Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 09:32:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crq_30456/04_2023/7crq_30456_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crq_30456/04_2023/7crq_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crq_30456/04_2023/7crq_30456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crq_30456/04_2023/7crq_30456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crq_30456/04_2023/7crq_30456_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crq_30456/04_2023/7crq_30456_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "D GLU 102": "OE1" <-> "OE2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "I ARG 1097": "NH1" <-> "NH2" Residue "I GLU 1122": "OE1" <-> "OE2" Residue "I ARG 1133": "NH1" <-> "NH2" Residue "I ARG 1142": "NH1" <-> "NH2" Residue "I ARG 1160": "NH1" <-> "NH2" Residue "I GLU 1182": "OE1" <-> "OE2" Residue "I GLU 1193": "OE1" <-> "OE2" Residue "I ARG 1220": "NH1" <-> "NH2" Residue "I ARG 1242": "NH1" <-> "NH2" Residue "I ARG 1270": "NH1" <-> "NH2" Residue "I GLU 1272": "OE1" <-> "OE2" Residue "I ARG 1287": "NH1" <-> "NH2" Residue "L GLU 1094": "OE1" <-> "OE2" Residue "L ARG 1097": "NH1" <-> "NH2" Residue "L GLU 1105": "OE1" <-> "OE2" Residue "L GLU 1122": "OE1" <-> "OE2" Residue "L ARG 1133": "NH1" <-> "NH2" Residue "L ARG 1142": "NH1" <-> "NH2" Residue "L GLU 1148": "OE1" <-> "OE2" Residue "L ARG 1160": "NH1" <-> "NH2" Residue "L ARG 1220": "NH1" <-> "NH2" Residue "L ARG 1242": "NH1" <-> "NH2" Residue "L ARG 1270": "NH1" <-> "NH2" Residue "L ARG 1287": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/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: {'ARG:plan': 1, 'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 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: {'ARG:plan': 1, 'NLE:plan-1': 3} 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: 9.04, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 7.58 Conformation dependent library (CDL) restraints added in 1.5 seconds 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... running ksdssp... Secondary structure from input PDB file: 40 helices and 4 sheets defined 38.4% alpha, 3.7% beta 121 base pairs and 288 stacking pairs defined. Time for finding SS restraints: 6.12 Creating SS restraints... Processing helix chain 'M' and resid 46 through 54 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) Processing helix chain 'M' and resid 64 through 76 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) Processing helix chain 'M' and resid 88 through 113 removed outlier: 3.826A pdb=" N ALA M 91 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU M 92 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN M 93 " --> pdb=" O NLE M 90 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU M 94 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER M 96 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU M 97 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL M 101 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE M 104 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU M 105 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR M 107 " --> pdb=" O PHE M 104 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN M 108 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 131 removed outlier: 3.736A pdb=" N LEU M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 32 through 41 removed outlier: 3.687A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 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 83 through 93 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 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 35 removed outlier: 3.659A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 73 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 80 through 87 removed outlier: 3.604A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 96 No H-bonds generated for 'chain 'C' and resid 93 through 96' Processing helix chain 'D' and resid 35 through 45 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 53 through 80 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 88 through 96 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) Processing helix chain 'D' and resid 102 through 119 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) Processing helix chain 'E' and resid 51 through 54 No H-bonds generated for 'chain 'E' and resid 51 through 54' Processing helix chain 'E' and resid 64 through 76 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) Processing helix chain 'E' and resid 92 through 113 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 123 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 51 through 75 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) Processing helix chain 'F' and resid 83 through 93 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 17 through 21 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 17 through 21' Processing helix chain 'G' and resid 27 through 35 removed outlier: 3.607A pdb=" N ARG G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 55 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) Processing helix chain 'G' and resid 57 through 73 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) removed outlier: 4.197A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 87 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) Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 38 through 45 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 55 through 80 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) Processing helix chain 'H' and resid 88 through 98 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) Processing helix chain 'H' and resid 106 through 120 removed outlier: 3.627A pdb=" N THR H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 1181 through 1193 Processing helix chain 'I' and resid 1218 through 1220 No H-bonds generated for 'chain 'I' and resid 1218 through 1220' Processing helix chain 'L' and resid 1115 through 1118 No H-bonds generated for 'chain 'L' and resid 1115 through 1118' Processing helix chain 'L' and resid 1181 through 1193 Processing sheet with id= A, first strand: chain 'I' and resid 1177 through 1179 removed outlier: 6.585A pdb=" N ILE I1210 " --> pdb=" O THR I1203 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THR