Starting phenix.real_space_refine on Wed Feb 21 06:32:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crq_30456/02_2024/7crq_30456_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crq_30456/02_2024/7crq_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_30456/02_2024/7crq_30456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crq_30456/02_2024/7crq_30456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crq_30456/02_2024/7crq_30456_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crq_30456/02_2024/7crq_30456_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-dev-5238/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: 9.71, per 1000 atoms: 0.58 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: 7.57 Conformation dependent library (CDL) restraints added in 2.0 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: 8.54 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: 6.49 Time building geometry restraints manager: 8.16 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: 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: 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.010 Extract box with map and model: 3.450 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 55.870 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.300 ------------------------------------------------------------------------------- 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 : 26.258 137.115 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 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L1157 HIS 0.005 0.001 HIS E 113 PHE 0.016 0.002 PHE I1170 TYR 0.024 0.002 TYR C 50 ARG 0.005 0.000 ARG E 129 *********************** 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 : 1.367 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: 0.4650 time to fit residues: 112.3821 Evaluate side-chains 136 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 127 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 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: 0.7727 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17618 Z= 0.164 Angle : 0.552 5.232 25233 Z= 0.321 Chirality : 0.036 0.149 2834 Planarity : 0.004 0.041 2056 Dihedral : 29.181 141.410 5102 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.78 % Allowed : 8.28 % Favored : 90.94 % 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: 543 sheet: -2.81 (0.54), residues: 66 loop : -3.36 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L1157 HIS 0.003 0.001 HIS H 79 PHE 0.011 0.001 PHE H 67 TYR 0.011 0.001 TYR M 99 ARG 0.004 0.000 ARG M 42 *********************** 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 136 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.468 Fit side-chains REVERT: M 56 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8369 (ttpp) REVERT: D 39 TYR cc_start: 0.8125 (t80) cc_final: 0.7852 (t80) REVERT: D 83 ARG cc_start: 0.8384 (mmt-90) cc_final: 0.8145 (mmt90) REVERT: I 1077 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6686 (mmtp) REVERT: I 1215 LYS cc_start: 0.6668 (mptt) cc_final: 0.6102 (mmtt) REVERT: L 1135 GLN cc_start: 0.8102 (mt0) cc_final: 0.7890 (mt0) outliers start: 8 outliers final: 4 residues processed: 133 average time/residue: 0.4036 time to fit residues: 72.6474 Evaluate side-chains 130 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1251 ILE Chi-restraints excluded: chain I residue 1262 ASN 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: 6.9990 chunk 93 optimal weight: 40.0000 chunk 37 optimal weight: 7.9990 chunk 137 optimal weight: 30.0000 chunk 148 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1285 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= 0.470 Angle : 0.682 7.446 25233 Z= 0.388 Chirality : 0.043 0.219 2834 Planarity : 0.005 0.049 2056 Dihedral : 29.398 140.656 5095 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 1.85 % Allowed : 11.00 % Favored : 87.15 % 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: -3.78 (0.20), residues: 1189 helix: -1.88 (0.20), residues: 530 sheet: -2.51 (0.59), residues: 66 loop : -3.16 (0.21), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L1235 HIS 0.008 0.001 HIS M 113 PHE 0.017 0.002 PHE I1170 TYR 0.014 0.002 TYR D 118 ARG 0.005 0.001 ARG E 53 *********************** 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 147 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.472 Fit side-chains REVERT: M 56 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8460 (ttpp) REVERT: D 39 TYR cc_start: 0.8281 (t80) cc_final: 0.8011 (t80) REVERT: E 49 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8724 (ptm160) REVERT: I 1077 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6771 (mmtt) outliers start: 19 outliers final: 14 residues processed: 139 average time/residue: 0.4315 time to fit residues: 81.0868 Evaluate side-chains 144 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 81 ASP 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 1135 GLN Chi-restraints excluded: chain I residue 1251 ILE Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1237 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 92 optimal weight: 30.0000 chunk 137 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1499 