223: 6 0.223 - 0.297: 0 0.297 - 0.371: 1 Chirality restraints: 2568 Sorted by residual: chirality pdb=" CA ASP I1125 " pdb=" N ASP I1125 " pdb=" C ASP I1125 " pdb=" CB ASP I1125 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA SER G 113 " pdb=" N SER G 113 " pdb=" C SER G 113 " pdb=" CB SER G 113 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA ILE I1127 " pdb=" N ILE I1127 " pdb=" C ILE I1127 " pdb=" CB ILE I1127 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.24e-01 ... (remaining 2565 not shown) Planarity restraints: 1723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS I 998 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO I 999 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO I 999 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 999 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE I1097 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C ILE I1097 " -0.045 2.00e-02 2.50e+03 pdb=" O ILE I1097 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP I1098 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG A 141 " 0.036 2.00e-02 2.50e+03 1.50e-02 6.75e+00 pdb=" N9 DG A 141 " -0.034 2.00e-02 2.50e+03 pdb=" C8 DG A 141 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DG A 141 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG A 141 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG A 141 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG A 141 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DG A 141 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG A 141 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG A 141 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG A 141 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG A 141 " -0.002 2.00e-02 2.50e+03 ... (remaining 1720 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 3 2.12 - 2.81: 3736 2.81 - 3.51: 18095 3.51 - 4.20: 36158 4.20 - 4.90: 54691 Nonbonded interactions: 112683 Sorted by model distance: nonbonded pdb=" NH2 ARG I1126 " pdb=" OG1 THR I1159 " model vdw 1.421 3.120 nonbonded pdb=" CE1 HIS M 39 " pdb=" OE1 GLU I1149 " model vdw 1.762 3.260 nonbonded pdb=" O CYS I1198 " pdb="ZN ZN I1404 " model vdw 2.086 2.230 nonbonded pdb=" O GLU I1091 " pdb=" OG SER I1137 " model vdw 2.154 3.040 nonbonded pdb=" O TYR F 51 " pdb=" NH1 ARG F 55 " model vdw 2.162 3.120 ... (remaining 112678 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 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = (chain 'C' and (resid 10 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and (resid 10 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 117 or (resid 118 and (name N or n \ ame CA or name C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 27 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 121)) } ncs_group { reference = chain 'E' selection = (chain 'M' and resid 37 through 134) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.93 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 47.180 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.006 0.057 15755 Z= 0.343 Angle : 0.738 10.857 22728 Z= 0.454 Chirality : 0.041 0.371 2568 Planarity : 0.005 0.071 1723 Dihedral : 27.717 173.892 6737 Min Nonbonded Distance : 1.421 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.45 % Allowed : 5.08 % Favored : 93.47 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.38 (0.19), residues: 966 helix: -3.15 (0.17), residues: 483 sheet: -4.20 (0.78), residues: 25 loop : -4.05 (0.21), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I1075 HIS 0.005 0.001 HIS M 39 PHE 0.010 0.002 PHE I1039 TYR 0.020 0.002 TYR H 118 ARG 0.003 0.000 ARG I1035 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.152 Fit side-chains REVERT: B 84 MET cc_start: 0.8368 (mmm) cc_final: 0.8150 (mmt) REVERT: D 90 GLU cc_start: 0.8160 (mp0) cc_final: 0.7465 (mp0) REVERT: E 73 GLU cc_start: 0.8006 (tt0) cc_final: 0.7650 (tt0) REVERT: E 106 ASP cc_start: 0.8539 (m-30) cc_final: 0.8321 (m-30) REVERT: E 123 ASP cc_start: 0.8151 (m-30) cc_final: 0.7753 (m-30) REVERT: F 91 LYS cc_start: 0.8912 (tttm) cc_final: 0.8661 (tptt) REVERT: G 118 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.6396 (tptp) outliers start: 12 outliers final: 5 residues processed: 133 average time/residue: 0.4037 time to fit residues: 70.0306 Evaluate side-chains 99 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain I residue 1006 TYR Chi-restraints excluded: chain I residue 1102 CYS Chi-restraints excluded: chain I residue 1103 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 0.0050 chunk 51 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 74 optimal weight: 50.0000 chunk 115 optimal weight: 9.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 39 HIS B 25 ASN E 125 GLN F 25 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 993 HIS I 997 ASN I1034 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15755 Z= 0.215 Angle : 0.584 7.282 22728 Z= 0.342 Chirality : 0.036 0.135 2568 Planarity : 0.004 0.054 1723 Dihedral : 30.420 174.752 4810 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.93 % Allowed : 9.19 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.22), residues: 966 helix: -2.00 (0.21), residues: 494 sheet: -4.23 (0.75), residues: 17 loop : -3.71 (0.22), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I1075 HIS 0.004 0.001 HIS M 39 PHE 0.017 0.001 PHE I1088 TYR 0.022 0.001 TYR I1062 ARG 0.003 0.000 ARG I1060 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8227 (mmm) cc_final: 0.8002 (mmt) REVERT: C 56 GLU cc_start: 0.8314 (tt0) cc_final: 0.8077 (tt0) REVERT: E 106 ASP cc_start: 0.8520 (m-30) cc_final: 0.8232 (m-30) REVERT: G 36 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8418 (ttmm) REVERT: I 1143 SER cc_start: 0.8721 (t) cc_final: 0.7980 (m) outliers start: 16 outliers final: 10 residues processed: 101 average time/residue: 0.3872 time to fit residues: 54.7431 Evaluate side-chains 94 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 1089 VAL Chi-restraints excluded: chain I residue 1102 CYS Chi-restraints excluded: chain I residue 1193 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1579 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: