Starting phenix.real_space_refine on Sun Sep 13 14:56:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cro_30453/09_2026/7cro_30453.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cro_30453/09_2026/7cro_30453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cro_30453/09_2026/7cro_30453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cro_30453/09_2026/7cro_30453.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cro_30453/09_2026/7cro_30453.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cro_30453/09_2026/7cro_30453.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cro_30453/09_2026/7cro_30453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cro_30453/09_2026/7cro_30453.map" } resolution = 3.75 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12063 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 336 5.49 5 S 30 5.16 5 C 8235 2.51 5 N 2762 2.21 5 O 3431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 14797 Number of models: 1 Model: "" Number of chains: 12 Chain: "M" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 833 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'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: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 803 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'NLE:plan-1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "A" Number of atoms: 3420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3420 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "K" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3468 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "I" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1731 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 13, 'TRANS': 205} Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13279 SG CYS I1016 59.525 92.667 71.375 1.00 74.39 S ATOM 13293 SG CYS I1018 62.061 90.974 69.713 1.00 91.22 S ATOM 13354 SG CYS I1026 59.637 93.550 67.996 1.00 85.87 S ATOM 13398 SG CYS I1032 58.228 89.896 69.399 1.00 68.52 S ATOM 13475 SG CYS I1041 54.903 93.115 69.256 1.00 88.65 S ATOM 13556 SG CYS I1052 56.026 94.118 66.143 1.00 84.65 S ATOM 14669 SG CYS I1191 35.820 63.419 55.974 1.00110.31 S ATOM 14686 SG CYS I1193 37.494 65.438 53.715 1.00103.59 S ATOM 14715 SG CYS I1198 38.607 61.460 51.915 1.00105.52 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N SAM I1401 " occ=0.93 ... (25 atoms not shown) pdb=" O4' SAM I1401 " occ=0.93 Time building chain proxies: 2.93, per 1000 atoms: 0.20 Number of scatterers: 14797 At special positions: 0 Unit cell: (136.08, 151.2, 173.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 30 16.00 P 336 15.00 O 3431 8.00 N 2762 7.00 C 8235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 432.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I1402 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1026 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1032 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1018 " pdb="ZN ZN I1402 " - pdb=" SG CYS I1016 " pdb=" ZN I1403 " pdb="ZN ZN I1403 " - pdb=" SG CYS I1041 " pdb="ZN ZN I1403 " - pdb=" SG CYS I1052 " pdb=" ZN I1404 " pdb="ZN ZN I1404 " - pdb=" SG CYS I1191 " pdb="ZN ZN I1404 " - pdb=" SG CYS I1193 " pdb="ZN ZN I1404 " - pdb=" SG CYS I1198 " Number of angles added : 6 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 59.4% alpha, 0.0% beta 114 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'M' and resid 44 through 57 removed outlier: 4.582A pdb=" N LEU M 48 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU M 50 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE M 51 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER M 57 " --> pdb=" O ARG M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 77 removed outlier: 3.616A pdb=" N LEU M 70 " --> pdb=" O PRO M 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL M 71 " --> pdb=" O PHE M 67 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG M 72 " --> pdb=" O GLN M 68 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 removed outlier: 4.050A pdb=" N NLE M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA M 91 " --> pdb=" O SER M 87 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU M 92 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN M 93 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU M 94 " --> pdb=" O NLE M 90 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA M 95 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU M 97 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN M 108 " --> pdb=" O PHE M 104 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU M 109 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS M 110 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 132 removed outlier: 4.195A pdb=" N ILE M 124 " --> pdb=" O NLE M 120 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN M 125 " --> pdb=" O PRO M 121 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 42 removed outlier: 4.943A pdb=" N GLY B 28 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N