Starting phenix.real_space_refine on Mon Sep 14 00:43:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7crq_30456/09_2026/7crq_30456.cif Found real_map, /net/cci-nas-00/data/ceres_data/7crq_30456/09_2026/7crq_30456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7crq_30456/09_2026/7crq_30456.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7crq_30456/09_2026/7crq_30456.cif" model { file = "/net/cci-nas-00/data/ceres_data/7crq_30456/09_2026/7crq_30456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7crq_30456/09_2026/7crq_30456.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7crq_30456/09_2026/7crq_30456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7crq_30456/09_2026/7crq_30456.map" } resolution = 3.15 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13425 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 6 6.06 5 P 336 5.49 5 S 50 5.16 5 C 9355 2.51 5 N 3122 2.21 5 O 3764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16633 Number of models: 1 Model: "" Number of chains: 14 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: {'NLE:plan-1': 3, 'ARG:plan': 1} 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: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'NLE:plan-1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 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: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} 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: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1755 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "L" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1755 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 12, 'TRANS': 209} 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} Chain: "L" 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 13324 SG CYS I1098 58.034 126.432 71.341 1.00 57.77 S ATOM 13338 SG CYS I1100 60.761 124.188 69.488 1.00 68.64 S ATOM 13439 SG CYS I1114 57.471 122.507 68.951 1.00 51.71 S ATOM 13397 SG CYS I1108 58.450 125.943 67.441 1.00 67.39 S ATOM 13518 SG CYS I1123 54.177 126.109 69.120 1.00 65.08 S ATOM 13557 SG CYS I1128 57.048 129.244 68.831 1.00 69.30 S ATOM 14720 SG CYS I1273 35.858 97.229 54.423 1.00 95.53 S ATOM 16475 SG CYS L1273 100.091 62.562 77.111 1.00 94.11 S ATOM 15079 SG CYS L1098 84.287 77.976 112.000 1.00 61.91 S ATOM 15093 SG CYS L1100 80.734 76.863 110.364 1.00 71.33 S ATOM 15152 SG CYS L1108 83.224 74.633 111.459 1.00 74.24 S ATOM 15194 SG CYS L1114 83.930 75.924 108.166 1.00 63.88 S ATOM 15152 SG CYS L1108 83.224 74.633 111.459 1.00 74.24 S ATOM 15312 SG CYS L1128 85.348 74.884 114.264 1.00 71.27 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N SAM I1501 " occ=0.93 ... (25 atoms not shown) pdb=" O4' SAM I1501 " occ=0.93 residue: pdb=" N SAM L1504 " occ=0.93 ... (25 atoms not shown) pdb=" O4' SAM L1504 " occ=0.93 Time building chain proxies: 3.13, per 1000 atoms: 0.19 Number of scatterers: 16633 At special positions: 0 Unit cell: (143.64, 180.36, 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 6 29.99 S 50 16.00 P 336 15.00 O 3764 8.00 N 3122 7.00 C 9355 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 7728 O5' DG A 87 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 358.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I1502 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1114 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1100 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1098 " pdb=" ZN I1503 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1108 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1128 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1123 " pdb=" ZN I1504 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1273 " pdb=" ZN L1501 " pdb="ZN ZN L1501 " - pdb=" SG CYS L1273 " pdb=" ZN L1502 " pdb="ZN ZN L1502 " - pdb=" SG CYS L1114 " pdb="ZN ZN L1502 " - pdb=" SG CYS L1108 " pdb="ZN ZN L1502 " - pdb=" SG CYS L1098 " pdb="ZN ZN L1502 " - pdb=" SG CYS L1100 " pdb=" ZN L1503 " pdb="ZN ZN L1503 " - pdb=" SG CYS L1108 " pdb="ZN ZN L1503 " - pdb=" SG CYS L1128 " Number of angles added : 6 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 51.5% alpha, 0.0% beta 121 base pairs and 288 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'M' and resid 44 through 57 removed outlier: 3.786A pdb=" N GLU M 50 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE M 51 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER M 57 " --> pdb=" O ARG M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 77 removed outlier: 3.647A pdb=" N LEU M 70 " --> pdb=" O PRO M 66 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL M 71 " --> pdb=" O PHE M 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG M 72 " --> pdb=" O GLN M 68 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.823A pdb=" N NLE M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA M 91 " --> pdb=" O SER M 87 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU M 92 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN M 93 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU M 94 " --> pdb=" O NLE M 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA M 95 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU M 97 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU M 105 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN M 108 " --> pdb=" O PHE M 104 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU M 109 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS M 110 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 132 removed outlier: 4.136A pdb=" N ILE M 124 " --> pdb=" O NLE M 120 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN M 125 " --> pdb=" O PRO M 121 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 42 removed outlier: 4.919A pdb=" N GLY B 28 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N THR B 30 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS B 31 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 3.687A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.526A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.066A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 4.119A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.722A 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: 3.659A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.985A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU C 61 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 97 removed outlier: 3.761A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLU C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLU C 92 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.513A 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: 3.776A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.712A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 120 removed outlier: 3.647A pdb=" N VAL D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Proline residue: D 100 - end of helix removed outlier: 6.240A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.759A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.697A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.136A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N NLE E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU E 94 " --> pdb=" O NLE E 90 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 4.153A pdb=" N ILE E 124 " --> pdb=" O NLE E 120 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 41 removed outlier: 5.372A pdb=" N GLY F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS F 31 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Proline residue: F 32 - end of helix removed outlier: 3.636A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.010A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.078A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.801A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.685A 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: 3.607A pdb=" N ARG G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.988A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 97 removed outlier: 3.747A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU G 91 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU G 92 " --> pdb=" O ARG G 88 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU G 93 " --> pdb=" O ASN G 89 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.856A 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: 3.852A pdb=" N TYR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 4.197A pdb=" N SER H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 121 removed outlier: 3.710A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR H 93 " --> pdb=" O ARG H 89 " (cutoff:3.500A) Proline residue: H 100 - end of helix removed outlier: 6.476A pdb=" N LEU H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 1091 through 1095 removed outlier: 4.522A pdb=" N ILE I1095 " --> pdb=" O ASP I1091 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1091 through 1095' Processing helix chain 'I' and resid 1114 through 1119 removed outlier: 4.028A pdb=" N LEU I1119 " --> pdb=" O LEU I1115 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1142 removed outlier: 4.605A pdb=" N LYS I1141 " --> pdb=" O GLN I1137 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG I1142 " --> pdb=" O CYS I1138 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1137 through 1142' Processing helix chain 'I' and resid 1180 through 