Starting phenix.real_space_refine on Sun Dec 10 09:29:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn3_33309/12_2023/7xn3_33309.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn3_33309/12_2023/7xn3_33309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn3_33309/12_2023/7xn3_33309.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn3_33309/12_2023/7xn3_33309.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn3_33309/12_2023/7xn3_33309.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn3_33309/12_2023/7xn3_33309.pdb" } resolution = 2.9 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 78 5.16 5 C 8682 2.51 5 N 2478 2.21 5 O 2766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 52": "OD1" <-> "OD2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B ARG 99": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "F ASP 52": "OD1" <-> "OD2" Residue "F ASP 75": "OD1" <-> "OD2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 99": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ASP 115": "OD1" <-> "OD2" Residue "F ARG 239": "NH1" <-> "NH2" Residue "F ASP 267": "OD1" <-> "OD2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "F GLU 307": "OE1" <-> "OE2" Residue "E ASP 52": "OD1" <-> "OD2" Residue "E ASP 75": "OD1" <-> "OD2" Residue "E ARG 78": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E ARG 99": "NH1" <-> "NH2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ASP 115": "OD1" <-> "OD2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E ASP 267": "OD1" <-> "OD2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "E GLU 307": "OE1" <-> "OE2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C ASP 75": "OD1" <-> "OD2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ASP 115": "OD1" <-> "OD2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D ASP 267": "OD1" <-> "OD2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D GLU 307": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14016 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2317 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Chain: "B" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2317 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Chain: "F" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2317 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Chain: "E" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2317 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Chain: "C" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2317 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Chain: "D" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2317 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {'PO4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {'PO4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 7.67, per 1000 atoms: 0.55 Number of scatterers: 14016 At special positions: 0 Unit cell: (119.78, 130.38, 83.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 12 15.00 O 2766 8.00 N 2478 7.00 C 8682 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.37 Conformation dependent library (CDL) restraints added in 2.7 seconds 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 24 sheets defined 39.3% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 62 through 79 Processing helix chain 'A' and resid 92 through 96 removed outlier: 4.224A pdb=" N ALA A 95 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 96' Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.755A pdb=" N PHE A 139 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 157 Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.516A pdb=" N ARG A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 284 removed outlier: 3.678A pdb=" N LEU A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 305 Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 62 through 79 Processing helix chain 'B' and resid 92 through 96 removed outlier: 4.224A pdb=" N ALA B 95 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG B 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 96' Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.755A pdb=" N PHE B 139 " --> pdb=" O GLN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 Processing helix chain 'B' and resid 174 through 184 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.517A pdb=" N ARG B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 284 removed outlier: 3.678A pdb=" N LEU B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 305 Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'F' and resid 12 through 23 Processing helix chain 'F' and resid 62 through 79 Processing helix chain 'F' and resid 92 through 96 removed outlier: 4.224A pdb=" N ALA F 95 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG F 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 96' Processing helix chain 'F' and resid 108 through 121 Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.756A pdb=" N PHE F 139 " --> pdb=" O GLN F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 157 Processing helix chain 'F' and resid 174 through 184 Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 258 through 263 removed outlier: 3.516A pdb=" N ARG F 262 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 284 removed outlier: 3.678A pdb=" N LEU F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 305 Processing helix chain 'F' and resid 309 through 313 Processing helix chain 'E' and resid 12 through 23 Processing helix chain 'E' and resid 62 through 79 Processing helix chain 'E' and resid 92 through 96 removed outlier: 4.224A pdb=" N ALA E 95 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 96' Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.755A pdb=" N PHE E 139 " --> pdb=" O GLN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'E' and resid 174 through 184 Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 258 through 263 removed outlier: 3.516A pdb=" N ARG E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 284 removed outlier: 3.678A pdb=" N LEU E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 305 Processing helix chain 'E' and resid 309 through 313 Processing helix chain 'C' and resid 12 through 23 Processing helix chain 'C' and resid 62 through 79 Processing helix chain 'C' and resid 92 through 96 removed outlier: 4.224A pdb=" N ALA C 95 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG C 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 96' Processing helix chain 'C' and resid 108 through 121 Processing helix chain 'C' and resid 134 through 139 removed outlier: 3.755A pdb=" N PHE C 139 " --> pdb=" O GLN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 157 Processing helix chain 'C' and resid 174 through 184 Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.516A pdb=" N ARG C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 284 removed outlier: 3.678A pdb=" N LEU C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 305 Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 62 through 79 Processing helix chain 'D' and resid 92 through 96 removed outlier: 4.224A pdb=" N ALA D 95 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG D 96 " --> pdb=" O GLY D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 96' Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 134 through 139 removed outlier: 3.755A pdb=" N PHE D 139 " --> pdb=" O GLN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 174 through 184 Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.517A pdb=" N ARG D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 284 removed outlier: 3.678A pdb=" N LEU D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 309 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.503A pdb=" N ILE A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL A 88 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 128 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 125 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL A 146 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR A 127 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 206 through 208 removed outlier: 4.174A pdb=" N ASP A 188 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 166 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 165 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL A 219 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A 167 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS A 216 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR A 247 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 218 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 244 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 270 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA A 246 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL A 269 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.503A pdb=" N ILE B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL B 88 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 128 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 125 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL B 146 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR B 127 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA7, first strand: chain 'B' and resid 206 through 208 removed outlier: 4.174A pdb=" N ASP B 188 " --> pdb=" O PRO B 164 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 166 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE B 165 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL B 219 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B 167 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS B 216 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N TYR B 247 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B 218 " --> pdb=" O TYR B 247 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL B 244 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL B 270 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA B 246 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL B 269 " --> pdb=" O ARG B 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 222 through 223 Processing sheet with id=AA9, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.503A pdb=" N ILE F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL F 88 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL F 128 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL F 125 " --> pdb=" O ASP F 144 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL F 146 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR F 127 " --> pdb=" O VAL F 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AB2, first strand: chain 'F' and resid 206 through 208 removed outlier: 4.174A pdb=" N ASP F 188 " --> pdb=" O PRO F 164 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL F 166 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE F 165 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL F 219 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL F 167 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS F 216 " --> pdb=" O PHE F 245 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N TYR F 247 " --> pdb=" O CYS F 216 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU F 218 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL F 244 " --> pdb=" O GLU F 268 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL F 270 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA F 246 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL F 269 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 222 through 223 Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.503A pdb=" N ILE E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL E 88 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL E 128 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL E 125 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL E 146 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR E 127 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 34 Processing sheet with id=AB6, first strand: chain 'E' and resid 206 through 208 removed outlier: 4.174A pdb=" N ASP E 188 " --> pdb=" O PRO E 164 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL E 166 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE E 165 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL E 219 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL E 167 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS E 216 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR E 247 " --> pdb=" O CYS E 216 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU E 218 " --> pdb=" O TYR E 247 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL E 244 " --> pdb=" O GLU E 268 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL E 270 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA E 246 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL E 269 " --> pdb=" O ARG E 288 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 222 through 223 Processing sheet with id=AB8, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.503A pdb=" N ILE C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL C 88 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 128 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL C 125 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL C 146 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR C 127 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AC1, first strand: chain 'C' and resid 206 