Starting phenix.real_space_refine on Fri Mar 6 01:20:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7crq_30456/03_2026/7crq_30456.cif Found real_map, /net/cci-nas-00/data/ceres_data/7crq_30456/03_2026/7crq_30456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7crq_30456/03_2026/7crq_30456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7crq_30456/03_2026/7crq_30456.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7crq_30456/03_2026/7crq_30456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7crq_30456/03_2026/7crq_30456.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13425 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 336 5.49 5 S 50 5.16 5 C 9355 2.51 5 N 3122 2.21 5 O 3764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16633 Number of models: 1 Model: "" Number of chains: 14 Chain: "M" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 833 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'NLE:plan-1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'NLE:plan-1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "A" Number of atoms: 3420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3420 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "K" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3468 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "I" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1755 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "L" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1755 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13324 SG CYS I1098 58.034 126.432 71.341 1.00 57.77 S ATOM 13338 SG CYS I1100 60.761 124.188 69.488 1.00 68.64 S ATOM 13439 SG CYS I1114 57.471 122.507 68.951 1.00 51.71 S ATOM 13397 SG CYS I1108 58.450 125.943 67.441 1.00 67.39 S ATOM 13518 SG CYS I1123 54.177 126.109 69.120 1.00 65.08 S ATOM 13557 SG CYS I1128 57.048 129.244 68.831 1.00 69.30 S ATOM 14720 SG CYS I1273 35.858 97.229 54.423 1.00 95.53 S ATOM 16475 SG CYS L1273 100.091 62.562 77.111 1.00 94.11 S ATOM 15079 SG CYS L1098 84.287 77.976 112.000 1.00 61.91 S ATOM 15093 SG CYS L1100 80.734 76.863 110.364 1.00 71.33 S ATOM 15152 SG CYS L1108 83.224 74.633 111.459 1.00 74.24 S ATOM 15194 SG CYS L1114 83.930 75.924 108.166 1.00 63.88 S ATOM 15152 SG CYS L1108 83.224 74.633 111.459 1.00 74.24 S ATOM 15312 SG CYS L1128 85.348 74.884 114.264 1.00 71.27 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N SAM I1501 " occ=0.93 ... (25 atoms not shown) pdb=" O4' SAM I1501 " occ=0.93 residue: pdb=" N SAM L1504 " occ=0.93 ... (25 atoms not shown) pdb=" O4' SAM L1504 " occ=0.93 Time building chain proxies: 3.77, per 1000 atoms: 0.23 Number of scatterers: 16633 At special positions: 0 Unit cell: (143.64, 180.36, 173.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 50 16.00 P 336 15.00 O 3764 8.00 N 3122 7.00 C 9355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 7728 O5' DG A 87 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 527.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I1502 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1114 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1100 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1098 " pdb=" ZN I1503 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1108 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1128 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1123 " pdb=" ZN I1504 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1273 " pdb=" ZN L1501 " pdb="ZN ZN L1501 " - pdb=" SG CYS L1273 " pdb=" ZN L1502 " pdb="ZN ZN L1502 " - pdb=" SG CYS L1114 " pdb="ZN ZN L1502 " - pdb=" SG CYS L1108 " pdb="ZN ZN L1502 " - pdb=" SG CYS L1098 " pdb="ZN ZN L1502 " - pdb=" SG CYS L1100 " pdb=" ZN L1503 " pdb="ZN ZN L1503 " - pdb=" SG CYS L1108 " pdb="ZN ZN L1503 " - pdb=" SG CYS L1128 " Number of angles added : 6 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 51.5% alpha, 0.0% beta 121 base pairs and 288 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'M' and resid 44 through 57 removed outlier: 3.786A pdb=" N GLU M 50 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE M 51 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER M 57 " --> pdb=" O ARG M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 77 removed outlier: 3.647A pdb=" N LEU M 70 " --> pdb=" O PRO M 66 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL M 71 " --> pdb=" O PHE M 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG M 72 " --> pdb=" O GLN M 68 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.823A pdb=" N NLE M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA M 91 " --> pdb=" O SER M 87 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU M 92 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN M 93 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU M 94 " --> pdb=" O NLE M 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA M 95 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU M 97 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU M 105 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN M 108 " --> pdb=" O PHE M 104 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU M 109 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS M 110 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 132 removed outlier: 4.136A pdb=" N ILE M 124 " --> pdb=" O NLE M 120 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN M 125 " --> pdb=" O PRO M 121 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 42 removed outlier: 4.919A pdb=" N GLY B 28 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N THR B 30 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS B 31 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 3.687A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.526A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.066A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 4.119A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 21' Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.659A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.985A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU C 61 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 97 removed outlier: 3.761A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLU C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLU C 92 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.513A pdb=" N LEU C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 116' Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.776A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.712A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 120 removed outlier: 3.647A pdb=" N VAL D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Proline residue: D 100 - end of helix removed outlier: 6.240A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.759A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.697A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.136A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N NLE E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU E 94 " --> pdb=" O NLE E 90 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 4.153A pdb=" N ILE E 124 " --> pdb=" O NLE E 120 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 41 removed outlier: 5.372A pdb=" N GLY F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS F 31 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Proline residue: F 32 - end of helix removed outlier: 3.636A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.010A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.078A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.801A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 16 through 21' Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.607A pdb=" N ARG G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.988A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 97 removed outlier: 3.747A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU G 91 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU G 92 " --> pdb=" O ARG G 88 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU G 93 " --> pdb=" O ASN G 89 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.856A pdb=" N LEU G 116 " --> pdb=" O GLN G 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 112 through 116' Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.852A pdb=" N TYR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 4.197A pdb=" N SER H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 121 removed outlier: 3.710A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR H 93 " --> pdb=" O ARG H 89 " (cutoff:3.500A) Proline residue: H 100 - end of helix removed outlier: 6.476A pdb=" N LEU H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 1091 through 1095 removed outlier: 4.522A pdb=" N ILE I1095 " --> pdb=" O ASP I1091 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1091 through 1095' Processing helix chain 'I' and resid 1114 through 1119 removed outlier: 4.028A pdb=" N LEU I1119 " --> pdb=" O LEU I1115 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1142 removed outlier: 4.605A pdb=" N LYS I1141 " --> pdb=" O GLN I1137 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG I1142 " --> pdb=" O CYS I1138 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1137 through 1142' Processing helix chain 'I' and resid 1180 through 1194 Processing helix chain 'I' and resid 1217 through 1222 removed outlier: 4.353A pdb=" N PHE I1221 " --> pdb=" O ASN