1194 Processing helix chain 'I' and resid 1217 through 1222 removed outlier: 4.353A pdb=" N PHE I1221 " --> pdb=" O ASN I1217 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N MET I1222 " --> pdb=" O TYR I1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1217 through 1222' Processing helix chain 'L' and resid 1091 through 1095 removed outlier: 4.753A pdb=" N ILE L1095 " --> pdb=" O ASP L1091 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1091 through 1095' Processing helix chain 'L' and resid 1114 through 1119 removed outlier: 3.865A pdb=" N LEU L1119 " --> pdb=" O LEU L1115 " (cutoff:3.500A) Processing helix chain 'L' and resid 1137 through 1142 removed outlier: 4.848A pdb=" N LYS L1141 " --> pdb=" O GLN L1137 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG L1142 " --> pdb=" O CYS L1138 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1137 through 1142' Processing helix chain 'L' and resid 1180 through 1194 Processing helix chain 'L' and resid 1217 through 1222 removed outlier: 4.608A pdb=" N PHE L1221 " --> pdb=" O ASN L1217 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET L1222 " --> pdb=" O TYR L1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1217 through 1222' 259 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 321 hydrogen bonds 642 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 288 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 2.08 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: 3309 1.33 - 1.45: 5328 1.45 - 1.57: 8244 1.57 - 1.69: 669 1.69 - 1.81: 68 Bond restraints: 17618 Sorted by residual: bond pdb=" O3' DC A 163 " pdb=" P DC A 164 " ideal model delta sigma weight residual 1.607 1.563 0.044 1.20e-02 6.94e+03 1.33e+01 bond pdb=" C3' DG A 114 " pdb=" C2' DG A 114 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" CA LYS I1077 " pdb=" C LYS I1077 " ideal model delta sigma weight residual 1.519 1.559 -0.040 1.19e-02 7.06e+03 1.13e+01 bond pdb=" C3' DT K 17 " pdb=" C2' DT K 17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG K 114 " pdb=" C2' DG K 114 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.02e+01 ... (remaining 17613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 23777 1.82 - 3.65: 1362 3.65 - 5.47: 72 5.47 - 7.30: 13 7.30 - 9.12: 9 Bond angle restraints: 25233 Sorted by residual: angle pdb=" N LYS I1181 " pdb=" CA LYS I1181 " pdb=" C LYS I1181 " ideal model delta sigma weight residual 110.97 116.84 -5.87 1.09e+00 8.42e-01 2.90e+01 angle pdb=" N LYS L1234 " pdb=" CA LYS L1234 " pdb=" C LYS L1234 " ideal model delta sigma weight residual 109.46 117.84 -8.38 1.66e+00 3.63e-01 2.55e+01 angle pdb=" N VAL G 54 " pdb=" CA VAL G 54 " pdb=" C VAL G 54 " ideal model delta sigma weight residual 111.81 107.50 4.31 8.60e-01 1.35e+00 2.52e+01 angle pdb=" N SER G 113 " pdb=" CA SER G 113 " pdb=" C SER G 113 " ideal model delta sigma weight residual 111.28 116.62 -5.34 1.09e+00 8.42e-01 2.40e+01 angle pdb=" O4' DA A 27 " pdb=" C4' DA A 27 " pdb=" C3' DA A 27 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.22e+01 ... (remaining 25228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.42: 7528 27.42 - 54.85: 1910 54.85 - 82.27: 276 82.27 - 109.69: 2 109.69 - 137.12: 2 Dihedral angle restraints: 9718 sinusoidal: 6176 harmonic: 3542 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C4' DC K 36 " pdb=" C3' DC K 36 " pdb=" O3' DC K 36 " pdb=" P DT K 37 " ideal model delta sinusoidal sigma weight residual -140.00 -2.88 -137.12 1 3.50e+01 8.16e-04 1.36e+01 dihedral pdb=" C4' DC A 150 " pdb=" C3' DC A 150 " pdb=" O3' DC A 150 " pdb=" P DA A 151 " ideal model delta sinusoidal sigma weight residual 220.00 83.97 136.03 1 3.50e+01 8.16e-04 1.35e+01 ... (remaining 9715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2332 0.062 - 0.123: 463 0.123 - 0.185: 37 0.185 - 0.247: 1 0.247 - 0.308: 1 Chirality restraints: 2834 Sorted by residual: chirality pdb=" C4' DC A 163 " pdb=" C5' DC A 163 " pdb=" O4' DC A 163 " pdb=" C3' DC A 163 " both_signs ideal model delta sigma weight residual False -2.53 -2.22 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C2' SAM I1501 " pdb=" C1' SAM I1501 " pdb=" C3' SAM I1501 " pdb=" O2' SAM I1501 " both_signs ideal model delta sigma weight residual False -2.76 -2.57 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CA LYS L1234 " pdb=" N LYS L1234 " pdb=" C LYS L1234 " pdb=" CB LYS L1234 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 2831 not shown) Planarity restraints: 2056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 99 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO H 100 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN L1233 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" C GLN L1233 " -0.038 