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= 0.167 Angle : 0.555 7.429 25233 Z= 0.324 Chirality : 0.036 0.141 2834 Planarity : 0.004 0.042 2056 Dihedral : 29.225 141.189 5095 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.85 % Allowed : 11.78 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.21), residues: 1189 helix: -1.27 (0.21), residues: 525 sheet: -2.46 (0.59), residues: 66 loop : -2.88 (0.21), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L1157 HIS 0.003 0.001 HIS H 79 PHE 0.012 0.001 PHE H 67 TYR 0.010 0.001 TYR M 99 ARG 0.004 0.000 ARG D 30 *********************** 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 fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.436 Fit side-chains REVERT: M 56 LYS cc_start: 0.8661 (ttpt) cc_final: 0.8401 (ttpp) REVERT: C 75 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8692 (mtpt) REVERT: D 30 ARG cc_start: 0.7757 (mtp85) cc_final: 0.7141 (mmt-90) REVERT: D 39 TYR cc_start: 0.8163 (t80) cc_final: 0.7897 (t80) REVERT: D 68 GLU cc_start: 0.7756 (pp20) cc_final: 0.7494 (pp20) REVERT: E 37 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7935 (mtmt) REVERT: I 1077 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6616 (mmtt) REVERT: L 1135 GLN cc_start: 0.8076 (mt0) cc_final: 0.7873 (mt0) REVERT: L 1257 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6645 (pp) outliers start: 19 outliers final: 9 residues processed: 140 average time/residue: 0.4085 time to fit residues: 77.6122 Evaluate side-chains 136 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1257 LEU Chi-restraints excluded: chain L residue 1262 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17618 Z= 0.382 Angle : 0.628 7.200 25233 Z= 0.360 Chirality : 0.040 0.161 2834 Planarity : 0.005 0.045 2056 Dihedral : 29.305 141.472 5095 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.63 % Allowed : 12.56 % Favored : 84.81 % 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: -3.22 (0.21), residues: 1189 helix: -1.39 (0.20), residues: 531 sheet: -1.88 (0.68), residues: 56 loop : -2.93 (0.21), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP I1157 HIS 0.006 0.001 HIS M 113 PHE 0.013 0.002 PHE I1170 TYR 0.013 0.002 TYR D 118 ARG 0.004 0.000 ARG F 92 *********************** 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 156 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 1.310 Fit side-chains REVERT: M 56 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8436 (ttpp) REVERT: C 75 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8748 (mtpt) REVERT: D 39 TYR cc_start: 0.8239 (t80) cc_final: 0.7952 (t80) REVERT: E 37 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8155 (mtmt) REVERT: G 95 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8679 (mtpp) REVERT: I 1077 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6629 (mmtt) REVERT: L 1135 GLN cc_start: 0.8103 (mt0) cc_final: 0.7880 (mt0) REVERT: L 1234 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8598 (pttm) REVERT: L 1257 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6662 (pp) outliers start: 27 outliers final: 16 residues processed: 147 average time/residue: 0.4290 time to fit residues: 85.6688 Evaluate side-chains 149 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 32 GLU 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 1135 GLN Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1257 LEU Chi-restraints excluded: chain L residue 1262 ASN Chi-restraints excluded: chain L residue 1271 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** I1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17618 Z= 0.169 Angle : 0.559 7.543 25233 Z= 0.327 Chirality : 0.036 0.139 2834 Planarity : 0.004 0.055 2056 Dihedral : 29.241 141.336 5095 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.95 % Allowed : 13.92 % Favored : 84.13 % 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: -2.86 (0.22), residues: 1189 helix: -0.97 (0.21), residues: 527 sheet: -1.81 (0.69), residues: 56 loop : -2.84 (0.21), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L1157 HIS 0.004 0.001 HIS H 79 PHE 0.016 0.001 PHE H 67 TYR 0.012 0.001 TYR M 99 ARG 0.006 0.000 ARG D 30 *********************** 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 148 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 1.398 Fit side-chains REVERT: M 56 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8397 (ttpp) REVERT: D 30 ARG cc_start: 0.7689 (mtp85) cc_final: 0.7002 (mmt-90) REVERT: D 39 TYR cc_start: 0.8185 (t80) cc_final: 0.7896 (t80) REVERT: E 37 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8016 (mtmt) REVERT: G 95 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8667 (mtpp) REVERT: I 1077 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6585 (mmtt) REVERT: L 1234 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8528 (pttm) REVERT: L 1257 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6656 (pp) outliers start: 20 outliers final: 12 residues processed: 142 average time/residue: 0.3843 time to fit residues: 74.1945 Evaluate side-chains 140 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 E residue 37 LYS Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 32 GLU 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 