I1217 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N MET I1222 " --> pdb=" O TYR I1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1217 through 1222' Processing helix chain 'L' and resid 1091 through 1095 removed outlier: 4.753A pdb=" N ILE L1095 " --> pdb=" O ASP L1091 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1091 through 1095' Processing helix chain 'L' and resid 1114 through 1119 removed outlier: 3.865A pdb=" N LEU L1119 " --> pdb=" O LEU L1115 " (cutoff:3.500A) Processing helix chain 'L' and resid 1137 through 1142 removed outlier: 4.848A pdb=" N LYS L1141 " --> pdb=" O GLN L1137 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG L1142 " --> pdb=" O CYS L1138 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1137 through 1142' Processing helix chain 'L' and resid 1180 through 1194 Processing helix chain 'L' and resid 1217 through 1222 removed outlier: 4.608A pdb=" N PHE L1221 " --> pdb=" O ASN L1217 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET L1222 " --> pdb=" O TYR L1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1217 through 1222' 259 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 321 hydrogen bonds 642 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 288 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3309 1.33 - 1.45: 5328 1.45 - 1.57: 8244 1.57 - 1.69: 669 1.69 - 1.81: 68 Bond restraints: 17618 Sorted by residual: bond pdb=" CA LYS I1077 " pdb=" C LYS I1077 " ideal model delta sigma weight residual 1.519 1.559 -0.040 1.19e-02 7.06e+03 1.13e+01 bond pdb=" O3' DC A 163 " pdb=" P DC A 164 " ideal model delta sigma weight residual 1.607 1.563 0.044 1.50e-02 4.44e+03 8.50e+00 bond pdb=" C2 SAM L1504 " pdb=" N3 SAM L1504 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.49e+00 bond pdb=" C2 SAM I1501 " pdb=" N3 SAM I1501 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.25e+00 bond pdb=" C2 SAM L1504 " pdb=" N1 SAM L1504 " ideal model delta sigma weight residual 1.329 1.381 -0.052 2.00e-02 2.50e+03 6.85e+00 ... (remaining 17613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 24368 1.82 - 3.65: 775 3.65 - 5.47: 68 5.47 - 7.30: 13 7.30 - 9.12: 9 Bond angle restraints: 25233 Sorted by residual: angle pdb=" N LYS I1181 " pdb=" CA LYS I1181 " pdb=" C LYS I1181 " ideal model delta sigma weight residual 110.97 116.84 -5.87 1.09e+00 8.42e-01 2.90e+01 angle pdb=" N LYS L1234 " pdb=" CA LYS L1234 " pdb=" C LYS L1234 " ideal model delta sigma weight residual 109.46 117.84 -8.38 1.66e+00 3.63e-01 2.55e+01 angle pdb=" N VAL G 54 " pdb=" CA VAL G 54 " pdb=" C VAL G 54 " ideal model delta sigma weight residual 111.81 107.50 4.31 8.60e-01 1.35e+00 2.52e+01 angle pdb=" C5' DC A 163 " pdb=" C4' DC A 163 " pdb=" O4' DC A 163 " ideal model delta sigma weight residual 109.40 116.86 -7.46 1.50e+00 4.44e-01 2.48e+01 angle pdb=" N SER G 113 " pdb=" CA SER G 113 " pdb=" C SER G 113 " ideal model delta sigma weight residual 111.28 116.62 -5.34 1.09e+00 8.42e-01 2.40e+01 ... (remaining 25228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.42: 7558 27.42 - 54.85: 1936 54.85 - 82.27: 284 82.27 - 109.69: 2 109.69 - 137.12: 2 Dihedral angle restraints: 9782 sinusoidal: 6240 harmonic: 3542 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C4' DC K 36 " pdb=" C3' DC K 36 " pdb=" O3' DC K 36 " pdb=" P DT K 37 " ideal model delta sinusoidal sigma weight residual -140.00 -2.88 -137.12 1 3.50e+01 8.16e-04 1.36e+01 dihedral pdb=" C4' DC A 150 " pdb=" C3' DC A 150 " pdb=" O3' DC A 150 " pdb=" P DA A 151 " ideal model delta sinusoidal sigma weight residual 220.00 83.97 136.03 1 3.50e+01 8.16e-04 1.35e+01 ... (remaining 9779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2473 0.060 - 0.121: 324 0.121 - 0.181: 31 0.181 - 0.241: 5 0.241 - 0.302: 1 Chirality restraints: 2834 Sorted by residual: chirality pdb=" C4' DC A 163 " pdb=" C5' DC A 163 " pdb=" O4' DC A 163 " pdb=" C3' DC A 163 " both_signs ideal model delta sigma weight residual False -2.53 -2.22 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C2' SAM I1501 " pdb=" C1' SAM I1501 " pdb=" C3' SAM I1501 " pdb=" O2' SAM I1501 " both_signs ideal model delta sigma weight residual False -2.76 -2.57 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CA LYS L1234 " pdb=" N LYS L1234 " pdb=" C LYS L1234 " pdb=" CB LYS L1234 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 2831 not shown) Planarity restraints: 2056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 99 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO H 100 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN L1233 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" C GLN L1233 " -0.038 2.00e-02 2.50e+03 pdb=" O GLN L1233 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS L1234 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 89 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C VAL E 89 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL E 89 " -0.014 2.00e-02 2.50e+03 pdb=" N NLE E 90 " -0.013 2.00e-02 2.50e+03 ... (remaining 2053 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 7 1.88 - 2.64: 236 2.64 - 3.39: 18368 3.39 - 4.15: 41615 4.15 - 4.90: 67967 Nonbonded interactions: 128193 Sorted by model distance: nonbonded pdb=" OP1 DG A 87 " pdb=" NH1 ARG L1287 " model vdw 1.131 3.120 nonbonded pdb=" OP1 DG A 87 " pdb=" CZ ARG L1287 " model vdw 1.402 3.270 nonbonded pdb=" O5' DG A 87 " pdb=" NH2 ARG L1287 " model vdw 1.412 3.120 nonbonded pdb=" OP1 DC K 165 " pdb=" NZ LYS I1074 " model vdw 1.605 3.120 nonbonded pdb=" OP1 DG A 87 " pdb=" NH2 ARG L1287 " model vdw 1.724 3.120 ... (remaining 128188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 27 through 121) } ncs_group { reference = chain 'E' selection = (chain 'M' and resid 35 through 134) } ncs_group { reference = (chain 'I' and (resid 1066 through 1287 or resid 1502 through 1503)) selection = (chain 'L' and (resid 1066 through 1287 or resid 1502 through 1503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.93 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.180 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.640 17632 Z= 0.336 Angle : 0.775 21.556 25239 Z= 0.447 Chirality : 0.042 0.302 2834 Planarity : 0.005 0.058 2056 Dihedral : 26.258 137.115 7500 Min Nonbonded Distance : 1.131 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.75 % Favored : 91.17 % Rotamer: Outliers : 1.36 % Allowed : 3.31 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.19 (0.17), residues: 1189 helix: -2.99 (0.16), residues: 548 sheet: -4.54 (0.47), residues: 54 loop : -3.85 (0.19), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 129 TYR 0.024 0.002 TYR C 50 PHE 0.016 0.002 PHE I1170 TRP 0.009 0.002 TRP L1157 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00579 (17618) covalent geometry : angle 0.74632 (25233) hydrogen bonds : bond 0.12823 ( 580) hydrogen bonds : angle 5.03643 ( 1419) metal coordination : bond 0.22016 ( 14) metal coordination : angle 13.46756 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: M 56 LYS cc_start: 0.8685 (ttpt) cc_final: 0.8449 (ttpp) REVERT: D 39 TYR cc_start: 0.8196 (t80) cc_final: 0.7920 (t80) REVERT: D 83 ARG cc_start: 0.8450 (mmt-90) cc_final: 0.8191 (mmt90) REVERT: H 68 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7207 (pt0) REVERT: I 1077 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6802 (mmtt) outliers start: 14 outliers final: 4 residues processed: 182 average time/residue: 0.2010 time to fit residues: 48.1934 Evaluate side-chains 136 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1262 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 70.0000 chunk 149 optimal weight: 8.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 125 GLN G 38 ASN I1066 ASN I1192 HIS I1233 GLN I1262 ASN L1075 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.191329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.136274 restraints weight = 22277.907| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 4.02 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17632 Z= 0.235 Angle : 0.640 5.818 25239 Z= 0.367 Chirality : 0.040 0.149 2834 Planarity : 0.005 0.053 2056 Dihedral : 29.415 140.707 5102 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 1.46 % Allowed : 9.64 % Favored : 88.90 % 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: -4.21 (0.20), residues: 1189 helix: -2.05 (0.19), residues: 550 sheet: -3.38 (0.45), residues: 90 loop : -3.50 (0.21), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L1287 TYR 0.013 0.002 TYR D 118 PHE 0.013 0.002 PHE I1170 TRP 0.009 0.002 TRP L1157 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00544 (17618) covalent geometry : angle 0.63814 (25233) hydrogen bonds : bond 0.07289 ( 580) hydrogen bonds : angle 2.85813 ( 1419) metal coordination : bond 0.00348 ( 14) metal coordination : angle 3.06686 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: M 56 LYS cc_start: 0.8514 (ttpt) cc_final: 0.8281 (ttpp) REVERT: D 39 TYR cc_start: 0.8186 (t80) cc_final: 0.7953 (t80) REVERT: I 1077 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6855 (mmtt) REVERT: L 1135 GLN cc_start: 0.7956 (mt0) cc_final: 0.7742 (mt0) REVERT: L 1234 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8600 (pttm) outliers start: 15 outliers final: 9 residues processed: 139 average time/residue: 0.1819 time to fit residues: 34.3387 Evaluate side-chains 137 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1251 ILE Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 