2.00e-02 2.50e+03 pdb=" O GLN L1233 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS L1234 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 89 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C VAL E 89 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL E 89 " -0.014 2.00e-02 2.50e+03 pdb=" N NLE E 90 " -0.013 2.00e-02 2.50e+03 ... (remaining 2053 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 7 1.88 - 2.64: 236 2.64 - 3.39: 18368 3.39 - 4.15: 41615 4.15 - 4.90: 67967 Nonbonded interactions: 128193 Sorted by model distance: nonbonded pdb=" OP1 DG A 87 " pdb=" NH1 ARG L1287 " model vdw 1.131 3.120 nonbonded pdb=" OP1 DG A 87 " pdb=" CZ ARG L1287 " model vdw 1.402 3.270 nonbonded pdb=" O5' DG A 87 " pdb=" NH2 ARG L1287 " model vdw 1.412 3.120 nonbonded pdb=" OP1 DC K 165 " pdb=" NZ LYS I1074 " model vdw 1.605 3.120 nonbonded pdb=" OP1 DG A 87 " pdb=" NH2 ARG L1287 " model vdw 1.724 3.120 ... (remaining 128188 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' selection = (chain 'G' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 27 through 121) } ncs_group { reference = chain 'E' selection = (chain 'M' and resid 35 through 134) } ncs_group { reference = (chain 'I' and (resid 1066 through 1287 or resid 1502 through 1503)) selection = (chain 'L' and (resid 1066 through 1287 or resid 1502 through 1503)) } 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 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.150 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.009 0.640 17632 Z= 0.594 Angle : 0.891 21.556 25239 Z= 0.698 Chirality : 0.048 0.308 2834 Planarity : 0.005 0.058 2056 Dihedral : 26.164 137.115 7436 Min Nonbonded Distance : 1.131 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.75 % Favored : 91.17 % Rotamer: Outliers : 1.36 % Allowed : 3.31 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.19 (0.17), residues: 1189 helix: -2.99 (0.16), residues: 548 sheet: -4.54 (0.47), residues: 54 loop : -3.85 (0.19), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 129 TYR 0.024 0.002 TYR C 50 PHE 0.016 0.002 PHE I1170 TRP 0.009 0.002 TRP L1157 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.56 (17618) covalent geometry : angle 0.86661 / 0.70 (25233) hydrogen bonds : bond 0.12823 / 8.70 ( 580) hydrogen bonds : angle 5.03643 / 3.42 ( 1419) metal coordination : bond 0.22016 / 14.43 ( 14) metal coordination : angle 13.46756 / 7.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: M 56 LYS cc_start: 0.8685 (ttpt) cc_final: 0.8449 (ttpp) REVERT: D 39 TYR cc_start: 0.8196 (t80) cc_final: 0.7918 (t80) REVERT: D 83 ARG cc_start: 0.8450 (mmt-90) cc_final: 0.8191 (mmt90) REVERT: H 68 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7207 (pt0) REVERT: I 1077 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6802 (mmtt) outliers start: 14 outliers final: 4 residues processed: 182 average time/residue: 0.1957 time to fit residues: 47.0987 Evaluate side-chains 136 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1262 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 50.0000 chunk 149 optimal weight: 8.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 104 GLN D 44 GLN E 125 GLN F 25 ASN G 38 ASN I1066 ASN I1192 HIS I1224 HIS I1233 GLN L1075 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.191239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134288 restraints weight = 22258.684| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.94 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17632 Z= 0.235 Angle : 0.720 7.999 25239 Z= 0.409 Chirality : 0.052 0.251 2834 Planarity : 0.005 0.053 2056 Dihedral : 29.641 142.587 5038 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 1.46 % Allowed : 9.54 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.34 (0.20), residues: 1189 helix: -2.16 (0.19), residues: 548 sheet: -4.50 (0.48), residues: 54 loop : -3.48 (0.20), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L1287 TYR 0.014 0.002 TYR D 118 PHE 0.014 0.002 PHE F 61 TRP 0.009 0.002 TRP L1157 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (17618) covalent geometry : angle 0.71919 / 0.41 (25233) hydrogen bonds : bond 0.08524 / 5.62 ( 580) hydrogen bonds : angle 3.01798 / 2.00 ( 1419) metal coordination : bond 0.01745 / 1.11 ( 14) metal coordination : angle 2.90108 / 1.