THR B 30 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS B 31 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 3.779A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.507A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.331A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.605A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 21' Processing helix chain 'C' and resid 26 through 36 removed outlier: 4.094A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 5.367A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 61 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 66 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 97 removed outlier: 3.776A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLU C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N GLU C 92 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 5.031A pdb=" N LEU C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 116' Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.754A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.654A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 120 removed outlier: 3.842A pdb=" N THR D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Proline residue: D 100 - end of helix removed outlier: 5.878A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 4.680A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.944A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.068A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N NLE E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU E 94 " --> pdb=" O NLE E 90 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 4.112A pdb=" N ILE E 124 " --> pdb=" O NLE E 120 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 41 removed outlier: 5.673A pdb=" N GLY F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N THR F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS F 31 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Proline residue: F 32 - end of helix Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.127A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.290A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.759A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 16 through 21' Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.920A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 72 removed outlier: 5.426A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 97 removed outlier: 3.753A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU G 91 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N GLU G 92 " --> pdb=" O ARG G 88 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU G 93 " --> pdb=" O ASN G 89 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 4.610A pdb=" N LEU G 116 " --> pdb=" O GLN G 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 112 through 116' Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.905A pdb=" N TYR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.982A pdb=" N SER H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N MET H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA H 74 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 121 removed outlier: 4.324A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR H 93 " --> pdb=" O ARG H 89 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG H 96 " --> pdb=" O GLN H 92 " (cutoff:3.500A) Proline residue: H 100 - end of helix removed outlier: 6.269A pdb=" N LEU H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYR H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 1009 through 1013 removed outlier: 4.262A pdb=" N ILE I1013 " --> pdb=" O ASP I1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1009 through 1013' Processing helix chain 'I' and resid 1032 through 1037 removed outlier: 4.038A pdb=" N LEU I1037 " --> pdb=" O LEU I1033 " (cutoff:3.500A) Processing helix chain 'I' and resid 1055 through 1060 removed outlier: 3.810A pdb=" N LYS I1059 " --> pdb=" O GLN I1055 " (cutoff:3.500A) Processing helix chain 'I' and resid 1098 through 1112 removed outlier: 3.514A pdb=" N ALA I1104 " --> pdb=" O GLU I1100 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA I1109 " --> pdb=" O ARG I1105 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU I1111 " --> pdb=" O LYS I1107 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASN I1112 " --> pdb=" O HIS I1108 " (cutoff:3.500A) Processing helix chain 'I' and resid 1135 through 1140 removed outlier: 4.470A pdb=" N PHE I1139 " --> pdb=" O ASN I1135 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N MET I1140 " --> pdb=" O TYR I1136 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1135 through 1140' 246 hydrogen bonds defined for protein. 