94 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 147 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN F 25 ASN I1224 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.192386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140972 restraints weight = 22429.484| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.43 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17632 Z= 0.170 Angle : 0.593 5.998 25239 Z= 0.345 Chirality : 0.038 0.144 2834 Planarity : 0.004 0.049 2056 Dihedral : 29.370 140.420 5099 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.97 % Allowed : 12.07 % Favored : 86.95 % 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: -3.63 (0.21), residues: 1189 helix: -1.46 (0.20), residues: 547 sheet: -3.27 (0.45), residues: 90 loop : -3.28 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L1287 TYR 0.012 0.001 TYR D 118 PHE 0.013 0.001 PHE H 67 TRP 0.007 0.001 TRP L1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00376 (17618) covalent geometry : angle 0.59208 (25233) hydrogen bonds : bond 0.06265 ( 580) hydrogen bonds : angle 2.75350 ( 1419) metal coordination : bond 0.00385 ( 14) metal coordination : angle 2.29801 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.467 Fit side-chains REVERT: M 56 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8305 (ttpp) REVERT: D 39 TYR cc_start: 0.8252 (t80) cc_final: 0.7985 (t80) REVERT: D 83 ARG cc_start: 0.8450 (mmt-90) cc_final: 0.8153 (mmt90) REVERT: I 1077 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6822 (mmtt) REVERT: L 1278 ASP cc_start: 0.4580 (OUTLIER) cc_final: 0.3911 (t0) outliers start: 10 outliers final: 5 residues processed: 134 average time/residue: 0.1881 time to fit residues: 33.8996 Evaluate side-chains 134 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1251 ILE Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 101 optimal weight: 7.9990 chunk 137 optimal weight: 50.0000 chunk 65 optimal weight: 0.0980 chunk 12 optimal weight: 0.0270 chunk 104 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 81 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 overall best weight: 3.8244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.191050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139952 restraints weight = 22320.382| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.37 r_work: 0.2736 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17632 Z= 0.241 Angle : 0.625 6.642 25239 Z= 0.360 Chirality : 0.040 0.163 2834 Planarity : 0.004 0.051 2056 Dihedral : 29.369 140.991 5095 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 1.75 % Allowed : 13.24 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.21), residues: 1189 helix: -1.26 (0.20), residues: 550 sheet: -3.21 (0.46), residues: 90 loop : -3.10 (0.22), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L1287 TYR 0.013 0.002 TYR D 118 PHE 0.014 0.002 PHE I1170 TRP 0.007 0.002 TRP L1157 HIS 0.005 0.001 HIS M 113 Details of bonding type rmsd covalent geometry : bond 0.00561 (17618) covalent geometry : angle 0.62320 (25233) hydrogen bonds : bond 0.07364 ( 580) hydrogen bonds : angle 2.76989 ( 1419) metal coordination : bond 0.00339 ( 14) metal coordination : angle 2.70766 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.357 Fit side-chains REVERT: M 56 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8777 (ttpp) REVERT: D 39 TYR cc_start: 0.9021 (t80) cc_final: 0.8807 (t80) REVERT: D 68 GLU cc_start: 0.8636 (pp20) cc_final: 0.8434 (pp20) REVERT: I 1077 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6603 (mmtt) REVERT: L 1169 GLU cc_start: 0.7890 (mp0) cc_final: 0.7047 (mp0) REVERT: L 1278 ASP cc_start: 0.5269 (OUTLIER) cc_final: 0.4267 (t0) outliers start: 18 outliers final: 11 residues processed: 144 average time/residue: 0.1787 time to fit residues: 35.0582 Evaluate side-chains 144 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1237 VAL Chi-restraints excluded: chain I residue 1251 ILE Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 22 optimal weight: 1.9990 chunk 135 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 131 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1233 GLN L1126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.192030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.135577 restraints weight = 22270.039| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.62 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17632 Z= 0.173 Angle : 0.594 8.919 25239 Z= 0.344 Chirality : 0.037 0.147 2834 Planarity : 0.004 0.050 2056 Dihedral : 29.340 141.051 5095 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.66 % Allowed : 14.12 % Favored : 84.23 % 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: -3.08 (0.22), residues: 1189 helix: -0.96 (0.21), residues: 548 sheet: -3.15 (0.46), residues: 90 loop : -3.02 (0.22), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 30 TYR 0.012 0.001 TYR D 118 PHE 0.013 0.001 PHE H 67 TRP 0.007 0.001 TRP L1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00386 (17618) covalent geometry : angle 0.59293 (25233) hydrogen bonds : bond 0.06407 ( 580) hydrogen bonds : angle 2.74162 ( 1419) metal coordination : bond 0.00306 ( 14) metal coordination : angle 2.32525 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.469 Fit side-chains REVERT: M 56 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8232 (ttpp) REVERT: D 30 ARG cc_start: 0.7724 (mtp85) cc_final: 0.6898 (mpt180) REVERT: D 39 TYR cc_start: 0.8181 (t80) cc_final: 0.7939 (t80) REVERT: D 83 ARG cc_start: 0.8401 (mmt180) cc_final: 0.8133 (mmt90) REVERT: E 37 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8071 (mtmt) REVERT: E 53 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8349 (ptt90) REVERT: I 1077 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6780 (mmtt) REVERT: L 1169 GLU cc_start: 0.6764 (mp0) cc_final: 0.6490 (mp0) REVERT: L 1278 ASP cc_start: 0.4842 (OUTLIER) cc_final: 0.4103 (t0) outliers start: 17 outliers final: 10 residues processed: 144 average time/residue: 0.1731 time to fit residues: 33.7703 Evaluate side-chains 145 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1237 VAL Chi-restraints excluded: chain I residue 1251 ILE Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1135 GLN Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 7 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 149 optimal weight: 0.0970 chunk 18 optimal weight: 0.0970 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 137 optimal weight: 50.0000 chunk 27 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.192551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138710 restraints weight = 22310.294| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.48 r_work: 0.2749 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 17632 Z= 0.161 Angle : 0.580 10.840 25239 Z= 0.336 Chirality : 0.037 0.157 2834 Planarity : 0.004 0.052 2056 Dihedral : 29.310 141.208 5095 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.66 % Allowed : 14.41 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.22), residues: 1189 helix: -0.76 (0.21), residues: 548 sheet: -3.13 (0.46), residues: 90 loop : -2.95 (0.22), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L1287 TYR 0.010 0.001 TYR D 118 PHE 0.013 0.001 PHE H 67 TRP 0.009 0.001 TRP L1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00355 (17618) covalent geometry : angle 0.57944 (25233) hydrogen bonds : bond 0.06006 ( 580) hydrogen bonds : angle 2.67980 ( 1419) metal coordination : bond 0.00300 ( 14) metal coordination : angle 2.19527 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.415 Fit side-chains REVERT: M 56 LYS cc_start: 0.8953 (ttpt) cc_final: 0.8716 (ttpp) REVERT: D 30 ARG cc_start: 0.7779 (mtp85) cc_final: 0.6803 (mmt-90) REVERT: D 39 TYR cc_start: 0.9024 (t80) cc_final: 0.8811 (t80) REVERT: D 83 ARG cc_start: 0.8850 (mmt180) cc_final: 0.8552 (mmt90) REVERT: E 37 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8165 (mtmt) REVERT: I 1077 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6530 (mmtt) REVERT: I 1132 ASP cc_start: 0.7615 (m-30) cc_final: 0.7386 (t0) REVERT: L 1169 GLU cc_start: 0.7913 (mp0) cc_final: 0.7041 (mp0) REVERT: L 1255 MET cc_start: 0.6239 (pmm) cc_final: 0.5571 (pmm) REVERT: L 1278 ASP cc_start: 0.5140 (OUTLIER) cc_final: 0.4166 (t0) outliers start: 17 outliers final: 9 residues processed: 142 average time/residue: 0.1889 time to fit residues: 36.2032 Evaluate side-chains 141 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1237 VAL Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1135 GLN Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 136 optimal weight: 0.0000 chunk 92 optimal weight: 30.0000 chunk 19 optimal weight: 0.0970 chunk 67 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.193309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.134621 restraints weight = 22164.489| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.40 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17632 Z= 0.143 Angle : 0.562 7.522 25239 Z= 0.328 Chirality : 0.036 0.153 2834 Planarity : 0.004 0.051 2056 Dihedral : 29.284 141.286 5095 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.56 % Allowed : 14.70 % Favored : 83.74 % 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: -2.65 (0.22), residues: 1189 helix: -0.51 (0.21), residues: 548 sheet: -3.13 (0.46), residues: 90 loop : -2.86 (0.23), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I1185 