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.381 Fit side-chains REVERT: M 56 LYS cc_start: 0.8513 (ttpt) cc_final: 0.8279 (ttpp) REVERT: D 39 TYR cc_start: 0.8113 (t80) cc_final: 0.7900 (t80) REVERT: E 49 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8298 (ptm160) REVERT: I 1077 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6920 (mmtt) REVERT: I 1215 LYS cc_start: 0.6918 (mptt) cc_final: 0.6254 (mmtt) REVERT: L 1135 GLN cc_start: 0.8074 (mt0) cc_final: 0.7830 (mt0) REVERT: L 1234 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8486 (pttm) outliers start: 15 outliers final: 12 residues processed: 138 average time/residue: 0.1754 time to fit residues: 33.0867 Evaluate side-chains 142 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1251 ILE Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1262 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 94 optimal weight: 50.0000 chunk 64 optimal weight: 0.9990 chunk 147 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 86 optimal weight: 30.0000 chunk 78 optimal weight: 40.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.192638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135577 restraints weight = 22456.553| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.86 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17632 Z= 0.170 Angle : 0.638 7.571 25239 Z= 0.368 Chirality : 0.048 0.236 2834 Planarity : 0.004 0.049 2056 Dihedral : 29.700 142.957 5037 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.17 % Allowed : 12.46 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.21), residues: 1189 helix: -1.57 (0.20), residues: 546 sheet: -3.33 (0.44), residues: 90 loop : -3.28 (0.21), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 42 TYR 0.011 0.001 TYR D 118 PHE 0.011 0.001 PHE H 67 TRP 0.008 0.002 TRP L1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (17618) covalent geometry : angle 0.63699 / 0.37 (25233) hydrogen bonds : bond 0.07029 / 4.63 ( 580) hydrogen bonds : angle 2.80772 / 1.87 ( 1419) metal coordination : bond 0.00541 / 0.33 ( 14) metal coordination : angle 2.65727 / 1.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.475 Fit side-chains REVERT: M 56 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8253 (ttpp) REVERT: D 39 TYR cc_start: 0.8093 (t80) cc_final: 0.7870 (t80) REVERT: D 83 ARG cc_start: 0.8324 (mmt-90) cc_final: 0.8107 (mmt90) REVERT: I 1077 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6824 (mmtp) REVERT: L 1135 GLN cc_start: 0.8040 (mt0) cc_final: 0.7811 (mt0) REVERT: L 1278 ASP cc_start: 0.4749 (OUTLIER) cc_final: 0.3918 (t0) outliers start: 12 outliers final: 5 residues processed: 131 average time/residue: 0.1722 time to fit residues: 30.8471 Evaluate side-chains 129 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1251 ILE Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 101 optimal weight: 20.0000 chunk 137 optimal weight: 50.0000 chunk 65 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 104 optimal weight: 30.0000 chunk 139 optimal weight: 0.8980 chunk 81 optimal weight: 20.0000 chunk 78 optimal weight: 40.0000 chunk 114 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.193465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142608 restraints weight = 22470.468| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.36 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17632 Z= 0.139 Angle : 0.614 7.567 25239 Z= 0.356 Chirality : 0.046 0.231 2834 Planarity : 0.004 0.046 2056 Dihedral : 29.690 143.066 5031 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.75 % Allowed : 12.37 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.21), residues: 1189 helix: -1.09 (0.21), residues: 546 sheet: -3.19 (0.45), residues: 90 loop : -3.12 (0.22), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L1287 TYR 0.009 0.001 TYR D 118 PHE 0.013 0.001 PHE H 67 TRP 0.009 0.001 TRP I1157 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (17618) covalent geometry : angle 0.61264 / 0.36 (25233) hydrogen bonds : bond 0.06303 / 4.13 ( 580) hydrogen bonds : angle 2.74012 / 1.82 ( 1419) metal coordination : bond 0.00339 / 0.23 ( 14) metal coordination : angle 2.24047 / 1.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: M 56 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8298 (ttpp) REVERT: D 39 TYR cc_start: 0.8225 (t80) cc_final: 0.7944 (t80) REVERT: D 83 ARG cc_start: 0.8408 (mmt-90) cc_final: 0.8111 (mmt90) REVERT: I 1077 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6809 (mmtp) REVERT: L 1234 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8527 (pttm) REVERT: L 1257 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6562 (pp) REVERT: L 1278 ASP cc_start: 0.4613 (OUTLIER) cc_final: 0.3982 (t0) outliers start: 18 outliers final: 7 residues processed: 145 average time/residue: 0.1653 time to fit residues: 33.3319 Evaluate side-chains 139 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1251 ILE Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1257 LEU Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 22 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 78 optimal weight: 40.0000 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 122 optimal weight: 40.0000 chunk 77 optimal weight: 50.