738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 300 hydrogen bonds 600 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2912 1.33 - 1.45: 4975 1.45 - 1.57: 7155 1.57 - 1.69: 670 1.69 - 1.81: 43 Bond restraints: 15755 Sorted by residual: bond pdb=" C3' DT K 35 " pdb=" C2' DT K 35 " 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 A 11 " pdb=" C2' DG A 11 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC A 73 " pdb=" C2' DC A 73 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.91e+00 bond pdb=" C3' DC A 74 " pdb=" C2' DC A 74 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.86e+00 bond pdb=" C3' DT K 27 " pdb=" C2' DT K 27 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.58e+00 ... (remaining 15750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 21219 1.75 - 3.50: 1434 3.50 - 5.25: 59 5.25 - 7.01: 11 7.01 - 8.76: 5 Bond angle restraints: 22728 Sorted by residual: angle pdb=" O4' DG K 45 " pdb=" C4' DG K 45 " pdb=" C3' DG K 45 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.77e+01 angle pdb=" O4' DG K 126 " pdb=" C4' DG K 126 " pdb=" C3' DG K 126 " ideal model delta sigma weight residual 106.00 102.87 3.13 6.00e-01 2.78e+00 2.72e+01 angle pdb=" O4' DA K 159 " pdb=" C4' DA K 159 " pdb=" C3' DA K 159 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.48e+01 angle pdb=" O4' DG K 25 " pdb=" C4' DG K 25 " pdb=" C3' DG K 25 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.46e+01 angle pdb=" N3 DT K 103 " pdb=" C4 DT K 103 " pdb=" O4 DT K 103 " ideal model delta sigma weight residual 119.90 122.87 -2.97 6.00e-01 2.78e+00 2.46e+01 ... (remaining 22723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 6931 34.78 - 69.56: 1600 69.56 - 104.34: 33 104.34 - 139.11: 0 139.11 - 173.89: 1 Dihedral angle restraints: 8565 sinusoidal: 5677 harmonic: 2888 Sorted by residual: dihedral pdb=" CA HIS E 39 " pdb=" C HIS E 39 " pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta harmonic sigma weight residual 180.00 155.32 24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" N ASP I1125 " pdb=" C ASP I1125 " pdb=" CA ASP I1125 " pdb=" CB ASP I1125 " ideal model delta harmonic sigma weight residual 122.80 133.29 -10.49 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" CA TYR I1062 " pdb=" C TYR I1062 " pdb=" N PRO I1063 " pdb=" CA PRO I1063 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 8562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2289 0.074 - 0.149: 271 0.149 - 0.223: 6 0.223 - 0.297: 1 0.297 - 0.371: 1 Chirality restraints: 2568 Sorted by residual: chirality pdb=" CA ASP I1125 " pdb=" N ASP I1125 " pdb=" C ASP I1125 " pdb=" CB ASP I1125 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C3' DG A 91 " pdb=" C4' DG A 91 " pdb=" O3' DG A 91 " pdb=" C2' DG A 91 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA SER G 113 " pdb=" N SER G 113 " pdb=" C SER G 113 " pdb=" CB SER G 113 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.37e-01 ... (remaining 2565 not shown) Planarity restraints: 1723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS I 998 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO I 999 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO I 999 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 999 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE I1097 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C ILE I1097 " -0.045 2.00e-02 2.50e+03 pdb=" O ILE I1097 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP I1098 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG A 141 " 0.036 2.00e-02 2.50e+03 1.50e-02 6.75e+00 pdb=" N9 DG A 141 " -0.034 2.00e-02 2.50e+03 pdb=" C8 DG A 141 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DG A 141 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG A 141 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG A 141 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG A 141 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DG A 141 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG A 141 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG A 141 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG A 141 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG A 141 " -0.002 2.00e-02 2.50e+03 ... (remaining 1720 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 3 2.12 - 2.81: 3736 2.81 - 3.51: 18095 3.51 - 4.20: 36158 4.20 - 4.90: 54691 Nonbonded interactions: 112683 Sorted by model distance: nonbonded pdb=" NH2 ARG I1126 " pdb=" OG1 THR I1159 " model vdw 1.421 3.120 nonbonded pdb=" CE1 HIS M 39 " pdb=" OE1 GLU I1149 " model vdw 1.762 3.260 nonbonded pdb=" O CYS I1198 " pdb="ZN ZN I1404 " model vdw 2.086 2.230 nonbonded pdb=" O GLU I1091 " pdb=" OG SER I1137 " model vdw 2.154 3.040 nonbonded pdb=" O TYR F 51 " pdb=" NH1 ARG F 55 " model vdw 2.162 3.120 ... (remaining 112678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = (chain 'C' and (resid 10 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and (resid 10 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 117 or (resid 118 and (name N or n \ ame CA or name C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 27 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 121)) } ncs_group { reference = chain 'E' selection = (chain 'M' and resid 37 through 134) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.93 