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1257 LEU Chi-restraints excluded: chain L residue 1262 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 106 optimal weight: 40.0000 chunk 82 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 91 optimal weight: 70.0000 chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1603 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= 0.402 Angle : 0.642 10.048 25233 Z= 0.365 Chirality : 0.041 0.183 2834 Planarity : 0.005 0.056 2056 Dihedral : 29.305 141.722 5095 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.04 % Allowed : 15.09 % Favored : 82.86 % 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: -3.13 (0.22), residues: 1189 helix: -1.22 (0.21), residues: 531 sheet: -2.60 (0.56), residues: 80 loop : -2.86 (0.22), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP I1157 HIS 0.006 0.001 HIS M 113 PHE 0.013 0.002 PHE F 61 TYR 0.013 0.002 TYR D 118 ARG 0.004 0.001 ARG H 83 *********************** 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 148 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 1.357 Fit side-chains REVERT: M 56 LYS cc_start: 0.8716 (ttpt) cc_final: 0.8419 (ttpp) REVERT: C 75 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8751 (mtpt) REVERT: D 30 ARG cc_start: 0.7706 (mtp85) cc_final: 0.7048 (mmt-90) REVERT: D 39 TYR cc_start: 0.8239 (t80) cc_final: 0.7954 (t80) REVERT: E 37 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8152 (mtmt) REVERT: G 95 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8714 (mtpp) REVERT: I 1077 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6625 (mmtt) REVERT: L 1234 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8642 (pttm) REVERT: L 1257 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6890 (pp) outliers start: 21 outliers final: 13 residues processed: 141 average time/residue: 0.3993 time to fit residues: 76.2323 Evaluate side-chains 145 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 E residue 37 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain H residue 32 GLU 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 1135 GLN Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1257 LEU Chi-restraints excluded: chain L residue 1271 THR 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: 0.7980 chunk 28 optimal weight: 6.9990 chunk 92 optimal weight: 40.0000 chunk 99 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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** L1126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17618 Z= 0.289 Angle : 0.613 9.159 25233 Z= 0.351 Chirality : 0.038 0.133 2834 Planarity : 0.004 0.053 2056 Dihedral : 29.300 141.642 5095 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.04 % Allowed : 15.38 % Favored : 82.57 % 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: -3.09 (0.22), residues: 1189 helix: -1.17 (0.21), residues: 531 sheet: -2.58 (0.56), residues: 80 loop : -2.86 (0.22), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP I1157 HIS 0.005 0.001 HIS M 113 PHE 0.012 0.002 PHE H 67 TYR 0.012 0.001 TYR D 118 ARG 0.005 0.000 ARG I1160 *********************** 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 fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 1.406 Fit side-chains REVERT: M 56 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8422 (ttpp) REVERT: D 30 ARG cc_start: 0.7657 (mtp85) cc_final: 0.7089 (mmt-90) REVERT: D 39 TYR cc_start: 0.8224 (t80) cc_final: 0.7940 (t80) REVERT: E 37 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8146 (mtmt) REVERT: G 95 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8705 (mtpp) REVERT: I 1077 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6607 (mmtt) REVERT: L 1234 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8619 (pttm) REVERT: L 1257 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6892 (pp) outliers start: 21 outliers final: 16 residues processed: 138 average time/residue: 0.4016 time to fit residues: 74.9928 Evaluate side-chains 146 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 E residue 37 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 32 GLU 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 1135 GLN Chi-restraints excluded: chain I residue 1251 ILE Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1135 GLN Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1257 LEU Chi-restraints excluded: chain L residue 1262 ASN 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: 6.9990 chunk 81 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 40.0000 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 143 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.007 0.056 17618 Z= 0.411 Angle : 0.648 8.464 25233 Z= 0.368 Chirality : 0.041 0.192 2834 Planarity : 0.005 0.058 2056 Dihedral : 29.305 141.906 5095 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 2.53 % Allowed : 15.29 % Favored : 82.18 % 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: -3.21 (0.22), residues: 1189 helix: -1.32 (0.21), residues: 529 sheet: -2.63 (0.56), residues: 80 loop : -2.88 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L1235 HIS 0.007 0.001 HIS E 113 PHE 0.013 0.002 PHE F 61 TYR 0.013 0.002 TYR D 118 ARG 0.004 0.001 ARG H 69 *********************** 