I1203 " --> pdb=" O ILE I1210 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 1230 through 1237 removed outlier: 3.651A pdb=" N GLN I1233 " --> pdb=" O GLY I1244 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 1177 through 1179 removed outlier: 3.524A pdb=" N THR L1205 " --> pdb=" O ARG L1208 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE L1210 " --> pdb=" O THR L1203 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N THR L1203 " --> pdb=" O ILE L1210 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 1230 through 1237 removed outlier: 3.709A pdb=" N GLU L1231 " --> pdb=" O PHE L1246 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN L1233 " --> pdb=" O GLY L1244 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY L1244 " --> pdb=" O GLN L1233 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 645 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: 5.95 Time building geometry restraints manager: 7.67 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: 97.61 - 104.89: 1475 104.89 - 112.17: 9478 112.17 - 119.44: 5473 119.44 - 126.72: 7776 126.72 - 134.00: 1031 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: 7374 27.42 - 54.85: 1788 54.85 - 82.27: 276 82.27 - 109.69: 2 109.69 - 137.12: 2 Dihedral angle restraints: 9442 sinusoidal: 5900 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 9439 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: 235 2.64 - 3.39: 18394 3.39 - 4.15: 41681 4.15 - 4.90: 67980 Nonbonded interactions: 128297 Sorted by model distance: nonbonded pdb=" OP1 DG A 87 " pdb=" NH1 ARG L1287 " model vdw 1.131 2.520 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 2.520 nonbonded pdb=" OP1 DC K 165 " pdb=" NZ LYS I1074 " model vdw 1.605 2.520 nonbonded pdb=" OP1 DG A 87 " pdb=" NH2 ARG L1287 " model vdw 1.724 2.520 ... (remaining 128292 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 3.780 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 50.270 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.680 ------------------------------------------------------------------------------- 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 : 0.006 0.058 17618 Z= 0.349 Angle : 0.746 9.122 25233 Z= 0.446 Chirality : 0.042 0.302 2834 Planarity : 0.005 0.058 2056 Dihedral : 26.164 137.115 7160 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 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 1.404 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 182 average time/residue: 0.4516 time to fit residues: 108.7268 Evaluate side-chains 134 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 1.394 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2181 time to fit residues: 3.1028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 77 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 44 GLN E 125 GLN G 38 ASN I1066 ASN ** I1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1224 HIS I1233 GLN I1262 ASN L1075 HIS L1268 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 17618 Z= 0.161 Angle : 0.548 5.444 25233 Z= 0.321 Chirality : 0.036 0.151 2834 Planarity : 0.004 0.041 2056 Dihedral : 29.582 141.433 4749 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.20), residues: 1189 helix: -1.81 (0.20), residues: 541 sheet: -2.80 (0.54), residues: 66 loop : -3.35 (0.20), residues: 582 *********************** 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 137 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.537 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 134 average time/residue: 0.4292 time to fit residues: 78.3655 Evaluate side-chains 128 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 1.367 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1422 time to fit residues: 2.6903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 37 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 122 optimal weight: 50.0000 chunk 136 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1192 HIS I1224 HIS I1262 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.063 17618 Z= 0.483 Angle : 0.688 7.564 25233 Z= 0.391 Chirality : 0.044 0.217 2834 Planarity : 0.005 0.049 2056 Dihedral : 29.776 140.799 4749 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.20), residues: 1189 helix: -1.89 (0.20), residues: 530 sheet: -2.57 (0.58), residues: 66 loop : -3.18 (0.21), residues: 593 *********************** 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 146 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.246 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 139 average time/residue: 0.4227 time to fit residues: 79.1850 Evaluate side-chains 137 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1615 time to fit residues: 4.5279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 92 optimal weight: 30.0000 chunk 137 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1224 HIS I1262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 17618 Z= 0.203 Angle : 0.564 7.183 25233 Z= 0.330 Chirality : 0.036 0.139 2834 Planarity : 0.004 0.043 2056 Dihedral : 29.702 141.409 4749 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.21), residues: 1189 helix: -1.39 (0.21), residues: 525 sheet: -2.49 (0.59), residues: 66 loop : -2.96 (0.21), residues: 598 *********************** 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 141 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.463 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 136 average time/residue: 0.4138 time to fit residues: 76.0975 Evaluate side-chains 133 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.417 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1623 time to fit residues: 3.5466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 36 optimal weight: 0.5980 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1224 HIS I1262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 17618 Z= 0.432 Angle : 0.658 7.128 25233 Z= 0.376 Chirality : 0.042 0.211 2834 Planarity : 0.005 0.047 2056 Dihedral : 29.769 141.603 4749 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.21), residues: 1189 helix: -1.53 (0.20), residues: 532 sheet: -2.76 (0.53), residues: 80 loop : -2.99 (0.22), residues: 577 *********************** 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 fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.390 