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 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: 0.040 Process input model: 16.860 Find NCS groups from input model: 0.160 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 0.551 15764 Z= 0.608 Angle : 0.906 20.240 22734 Z= 0.735 Chirality : 0.048 0.371 2568 Planarity : 0.005 0.071 1723 Dihedral : 27.675 173.892 6705 Min Nonbonded Distance : 1.421 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.45 % Allowed : 5.08 % Favored : 93.47 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.38 (0.19), residues: 966 helix: -3.15 (0.17), residues: 483 sheet: -4.20 (0.78), residues: 25 loop : -4.05 (0.21), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I1035 TYR 0.020 0.002 TYR H 118 PHE 0.010 0.002 PHE I1039 TRP 0.013 0.002 TRP I1075 HIS 0.005 0.001 HIS M 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.58 (15755) covalent geometry : angle 0.87511 / 0.73 (22728) hydrogen bonds : bond 0.15983 / 9.92 ( 546) hydrogen bonds : angle 5.59504 / 3.89 ( 1338) metal coordination : bond 0.24541 / 16.04 ( 9) metal coordination : angle 14.39977 / 7.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.466 Fit side-chains REVERT: B 84 MET cc_start: 0.8368 (mmm) cc_final: 0.8150 (mmt) REVERT: D 90 GLU cc_start: 0.8159 (mp0) cc_final: 0.7465 (mp0) REVERT: E 73 GLU cc_start: 0.8006 (tt0) cc_final: 0.7650 (tt0) REVERT: E 106 ASP cc_start: 0.8539 (m-30) cc_final: 0.8321 (m-30) REVERT: E 123 ASP cc_start: 0.8151 (m-30) cc_final: 0.7753 (m-30) REVERT: F 91 LYS cc_start: 0.8912 (tttm) cc_final: 0.8661 (tptt) REVERT: G 118 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.6396 (tptp) outliers start: 12 outliers final: 5 residues processed: 133 average time/residue: 0.1925 time to fit residues: 33.6399 Evaluate side-chains 99 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain I residue 1006 TYR Chi-restraints excluded: chain I residue 1102 CYS Chi-restraints excluded: chain I residue 1103 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.0030 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 65 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.6174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN E 125 GLN F 25 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 997 ASN I1034 ASN I1116 HIS I1142 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.132060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.090831 restraints weight = 35655.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.089566 restraints weight = 37439.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.089601 restraints weight = 37115.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.089887 restraints weight = 27996.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.089974 restraints weight = 25075.310| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15764 Z= 0.160 Angle : 0.663 12.659 22734 Z= 0.384 Chirality : 0.045 0.246 2568 Planarity : 0.005 0.045 1723 Dihedral : 30.673 171.681 4778 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.81 % Allowed : 9.67 % Favored : 88.51 % 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: -4.24 (0.22), residues: 966 helix: -2.06 (0.20), residues: 490 sheet: -4.40 (0.71), residues: 15 loop : -3.68 (0.22), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I1192 TYR 0.027 0.001 TYR I1062 PHE 0.014 0.001 PHE I1088 TRP 0.012 0.001 TRP I1075 HIS 0.006 0.001 HIS M 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.16 (15755) covalent geometry : angle 0.65018 / 0.38 (22728) hydrogen bonds : bond 0.07626 / 4.84 ( 546) hydrogen bonds : angle 3.51774 / 2.37 ( 1338) metal coordination : bond 0.01110 / 0.65 ( 9) metal coordination : angle 7.96764 / 4.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.425 Fit side-chains REVERT: B 84 MET cc_start: 0.8142 (mmm) cc_final: 0.7886 (mmt) REVERT: C 13 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7359 (mmmm) REVERT: C 56 GLU cc_start: 0.8110 (tt0) cc_final: 0.7896 (tt0) REVERT: D 56 MET cc_start: 0.8728 (tpt) cc_final: 0.8232 (tpt) REVERT: D 90 GLU cc_start: 0.8010 (mp0) cc_final: 0.7449 (mp0) REVERT: E 73 GLU cc_start: 0.7954 (tt0) cc_final: 0.7705 (tt0) REVERT: E 106 ASP cc_start: 0.8459 (m-30) cc_final: 0.8164 (m-30) REVERT: F 25 ASN cc_start: 0.8273 (m110) cc_final: 0.7428 (m110) REVERT: G 36 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8375 (ttmm) REVERT: G 118 LYS cc_start: 0.6989 (OUTLIER) cc_final: 0.6602 (tptp) REVERT: I 1143 SER cc_start: 0.8582 (t) cc_final: 0.7844 (m) outliers start: 15 outliers final: 9 residues processed: 109 average time/residue: 0.1623 time to fit residues: 24.4600 Evaluate side-chains 98 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 1006 TYR Chi-restraints excluded: chain I residue 1089 VAL Chi-restraints excluded: chain I residue 1102 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 1 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 116 optimal weight: 30.0000 chunk 16 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 75 optimal weight: 50.0000 chunk 121 optimal weight: 0.3980 chunk 3 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 chunk 120 optimal weight: 8.