TYR 0.009 0.001 TYR H 39 PHE 0.012 0.001 PHE H 67 TRP 0.007 0.001 TRP L1157 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00296 (17618) covalent geometry : angle 0.56110 (25233) hydrogen bonds : bond 0.05452 ( 580) hydrogen bonds : angle 2.65381 ( 1419) metal coordination : bond 0.00313 ( 14) metal coordination : angle 1.96756 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.508 Fit side-chains REVERT: M 56 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8207 (ttpp) REVERT: D 30 ARG cc_start: 0.7592 (mtp85) cc_final: 0.6955 (mmt-90) REVERT: D 39 TYR cc_start: 0.8089 (t80) cc_final: 0.7863 (t80) REVERT: D 83 ARG cc_start: 0.8270 (mmt180) cc_final: 0.8024 (mmt90) REVERT: E 37 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8052 (mtmt) REVERT: H 83 ARG cc_start: 0.8238 (mmt90) cc_final: 0.8029 (mpt180) REVERT: I 1077 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6746 (mmtt) REVERT: L 1255 MET cc_start: 0.5419 (pmm) cc_final: 0.5045 (pmm) REVERT: L 1278 ASP cc_start: 0.4709 (OUTLIER) cc_final: 0.4001 (t0) outliers start: 16 outliers final: 9 residues processed: 141 average time/residue: 0.1769 time to fit residues: 33.9650 Evaluate side-chains 138 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1237 VAL Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1135 GLN Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 137 optimal weight: 0.9990 chunk 107 optimal weight: 0.0060 chunk 61 optimal weight: 0.0170 chunk 81 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 overall best weight: 1.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.193470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135270 restraints weight = 22338.431| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.66 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17632 Z= 0.155 Angle : 0.558 9.135 25239 Z= 0.324 Chirality : 0.036 0.158 2834 Planarity : 0.004 0.054 2056 Dihedral : 29.231 141.682 5095 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.85 % Allowed : 14.80 % Favored : 83.35 % 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: -2.42 (0.22), residues: 1189 helix: -0.31 (0.21), residues: 549 sheet: -2.82 (0.50), residues: 80 loop : -2.83 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I1133 TYR 0.009 0.001 TYR D 118 PHE 0.010 0.001 PHE H 67 TRP 0.011 0.001 TRP L1157 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00339 (17618) covalent geometry : angle 0.55733 (25233) hydrogen bonds : bond 0.05458 ( 580) hydrogen bonds : angle 2.52827 ( 1419) metal coordination : bond 0.00278 ( 14) metal coordination : angle 2.18635 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.321 Fit side-chains REVERT: M 56 LYS cc_start: 0.8439 (ttpt) cc_final: 0.8178 (ttpp) REVERT: D 30 ARG cc_start: 0.7578 (mtp85) cc_final: 0.6896 (mmt-90) REVERT: D 83 ARG cc_start: 0.8250 (mmt180) cc_final: 0.8036 (mmt90) REVERT: E 37 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8068 (mtmt) REVERT: I 1068 ARG cc_start: 0.3422 (OUTLIER) cc_final: 0.2768 (ttm170) REVERT: I 1077 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6710 (mmtp) REVERT: L 1255 MET cc_start: 0.5628 (pmm) cc_final: 0.5063 (pmm) REVERT: L 1278 ASP cc_start: 0.4779 (OUTLIER) cc_final: 0.4091 (t0) outliers start: 19 outliers final: 8 residues processed: 144 average time/residue: 0.1831 time to fit residues: 35.6620 Evaluate side-chains 136 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 1068 ARG Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1237 VAL Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1135 GLN Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 3 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 102 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 30.0000 chunk 18 optimal weight: 0.2980 chunk 96 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 106 optimal weight: 40.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.193967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142962 restraints weight = 22371.100| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.45 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17632 Z= 0.153 Angle : 0.547 9.193 25239 Z= 0.316 Chirality : 0.035 0.150 2834 Planarity : 0.004 0.055 2056 Dihedral : 29.148 141.880 5095 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.36 % Allowed : 15.09 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.23), residues: 1189 helix: -0.12 (0.22), residues: 552 sheet: -2.81 (0.51), residues: 80 loop : -2.68 (0.23), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I1160 TYR 0.008 0.001 TYR D 118 PHE 0.010 0.001 PHE H 67 TRP 0.008 0.001 TRP L1157 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00335 (17618) covalent geometry : angle 0.54607 (25233) hydrogen