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.192991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137088 restraints weight = 22314.006| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 4.01 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17632 Z= 0.161 Angle : 0.612 7.928 25239 Z= 0.352 Chirality : 0.046 0.212 2834 Planarity : 0.004 0.052 2056 Dihedral : 29.707 143.579 5031 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.46 % Allowed : 14.12 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.22), residues: 1189 helix: -0.77 (0.21), residues: 547 sheet: -3.09 (0.46), residues: 90 loop : -2.98 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L1287 TYR 0.010 0.001 TYR D 118 PHE 0.012 0.001 PHE H 67 TRP 0.007 0.001 TRP L1157 HIS 0.004 0.001 HIS M 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (17618) covalent geometry : angle 0.61119 / 0.35 (25233) hydrogen bonds : bond 0.06557 / 4.31 ( 580) hydrogen bonds : angle 2.68050 / 1.79 ( 1419) metal coordination : bond 0.00311 / 0.21 ( 14) metal coordination : angle 2.25455 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.422 Fit side-chains REVERT: M 56 LYS cc_start: 0.8488 (ttpt) cc_final: 0.8218 (ttpp) REVERT: D 39 TYR cc_start: 0.8124 (t80) cc_final: 0.7906 (t80) REVERT: D 83 ARG cc_start: 0.8367 (mmt-90) cc_final: 0.8141 (mmt90) REVERT: I 1077 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6837 (mmtt) REVERT: L 1234 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8545 (pttm) REVERT: L 1257 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6561 (pp) REVERT: L 1278 ASP cc_start: 0.4815 (OUTLIER) cc_final: 0.4090 (t0) outliers start: 15 outliers final: 7 residues processed: 142 average time/residue: 0.1681 time to fit residues: 32.9158 Evaluate side-chains 141 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1257 LEU Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 7 optimal weight: 2.9990 chunk 107 optimal weight: 0.0030 chunk 148 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 143 optimal weight: 6.9990 chunk 137 optimal weight: 50.0000 chunk 27 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.193727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.136316 restraints weight = 22369.759| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.65 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17632 Z= 0.134 Angle : 0.595 9.032 25239 Z= 0.343 Chirality : 0.045 0.209 2834 Planarity : 0.004 0.051 2056 Dihedral : 29.697 143.521 5031 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.85 % Allowed : 14.22 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.22), residues: 1189 helix: -0.55 (0.21), residues: 548 sheet: -3.08 (0.46), residues: 90 loop : -2.88 (0.22), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 30 TYR 0.009 0.001 TYR H 39 PHE 0.013 0.001 PHE H 67 TRP 0.009 0.001 TRP I1157 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (17618) covalent geometry : angle 0.59378 / 0.34 (25233) hydrogen bonds : bond 0.05963 / 3.91 ( 580) hydrogen bonds : angle 2.65940 / 1.78 ( 1419) metal coordination : bond 0.00231 / 0.15 ( 14) metal coordination : angle 2.12875 / 1.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.404 Fit side-chains REVERT: M 56 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8189 (ttpp) REVERT: D 30 ARG cc_start: 0.7703 (mtp85) cc_final: 0.6803 (mpt180) REVERT: D 39 TYR cc_start: 0.8039 (t80) cc_final: 0.7822 (t80) REVERT: D 83 ARG cc_start: 0.8270 (mmt-90) cc_final: 0.8056 (mmt90) REVERT: I 1077 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6712 (mmtt) REVERT: L 1169 GLU cc_start: 0.6866 (mp0) cc_final: 0.6502 (mp0) REVERT: L 1234 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8542 (pttm) REVERT: L 1257 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6575 (pp) REVERT: L 1278 ASP cc_start: 0.4820 (OUTLIER) cc_final: 0.4095 (t0) outliers start: 19 outliers final: 8 residues processed: 144 average time/residue: 0.1745 time to fit residues: 34.7182 Evaluate side-chains 139 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1135 GLN Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1257 LEU Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 92 optimal weight: 50.0000 chunk 19 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 116 optimal weight: 0.0980 chunk 103 optimal weight: 30.