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 993 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.129901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.089258 restraints weight = 35776.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.088027 restraints weight = 41358.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.088399 restraints weight = 37892.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.088683 restraints weight = 28158.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.088778 restraints weight = 26748.722| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15764 Z= 0.245 Angle : 0.714 10.827 22734 Z= 0.400 Chirality : 0.049 0.217 2568 Planarity : 0.005 0.047 1723 Dihedral : 30.870 170.724 4774 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.42 % Allowed : 13.06 % Favored : 84.52 % 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: -4.04 (0.23), residues: 966 helix: -1.88 (0.21), residues: 490 sheet: -3.96 (0.74), residues: 16 loop : -3.60 (0.23), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I1192 TYR 0.017 0.002 TYR H 118 PHE 0.010 0.001 PHE I1039 TRP 0.011 0.002 TRP I1075 HIS 0.006 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.24 (15755) covalent geometry : angle 0.70553 / 0.40 (22728) hydrogen bonds : bond 0.08684 / 5.52 ( 546) hydrogen bonds : angle 3.73841 / 2.51 ( 1338) metal coordination : bond 0.01077 / 0.58 ( 9) metal coordination : angle 6.95046 / 4.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8253 (mmm) cc_final: 0.8000 (mmt) REVERT: C 13 LYS cc_start: 0.7811 (mtpp) cc_final: 0.7390 (mmmm) REVERT: C 56 GLU cc_start: 0.8244 (tt0) cc_final: 0.8029 (tt0) REVERT: D 90 GLU cc_start: 0.8150 (mp0) cc_final: 0.7519 (mp0) REVERT: E 106 ASP cc_start: 0.8454 (m-30) cc_final: 0.8244 (m-30) REVERT: G 36 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8447 (ttmm) REVERT: I 1143 SER cc_start: 0.8657 (t) cc_final: 0.7878 (m) outliers start: 20 outliers final: 17 residues processed: 103 average time/residue: 0.1502 time to fit residues: 21.8876 Evaluate side-chains 101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 1089 VAL Chi-restraints excluded: chain I residue 1102 CYS Chi-restraints excluded: chain I residue 1193 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 30.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.132722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.091993 restraints weight = 35859.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.090786 restraints weight = 41084.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.091070 restraints weight = 40950.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.091392 restraints weight = 28711.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.091518 restraints weight = 26271.690| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15764 Z= 0.139 Angle : 0.588 9.293 22734 Z= 0.346 Chirality : 0.042 0.221 2568 Planarity : 0.004 0.040 1723 Dihedral : 30.672 171.676 4768 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.33 % Allowed : 15.11 % Favored : 83.56 % 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: -3.37 (0.24), residues: 966 helix: -1.35 (0.22), residues: 496 sheet: -3.90 (0.93), residues: 14 loop : -3.26 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I1126 TYR 0.011 0.001 TYR I1062 PHE 0.007 0.001 PHE I1117 TRP 0.011 0.001 TRP I1075 HIS 0.005 0.001 HIS I1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 (15755) covalent geometry : angle 0.57989 / 0.35 (22728) hydrogen bonds : bond 0.06382 / 4.07 ( 546) hydrogen bonds : angle 3.10557 / 2.09 ( 1338) metal coordination : bond 0.00798 / 0.44 ( 9) metal coordination : angle 5.90965 / 3.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8120 (mmm) cc_final: 0.7861 (mmt) REVERT: C 13 LYS cc_start: 0.7939 (mtpp) cc_final: 0.7530 (mmmm) REVERT: C 56 GLU cc_start: 0.8186 (tt0) cc_final: 0.7947 (tt0) REVERT: E 73 GLU cc_start: 0.7838 (tt0) cc_final: 0.7564 (tt0) REVERT: E 106 ASP cc_start: 0.8369 (m-30) cc_final: 0.8129 (m-30) REVERT: F 25 ASN cc_start: 0.8255 (m110) cc_final: 0.7709 (m110) REVERT: G 36 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8392 (ttmm) REVERT: I 1143 SER cc_start: 0.8403 (t) cc_final: 0.7638 (m) outliers start: 11 outliers final: 7 residues processed: 97 average time/residue: 0.1496 time to fit residues: 20.6629 Evaluate side-chains 95 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 1089 VAL Chi-restraints excluded: chain I residue 1102 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 60 optimal weight: 0.0770 chunk 43 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 73 optimal weight: 0.3980 chunk 78 optimal weight: 30.0000 chunk 75 optimal weight: 40.0000 chunk 40 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.132615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.091778 restraints weight = 35605.