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 153 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 1.350 Fit side-chains REVERT: M 56 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8427 (ttpp) REVERT: C 75 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8754 (mtpt) REVERT: D 30 ARG cc_start: 0.7598 (mtp85) cc_final: 0.7090 (mmt-90) REVERT: D 39 TYR cc_start: 0.8251 (t80) cc_final: 0.7959 (t80) REVERT: E 37 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8136 (mtmt) REVERT: G 95 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8706 (mtpp) REVERT: I 1077 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6617 (mmtt) REVERT: L 1234 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8650 (pttm) REVERT: L 1257 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6888 (pp) outliers start: 26 outliers final: 18 residues processed: 142 average time/residue: 0.4090 time to fit residues: 78.3671 Evaluate side-chains 149 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 37 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 32 GLU 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 1135 GLN Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1135 GLN Chi-restraints excluded: chain L residue 1146 ASP Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1257 LEU Chi-restraints excluded: chain L residue 1271 THR 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: 4.9990 chunk 99 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 138 optimal weight: 0.5980 chunk 119 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 92 optimal weight: 40.0000 chunk 73 optimal weight: 0.0170 chunk 95 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 overall best weight: 2.7224 ------------------------------------------------------------------------------- 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** L1126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17618 Z= 0.251 Angle : 0.600 8.561 25233 Z= 0.346 Chirality : 0.038 0.130 2834 Planarity : 0.004 0.056 2056 Dihedral : 29.282 141.720 5095 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.24 % Allowed : 15.48 % Favored : 82.28 % 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: -3.08 (0.22), residues: 1189 helix: -1.15 (0.21), residues: 527 sheet: -2.62 (0.56), residues: 80 loop : -2.85 (0.22), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L1157 HIS 0.004 0.001 HIS E 113 PHE 0.012 0.001 PHE H 67 TYR 0.011 0.001 TYR D 118 ARG 0.003 0.000 ARG H 83 ********************** 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 147 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 1.337 Fit side-chains REVERT: M 56 LYS cc_start: 0.8723 (ttpt) cc_final: 0.8420 (ttpp) REVERT: D 30 ARG cc_start: 0.7576 (mtp85) cc_final: 0.7083 (mmt-90) REVERT: D 39 TYR cc_start: 0.8211 (t80) cc_final: 0.7922 (t80) REVERT: E 37 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8036 (mtmt) REVERT: E 53 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8544 (ptt90) REVERT: G 95 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8683 (mtpp) REVERT: I 1077 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6596 (mmtt) REVERT: L 1234 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8631 (pttm) REVERT: L 1257 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6873 (pp) outliers start: 23 outliers final: 15 residues processed: 138 average time/residue: 0.4122 time to fit residues: 76.3243 Evaluate side-chains 144 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 E residue 37 LYS Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 32 GLU 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 1135 GLN Chi-restraints excluded: chain I residue 1262 ASN Chi-restraints excluded: chain L residue 1135 GLN Chi-restraints excluded: chain L residue 1146 ASP Chi-restraints excluded: chain L residue 1234 LYS Chi-restraints excluded: chain L residue 1237 VAL Chi-restraints excluded: chain L residue 1257 LEU Chi-restraints excluded: chain L residue 1262 ASN Chi-restraints excluded: chain L residue 1271 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 0.6980 chunk 110 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.0050 chunk 119 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 105 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** I1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.193038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139594 restraints weight = 22306.425| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 4.27 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17618 Z= 0.158 Angle : 0.570 10.592 25233 Z= 0.331 Chirality : 0.036 0.141 2834 Planarity : 0.004 0.054 2056 Dihedral : 29.225 141.603 5095 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.66 % Allowed : 16.46 % Favored : 81.89 % 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: -2.72 (0.22), residues: 1189 helix: -0.78 (0.21), residues: 525 sheet: -2.56 (0.56), residues: 80 loop : -2.71 (0.22), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L1157 HIS 0.003 0.001 HIS H 79 PHE 0.013 0.001 PHE H 67 TYR 0.010 0.001 TYR M 99 ARG 0.003 0.000 ARG H 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2922.82 seconds wall clock time: 53 minutes 46.14 seconds (3226.14 seconds total)