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.193976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140342 restraints weight = 22230.705| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.41 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17632 Z= 0.132 Angle : 0.592 7.909 25239 Z= 0.341 Chirality : 0.044 0.210 2834 Planarity : 0.004 0.052 2056 Dihedral : 29.692 143.610 5031 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.56 % Allowed : 14.61 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.22), residues: 1189 helix: -0.46 (0.21), residues: 548 sheet: -3.07 (0.46), residues: 90 loop : -2.84 (0.23), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 30 TYR 0.008 0.001 TYR D 118 PHE 0.011 0.001 PHE H 67 TRP 0.007 0.001 TRP I1157 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.13 (17618) covalent geometry : angle 0.59152 / 0.34 (25233) hydrogen bonds : bond 0.05874 / 3.85 ( 580) hydrogen bonds : angle 2.62850 / 1.75 ( 1419) metal coordination : bond 0.00294 / 0.19 ( 14) metal coordination : angle 1.99199 / 1.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.461 Fit side-chains REVERT: M 56 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8223 (ttpp) REVERT: D 30 ARG cc_start: 0.7703 (mtp85) cc_final: 0.7002 (mpt180) REVERT: D 39 TYR cc_start: 0.8151 (t80) cc_final: 0.7891 (t80) REVERT: D 83 ARG cc_start: 0.8365 (mmt-90) cc_final: 0.8083 (mmt90) REVERT: I 1077 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6812 (mmtt) REVERT: L 1234 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8542 (pttm) REVERT: L 1257 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6411 (pp) REVERT: L 1278 ASP cc_start: 0.4710 (OUTLIER) cc_final: 0.4110 (t0) outliers start: 16 outliers final: 11 residues processed: 137 average time/residue: 0.1809 time to fit residues: 34.0138 Evaluate side-chains 140 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1135 GLN Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1257 LEU Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 137 optimal weight: 0.0980 chunk 107 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.191503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133588 restraints weight = 22210.371| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.82 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17632 Z= 0.228 Angle : 0.661 7.669 25239 Z= 0.373 Chirality : 0.049 0.214 2834 Planarity : 0.005 0.055 2056 Dihedral : 29.720 143.777 5031 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 1.75 % Allowed : 14.70 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.22), residues: 1189 helix: -0.70 (0.21), residues: 551 sheet: -2.81 (0.50), residues: 80 loop : -2.93 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L1287 TYR 0.015 0.002 TYR E 54 PHE 0.013 0.002 PHE H 67 TRP 0.009 0.002 TRP I1157 HIS 0.006 0.001 HIS M 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.23 (17618) covalent geometry : angle 0.66009 / 0.37 (25233) hydrogen bonds : bond 0.07735 / 5.11 ( 580) hydrogen bonds : angle 2.77496 / 1.85 ( 1419) metal coordination : bond 0.00349 / 0.24 ( 14) metal coordination : angle 2.34628 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.507 Fit side-chains REVERT: M 56 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8174 (ttpp) REVERT: D 30 ARG cc_start: 0.7499 (mtp85) cc_final: 0.6885 (mmt-90) REVERT: D 39 TYR cc_start: 0.8118 (t80) cc_final: 0.7913 (t80) REVERT: D 83 ARG cc_start: 0.8346 (mmt-90) cc_final: 0.8135 (mmt90) REVERT: I 1077 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6725 (mmtt) REVERT: L 1234 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8624 (pttm) REVERT: L 1257 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6684 (pp) REVERT: L 1278 ASP cc_start: 0.4935 (OUTLIER) cc_final: 0.4155 (t0) outliers start: 18 outliers final: 10 residues processed: 140 average time/residue: 0.1807 time to fit residues: 34.4030 Evaluate side-chains 141 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1135 GLN Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1257 LEU Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 3 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 65 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 93 optimal weight: 50.0000 chunk 18 optimal weight: 0.4980 chunk 96 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 106 optimal weight: 50.