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.089993 restraints weight = 38867.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.090018 restraints weight = 40361.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.090301 restraints weight = 29382.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.090484 restraints weight = 26488.517| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15764 Z= 0.135 Angle : 0.573 8.524 22734 Z= 0.334 Chirality : 0.041 0.218 2568 Planarity : 0.004 0.040 1723 Dihedral : 30.662 170.673 4767 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.69 % Allowed : 16.20 % Favored : 82.10 % 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: -2.89 (0.25), residues: 966 helix: -0.92 (0.22), residues: 498 sheet: -3.49 (0.89), residues: 17 loop : -3.09 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I1060 TYR 0.011 0.001 TYR I1062 PHE 0.007 0.001 PHE I1117 TRP 0.009 0.001 TRP I1075 HIS 0.004 0.001 HIS I1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.14 (15755) covalent geometry : angle 0.56690 / 0.33 (22728) hydrogen bonds : bond 0.06301 / 4.01 ( 546) hydrogen bonds : angle 2.96471 / 2.00 ( 1338) metal coordination : bond 0.00708 / 0.37 ( 9) metal coordination : angle 5.20006 / 2.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8168 (mmm) cc_final: 0.7918 (mmt) REVERT: C 13 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7615 (mmmm) REVERT: E 73 GLU cc_start: 0.7794 (tt0) cc_final: 0.7484 (tt0) REVERT: E 106 ASP cc_start: 0.8299 (m-30) cc_final: 0.8067 (m-30) REVERT: F 25 ASN cc_start: 0.8158 (m110) cc_final: 0.7560 (m110) REVERT: G 36 LYS cc_start: 0.8571 (mtpp) cc_final: 0.8360 (ttmm) REVERT: I 1143 SER cc_start: 0.8432 (t) cc_final: 0.7702 (m) outliers start: 14 outliers final: 13 residues processed: 98 average time/residue: 0.1463 time to fit residues: 20.4948 Evaluate side-chains 99 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 1089 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 54 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 93 optimal weight: 30.0000 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 44 GLN G 110 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.131570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.090880 restraints weight = 35654.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.089166 restraints weight = 41326.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.089151 restraints weight = 44891.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.089463 restraints weight = 31100.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.089625 restraints weight = 28074.877| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15764 Z= 0.187 Angle : 0.612 8.508 22734 Z= 0.348 Chirality : 0.043 0.221 2568 Planarity : 0.004 0.040 1723 Dihedral : 30.711 170.261 4766 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.42 % Allowed : 16.93 % Favored : 80.65 % 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: -2.94 (0.25), residues: 966 helix: -0.93 (0.22), residues: 501 sheet: -3.43 (0.90), residues: 17 loop : -3.16 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 29 TYR 0.014 0.001 TYR H 118 PHE 0.010 0.001 PHE I1088 TRP 0.011 0.001 TRP I1075 HIS 0.007 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 (15755) covalent geometry : angle 0.60620 / 0.35 (22728) hydrogen bonds : bond 0.06919 / 4.39 ( 546) hydrogen bonds : angle 3.20220 / 2.16 ( 1338) metal coordination : bond 0.00812 / 0.42 ( 9) metal coordination : angle 5.01902 / 2.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8247 (mmm) cc_final: 0.8003 (mmt) REVERT: C 13 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7675 (mmmm) REVERT: E 73 GLU cc_start: 0.7824 (tt0) cc_final: 0.7526 (tt0) REVERT: F 25 ASN cc_start: 0.8187 (m110) cc_final: 0.7551 (m110) REVERT: F 53 GLU cc_start: 0.7963 (tp30) cc_final: 0.7706 (tp30) REVERT: G 36 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8387 (ttmm) REVERT: I 1143 SER cc_start: 0.8467 (t) cc_final: 0.7730 (m) outliers start: 20 outliers final: 15 residues processed: 103 average time/residue: 0.1529 time to fit residues: 22.1495 Evaluate side-chains 102 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 1006 TYR Chi-restraints excluded: chain I residue 1042 HIS Chi-restraints excluded: chain I residue 1089 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 21 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 98 optimal weight: 40.0000 chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.133596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.092203 restraints weight = 35574.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.090640 restraints weight = 36988.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.090631 restraints weight = 36480.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.090930 restraints weight = 27301.