bonds : bond 0.05205 ( 580) hydrogen bonds : angle 2.43550 ( 1419) metal coordination : bond 0.00264 ( 14) metal coordination : angle 2.27480 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.407 Fit side-chains REVERT: M 56 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8197 (ttpp) REVERT: D 30 ARG cc_start: 0.7484 (mtp85) cc_final: 0.7236 (mmt-90) REVERT: D 39 TYR cc_start: 0.8181 (t80) cc_final: 0.7867 (t80) REVERT: D 40 LYS cc_start: 0.9201 (mttt) cc_final: 0.8971 (mttt) REVERT: D 83 ARG cc_start: 0.8422 (mmt180) cc_final: 0.8108 (mmt90) REVERT: E 37 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7999 (mtmt) REVERT: I 1068 ARG cc_start: 0.3172 (OUTLIER) cc_final: 0.2552 (ttm170) REVERT: I 1077 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6619 (mmtt) REVERT: L 1278 ASP cc_start: 0.4676 (OUTLIER) cc_final: 0.4070 (t0) outliers start: 14 outliers final: 8 residues processed: 138 average time/residue: 0.1919 time to fit residues: 35.7156 Evaluate side-chains 137 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 1068 ARG Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1237 VAL Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1135 GLN Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 47 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.194798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144310 restraints weight = 22376.440| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.41 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17632 Z= 0.133 Angle : 0.545 9.893 25239 Z= 0.315 Chirality : 0.035 0.206 2834 Planarity : 0.004 0.056 2056 Dihedral : 29.136 141.785 5095 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.27 % Allowed : 15.09 % Favored : 83.64 % 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: -2.03 (0.23), residues: 1189 helix: 0.04 (0.22), residues: 554 sheet: -2.83 (0.51), residues: 80 loop : -2.63 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I1160 TYR 0.008 0.001 TYR H 39 PHE 0.011 0.001 PHE H 67 TRP 0.009 0.001 TRP L1157 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00272 (17618) covalent geometry : angle 0.54450 (25233) hydrogen bonds : bond 0.04735 ( 580) hydrogen bonds : angle 2.46597 ( 1419) metal coordination : bond 0.00252 ( 14) metal coordination : angle 2.11183 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.416 Fit side-chains REVERT: M 56 LYS cc_start: 0.8490 (ttpt) cc_final: 0.8189 (ttpp) REVERT: D 30 ARG cc_start: 0.7443 (mtp85) cc_final: 0.7241 (mmt-90) REVERT: D 39 TYR cc_start: 0.8122 (t80) cc_final: 0.7796 (t80) REVERT: D 40 LYS cc_start: 0.9208 (mttt) cc_final: 0.8972 (mttt) REVERT: D 83 ARG cc_start: 0.8380 (mmt180) cc_final: 0.8065 (mmt90) REVERT: E 37 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7988 (mtmt) REVERT: I 1068 ARG cc_start: 0.3026 (OUTLIER) cc_final: 0.2570 (ttm170) REVERT: I 1077 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6659 (mmtt) REVERT: L 1278 ASP cc_start: 0.4655 (OUTLIER) cc_final: 0.4085 (t0) outliers start: 13 outliers final: 7 residues processed: 135 average time/residue: 0.1842 time to fit residues: 33.3066 Evaluate side-chains 134 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1068 ARG Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1237 VAL Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1135 GLN Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1278 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 67 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 91 optimal weight: 80.0000 chunk 37 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.194406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139663 restraints weight = 22329.254| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.97 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17632 Z= 0.151 Angle : 0.540 7.516 25239 Z= 0.312 Chirality : 0.035 0.131 2834 Planarity : 0.004 0.056 2056 Dihedral : 29.089 142.123 5095 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.17 % Allowed : 15.38 % Favored : 83.45 % 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: -1.88 (0.23), residues: 1189 helix: 0.17 (0.22), residues: 551 sheet: -2.76 (0.52), residues: 80 loop : -2.55 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I1185 TYR 0.009 0.001 TYR D 118 PHE 0.011 0.001 PHE H 67 TRP 0.007 0.001 TRP I1157 HIS 0.003 0.001 HIS M 113 Details of bonding type rmsd covalent geometry : bond 0.00330 (17618) covalent geometry : angle 0.53916 (25233) hydrogen bonds : bond 0.05105 ( 580) hydrogen bonds : angle 2.37360 ( 1419) metal coordination : bond 0.00259 ( 14) metal coordination : angle 1.96713 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4073.22 seconds wall clock time: 69 minutes 54.32 seconds (4194.32 seconds total)