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1233 GLN L1126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.192746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138821 restraints weight = 22259.155| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.37 r_work: 0.2752 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17632 Z= 0.148 Angle : 0.614 7.926 25239 Z= 0.351 Chirality : 0.046 0.211 2834 Planarity : 0.004 0.055 2056 Dihedral : 29.700 143.597 5031 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.46 % Allowed : 15.29 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.22), residues: 1189 helix: -0.54 (0.21), residues: 550 sheet: -2.77 (0.50), residues: 80 loop : -2.87 (0.22), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.011 0.001 TYR D 118 PHE 0.014 0.001 PHE H 67 TRP 0.007 0.001 TRP I1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (17618) covalent geometry : angle 0.61297 / 0.35 (25233) hydrogen bonds : bond 0.06605 / 4.36 ( 580) hydrogen bonds : angle 2.73474 / 1.82 ( 1419) metal coordination : bond 0.00305 / 0.20 ( 14) metal coordination : angle 2.22769 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.411 Fit side-chains REVERT: M 56 LYS cc_start: 0.8966 (ttpt) cc_final: 0.8728 (ttpp) REVERT: D 30 ARG cc_start: 0.7592 (mtp85) cc_final: 0.6781 (mmt-90) REVERT: D 83 ARG cc_start: 0.8863 (mmt180) cc_final: 0.8568 (mmt90) REVERT: I 1077 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6486 (mmtt) REVERT: L 1234 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8470 (pttm) REVERT: L 1278 ASP cc_start: 0.5349 (OUTLIER) cc_final: 0.4416 (t0) outliers start: 15 outliers final: 9 residues processed: 138 average time/residue: 0.1667 time to fit residues: 31.4493 Evaluate side-chains 140 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1251 ILE Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1135 GLN Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 47 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 119 optimal weight: 0.0040 chunk 60 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 118 optimal weight: 0.1980 chunk 146 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.194473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.137257 restraints weight = 22311.381| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.67 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 17632 Z= 0.135 Angle : 0.614 17.075 25239 Z= 0.345 Chirality : 0.045 0.255 2834 Planarity : 0.004 0.061 2056 Dihedral : 29.666 143.627 5031 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.78 % Allowed : 16.16 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.23), residues: 1189 helix: -0.22 (0.22), residues: 552 sheet: -1.90 (0.62), residues: 56 loop : -2.81 (0.22), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I1160 TYR 0.022 0.001 TYR D 39 PHE 0.013 0.001 PHE H 67 TRP 0.011 0.002 TRP I1157 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 (17618) covalent geometry : angle 0.61290 / 0.34 (25233) hydrogen bonds : bond 0.05545 / 3.62 ( 580) hydrogen bonds : angle 2.72145 / 1.81 ( 1419) metal coordination : bond 0.00269 / 0.17 ( 14) metal coordination : angle 2.08469 / 1.18 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.455 Fit side-chains REVERT: M 56 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8163 (ttpp) REVERT: D 30 ARG cc_start: 0.7559 (mtp85) cc_final: 0.7003 (mmt-90) REVERT: D 83 ARG cc_start: 0.8241 (mmt180) cc_final: 0.8026 (mmt90) REVERT: I 1077 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6747 (mmtt) REVERT: L 1234 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8562 (pttm) REVERT: L 1278 ASP cc_start: 0.4720 (OUTLIER) cc_final: 0.4097 (t0) outliers start: 8 outliers final: 5 residues processed: 138 average time/residue: 0.1793 time to fit residues: 33.7969 Evaluate side-chains 135 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1135 GLN Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 67 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 70 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 3 optimal weight: 4.9990 chunk 91 optimal weight: 70.0000 chunk 37 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.194430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.138361 restraints weight = 22309.872| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 4.02 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17632 Z= 0.134 Angle : 0.575 8.817 25239 Z= 0.330 Chirality : 0.043 0.209 2834 Planarity : 0.004 0.056 2056 Dihedral : 29.595 144.310 5031 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.97 % Allowed : 15.97 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.23), residues: 1189 helix: -0.02 (0.22), residues: 554 sheet: -1.87 (0.63), residues: 56 loop : -2.71 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 83 TYR 0.009 0.001 TYR D 118 PHE 0.012 0.001 PHE H 67 TRP 0.007 0.001 TRP I1157 HIS 0.004 0.001 HIS M 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (17618) covalent geometry : angle 0.57458 / 0.33 (25233) hydrogen bonds : bond 0.05642 / 3.69 ( 580) hydrogen bonds : angle 2.52658 / 1.69 ( 1419) metal coordination : bond 0.00256 / 0.17 ( 14) metal coordination : angle 2.07833 / 1.19 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3821.73 seconds wall clock time: 65 minutes 41.32 seconds (3941.32 seconds total)