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.091113 restraints weight = 24535.738| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 15764 Z= 0.129 Angle : 0.549 8.379 22734 Z= 0.324 Chirality : 0.040 0.223 2568 Planarity : 0.004 0.035 1723 Dihedral : 30.575 170.987 4766 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.33 % Allowed : 18.50 % Favored : 80.17 % 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: -2.48 (0.25), residues: 966 helix: -0.54 (0.23), residues: 497 sheet: -3.18 (0.97), residues: 17 loop : -2.95 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 129 TYR 0.012 0.001 TYR I1062 PHE 0.018 0.001 PHE I1088 TRP 0.010 0.001 TRP I1075 HIS 0.004 0.001 HIS I1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.13 (15755) covalent geometry : angle 0.54460 / 0.32 (22728) hydrogen bonds : bond 0.05665 / 3.60 ( 546) hydrogen bonds : angle 2.81488 / 1.89 ( 1338) metal coordination : bond 0.00629 / 0.33 ( 9) metal coordination : angle 4.46288 / 2.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: M 81 ASP cc_start: 0.8128 (t70) cc_final: 0.7904 (t70) REVERT: B 84 MET cc_start: 0.8220 (mmm) cc_final: 0.7967 (mmt) REVERT: C 13 LYS cc_start: 0.8022 (mtpp) cc_final: 0.7622 (mmmm) REVERT: E 73 GLU cc_start: 0.7923 (tt0) cc_final: 0.7578 (tt0) REVERT: F 25 ASN cc_start: 0.8162 (m110) cc_final: 0.7448 (m110) REVERT: I 1143 SER cc_start: 0.8327 (t) cc_final: 0.7623 (m) outliers start: 11 outliers final: 10 residues processed: 100 average time/residue: 0.1532 time to fit residues: 21.6608 Evaluate side-chains 97 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 1042 HIS Chi-restraints excluded: chain I residue 1089 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 90 optimal weight: 50.0000 chunk 22 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.132618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.091985 restraints weight = 35790.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.090456 restraints weight = 40652.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.090309 restraints weight = 43993.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.090907 restraints weight = 29998.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.091010 restraints weight = 26062.788| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15764 Z= 0.161 Angle : 0.584 8.413 22734 Z= 0.335 Chirality : 0.041 0.223 2568 Planarity : 0.004 0.038 1723 Dihedral : 30.622 170.520 4766 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.06 % Allowed : 18.50 % Favored : 79.44 % 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: -2.45 (0.25), residues: 966 helix: -0.52 (0.23), residues: 498 sheet: -3.19 (0.96), residues: 17 loop : -2.93 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 29 TYR 0.010 0.001 TYR H 118 PHE 0.024 0.001 PHE I1088 TRP 0.010 0.001 TRP I1075 HIS 0.004 0.001 HIS I1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (15755) covalent geometry : angle 0.57934 / 0.33 (22728) hydrogen bonds : bond 0.06203 / 3.93 ( 546) hydrogen bonds : angle 2.97829 / 2.00 ( 1338) metal coordination : bond 0.00684 / 0.36 ( 9) metal coordination : angle 4.43182 / 2.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8226 (mmm) cc_final: 0.7992 (mmt) REVERT: C 13 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7548 (mmmm) REVERT: D 56 MET cc_start: 0.8548 (tpt) cc_final: 0.8110 (tpt) REVERT: E 73 GLU cc_start: 0.7891 (tt0) cc_final: 0.7585 (tt0) REVERT: F 25 ASN cc_start: 0.8195 (m110) cc_final: 0.7519 (m110) REVERT: I 1143 SER cc_start: 0.8390 (t) cc_final: 0.7684 (m) outliers start: 17 outliers final: 14 residues processed: 94 average time/residue: 0.1428 time to fit residues: 19.3772 Evaluate side-chains 95 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 1006 TYR Chi-restraints excluded: chain I residue 1042 HIS Chi-restraints excluded: chain I residue 1089 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 30.0000 chunk 123 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 88 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 50.0000 chunk 33 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.131023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.089979 restraints weight = 35507.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.088534 restraints weight = 42144.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.088430 restraints weight = 44893.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.088804 restraints weight = 31174.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.088982 restraints weight = 27902.400| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15764 Z= 0.204 Angle : 0.647 9.000 22734 Z= 0.362 Chirality : 0.045 0.219 2568 Planarity : 0.004 0.041 1723 Dihedral : 30.745 170.119 4766 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.06 % Allowed : 18.86 % Favored : 79.08 % 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: -2.75 (0.25), residues: 966 helix: -0.78 (0.22), residues: 496 sheet: -3.33 (0.94), residues: 17 loop : -3.05 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 29 TYR 0.017 0.002 TYR H 118 PHE 0.010 0.001 PHE H 67 TRP 0.009 0.001 TRP I1075 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (15755) covalent geometry : angle 0.64342 / 0.36 (22728) hydrogen bonds : bond 0.07498 / 4.74 ( 546) hydrogen bonds : angle 3.34573 / 2.24 ( 1338) metal coordination : bond 0.00798 / 0.41 ( 9) metal coordination : angle 4.46741 / 2.