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 142 average time/residue: 0.4238 time to fit residues: 82.0583 Evaluate side-chains 130 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 1.383 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1526 time to fit residues: 3.9963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 146 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN I1224 HIS I1262 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 17618 Z= 0.161 Angle : 0.566 7.552 25233 Z= 0.331 Chirality : 0.037 0.145 2834 Planarity : 0.004 0.053 2056 Dihedral : 29.709 141.553 4749 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.22), residues: 1189 helix: -0.98 (0.21), residues: 526 sheet: -2.69 (0.54), residues: 80 loop : -2.82 (0.22), residues: 583 *********************** 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 133 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 1.469 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 130 average time/residue: 0.4031 time to fit residues: 72.0679 Evaluate side-chains 124 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.411 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1435 time to fit residues: 2.2589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 106 optimal weight: 40.0000 chunk 82 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 91 optimal weight: 80.0000 chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN I1224 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.063 17618 Z= 0.468 Angle : 0.677 9.206 25233 Z= 0.384 Chirality : 0.043 0.194 2834 Planarity : 0.005 0.051 2056 Dihedral : 29.783 141.934 4749 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.21), residues: 1189 helix: -1.34 (0.21), residues: 531 sheet: -2.67 (0.55), residues: 80 loop : -2.91 (0.22), residues: 578 *********************** 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 139 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.540 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 132 average time/residue: 0.4314 time to fit residues: 77.8870 Evaluate side-chains 133 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2104 time to fit residues: 5.7724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 40.0000 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 92 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1224 HIS L1126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 17618 Z= 0.191 Angle : 0.588 9.096 25233 Z= 0.341 Chirality : 0.037 0.139 2834 Planarity : 0.004 0.046 2056 Dihedral : 29.747 141.658 4749 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.22), residues: 1189 helix: -1.03 (0.21), residues: 527 sheet: -2.62 (0.55), residues: 80 loop : -2.83 (0.22), residues: 582 *********************** 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 126 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 1.287 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 123 average time/residue: 0.4230 time to fit residues: 70.8287 Evaluate side-chains 121 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1531 time to fit residues: 2.5943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 30.0000 chunk 127 optimal weight: 30.0000 chunk 135 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 59 optimal weight: 0.0770 chunk 106 optimal weight: 40.0000 chunk 41 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 89 optimal weight: 30.0000 chunk 143 optimal weight: 20.0000 overall best weight: 1.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 17618 Z= 0.219 Angle : 0.580 8.767 25233 Z= 0.335 Chirality : 0.037 0.174 2834 Planarity : 0.004 0.056 2056 Dihedral : 29.713 142.176 4749 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.22), residues: 1189 helix: -0.89 (0.21), residues: 525 sheet: -2.56 (0.56), residues: 80 loop : -2.77 (0.22), residues: 584 *********************** 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 129 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.419 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 127 average time/residue: 0.4072 time to fit residues: 70.8755 Evaluate side-chains 125 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 1.671 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3165 time to fit residues: 3.0354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 150 optimal weight: 30.0000 chunk 138 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 92 optimal weight: 40.0000 chunk 73 optimal weight: 0.0670 chunk 95 optimal weight: 10.0000 chunk 127 optimal weight: 40.0000 overall best weight: 5.1526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.007 0.061 17618 Z= 0.435 Angle : 0.662 8.212 25233 Z= 0.377 Chirality : 0.042 0.186 2834 Planarity : 0.005 0.057 2056 Dihedral : 29.760 142.248 4749 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.22), residues: 1189 helix: -1.22 (0.21), residues: 529 sheet: -2.56 (0.47), residues: 100 loop : -2.91 (0.22), residues: 560 ********************** 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 124 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.434 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 122 average time/residue: 0.4147 time to fit residues: 68.7316 Evaluate side-chains 123 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1416 time to fit residues: 1.9620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 chunk 50 optimal weight: 0.5980 chunk 123 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 6 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.192817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136678 restraints weight = 22344.852| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 4.09 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 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 = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 17618 Z= 0.169 Angle : 0.583 8.653 25233 Z= 0.338 Chirality : 0.037 0.155 2834 Planarity : 0.004 0.053 2056 Dihedral : 29.708 141.815 4749 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.22), residues: 1189 helix: -0.80 (0.21), residues: 525 sheet: -2.53 (0.47), residues: 100 loop : -2.78 (0.23), residues: 564 =============================================================================== Job complete usr+sys time: 2728.99 seconds wall clock time: 50 minutes 19.90 seconds (3019.90 seconds total)