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8317 (mmm) cc_final: 0.8082 (mmt) REVERT: C 13 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7659 (mmmm) REVERT: E 73 GLU cc_start: 0.7950 (tt0) cc_final: 0.7607 (tt0) REVERT: F 25 ASN cc_start: 0.8187 (m110) cc_final: 0.7479 (m110) REVERT: F 53 GLU cc_start: 0.8179 (tp30) cc_final: 0.7910 (tp30) REVERT: I 1143 SER cc_start: 0.8360 (t) cc_final: 0.7665 (m) outliers start: 17 outliers final: 14 residues processed: 97 average time/residue: 0.1467 time to fit residues: 20.3667 Evaluate side-chains 99 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 1006 TYR Chi-restraints excluded: chain I residue 1042 HIS Chi-restraints excluded: chain I residue 1089 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 88 optimal weight: 30.0000 chunk 67 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 58 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.132479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091164 restraints weight = 35336.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.089674 restraints weight = 40521.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.089875 restraints weight = 40537.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090213 restraints weight = 29635.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.090269 restraints weight = 26857.695| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15764 Z= 0.147 Angle : 0.581 8.483 22734 Z= 0.336 Chirality : 0.042 0.219 2568 Planarity : 0.004 0.037 1723 Dihedral : 30.644 171.214 4766 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.93 % Allowed : 18.74 % Favored : 79.32 % 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: -2.45 (0.25), residues: 966 helix: -0.52 (0.23), residues: 496 sheet: -3.26 (0.96), residues: 17 loop : -2.91 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 30 TYR 0.011 0.001 TYR H 118 PHE 0.011 0.001 PHE I1088 TRP 0.009 0.001 TRP I1075 HIS 0.004 0.001 HIS I1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (15755) covalent geometry : angle 0.57759 / 0.34 (22728) hydrogen bonds : bond 0.06220 / 3.95 ( 546) hydrogen bonds : angle 3.03183 / 2.03 ( 1338) metal coordination : bond 0.00666 / 0.35 ( 9) metal coordination : angle 4.17471 / 2.35 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8301 (mmm) cc_final: 0.8087 (mmt) REVERT: C 13 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7658 (mmmm) REVERT: D 56 MET cc_start: 0.8552 (tpt) cc_final: 0.8141 (tpt) REVERT: E 73 GLU cc_start: 0.7827 (tt0) cc_final: 0.7275 (tt0) REVERT: F 25 ASN cc_start: 0.8191 (m110) cc_final: 0.7499 (m110) REVERT: I 1143 SER cc_start: 0.8306 (t) cc_final: 0.7642 (m) outliers start: 16 outliers final: 16 residues processed: 98 average time/residue: 0.1513 time to fit residues: 21.0481 Evaluate side-chains 101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 1006 TYR Chi-restraints excluded: chain I residue 1042 HIS Chi-restraints excluded: chain I residue 1089 VAL Chi-restraints excluded: chain I residue 1175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 56 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 97 optimal weight: 30.0000 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 chunk 10 optimal weight: 0.0370 chunk 80 optimal weight: 30.0000 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.132576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.091339 restraints weight = 35534.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.089829 restraints weight = 40038.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.090051 restraints weight = 40110.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.090346 restraints weight = 29031.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.090401 restraints weight = 26354.934| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15764 Z= 0.143 Angle : 0.577 8.256 22734 Z= 0.333 Chirality : 0.042 0.217 2568 Planarity : 0.004 0.038 1723 Dihedral : 30.635 171.144 4766 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.93 % Allowed : 18.98 % Favored : 79.08 % 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: -2.35 (0.26), residues: 966 helix: -0.43 (0.23), residues: 496 sheet: -3.29 (0.97), residues: 17 loop : -2.88 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 29 TYR 0.009 0.001 TYR H 118 PHE 0.012 0.001 PHE I1088 TRP 0.008 0.001 TRP I1075 HIS 0.004 0.001 HIS I1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (15755) covalent geometry : angle 0.57359 / 0.33 (22728) hydrogen bonds : bond 0.06199 / 3.93 ( 546) hydrogen bonds : angle 2.98963 / 2.01 ( 1338) metal coordination : bond 0.00647 / 0.34 ( 9) metal coordination : angle 4.12870 / 2.34 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2338.17 seconds wall clock time: 40 minutes 57.81 seconds (2457.81 seconds total)