through 208 removed outlier: 4.174A pdb=" N ASP C 188 " --> pdb=" O PRO C 164 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL C 166 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE C 165 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL C 219 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C 167 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS C 216 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N TYR C 247 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU C 218 " --> pdb=" O TYR C 247 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL C 244 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL C 270 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA C 246 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL C 269 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 222 through 223 Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.504A pdb=" N ILE D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL D 88 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL D 128 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL D 125 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL D 146 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR D 127 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AC5, first strand: chain 'D' and resid 206 through 208 removed outlier: 4.174A pdb=" N ASP D 188 " --> pdb=" O PRO D 164 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL D 166 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE D 165 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL D 219 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL D 167 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS D 216 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR D 247 " --> pdb=" O CYS D 216 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU D 218 " --> pdb=" O TYR D 247 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL D 244 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL D 270 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA D 246 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL D 269 " --> pdb=" O ARG D 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 222 through 223 540 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4805 1.34 - 1.45: 1072 1.45 - 1.57: 8109 1.57 - 1.69: 0 1.69 - 1.80: 132 Bond restraints: 14118 Sorted by residual: bond pdb=" O3 PO4 B1001 " pdb=" P PO4 B1001 " ideal model delta sigma weight residual 1.569 1.503 0.066 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O3 PO4 B1003 " pdb=" P PO4 B1003 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O3 PO4 F2602 " pdb=" P PO4 F2602 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O3 PO4 A1001 " pdb=" P PO4 A1001 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O3 PO4 C1001 " pdb=" P PO4 C1001 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 14113 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.29: 300 106.29 - 112.54: 7588 112.54 - 118.78: 3804 118.78 - 125.03: 7358 125.03 - 131.27: 96 Bond angle restraints: 19146 Sorted by residual: angle pdb=" CA GLU A 154 " pdb=" CB GLU A 154 " pdb=" CG GLU A 154 " ideal model delta sigma weight residual 114.10 121.90 -7.80 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CA GLU C 154 " pdb=" CB GLU C 154 " pdb=" CG GLU C 154 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CA GLU E 154 " pdb=" CB GLU E 154 " pdb=" CG GLU E 154 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 angle pdb=" CA GLU B 154 " pdb=" CB GLU B 154 " pdb=" CG GLU B 154 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 angle pdb=" CA GLU D 154 " pdb=" CB GLU D 154 " pdb=" CG GLU D 154 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 ... (remaining 19141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 7843 17.02 - 34.03: 627 34.03 - 51.05: 116 51.05 - 68.07: 42 68.07 - 85.08: 12 Dihedral angle restraints: 8640 sinusoidal: 3378 harmonic: 5262 Sorted by residual: dihedral pdb=" CA SER A 278 " pdb=" C SER A 278 " pdb=" N ASP A 279 " pdb=" CA ASP A 279 " ideal model delta harmonic sigma weight residual 180.00 -161.74 -18.26 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA SER E 278 " pdb=" C SER E 278 " pdb=" N ASP E 279 " pdb=" CA ASP E 279 " ideal model delta harmonic sigma weight residual -180.00 -161.74 -18.26 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA SER B 278 " pdb=" C SER B 278 " pdb=" N ASP B 279 " pdb=" CA ASP B 279 " ideal model delta harmonic sigma weight residual 180.00 -161.74 -18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 8637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1181 0.030 - 0.059: 654 0.059 - 0.089: 240 0.089 - 0.118: 206 0.118 - 0.148: 17 Chirality restraints: 2298 Sorted by residual: chirality pdb=" CA PRO B 276 " pdb=" N PRO B 276 " pdb=" C PRO B 276 " pdb=" CB PRO B 276 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA PRO A 276 " pdb=" N PRO A 276 " pdb=" C PRO A 276 " pdb=" CB PRO A 276 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA PRO F 276 " pdb=" N PRO F 276 " pdb=" C PRO F 276 " pdb=" CB PRO F 276 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 2295 not shown) Planarity restraints: 2514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 275 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO A 276 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 275 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO E 276 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 276 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 276 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 275 " 0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO C 276 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 276 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 276 " 0.031 5.00e-02 4.00e+02 ... (remaining 2511 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 692 2.72 - 3.26: 13702 3.26 - 3.81: 22304 3.81 - 4.35: 27704 4.35 - 4.90: 48603 Nonbonded interactions: 113005 Sorted by model distance: nonbonded pdb=" OD1 ASP A 224 " pdb=" OG SER A 254 " model vdw 2.174 2.440 nonbonded pdb=" OD1 ASP F 224 " pdb=" OG SER F 254 " model vdw 2.174 2.440 nonbonded pdb=" OD1 ASP B 224 " pdb=" OG SER B 254 " model vdw 2.174 2.440 nonbonded pdb=" OD1 ASP C 224 " pdb=" OG SER C 254 " model vdw 2.174 2.440 nonbonded pdb=" OD1 ASP D 224 " pdb=" OG SER D 254 " model vdw 2.175 2.440 ... (remaining 113000 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 'A' and (resid 3 through 315 or resid 1001)) selection = (chain 'B' and (resid 3 through 315 or resid 1001)) selection = (chain 'C' and (resid 3 through 315 or resid 1001)) selection = chain 'D' selection = chain 'E' selection = (chain 'F' and (resid 3 through 315 or resid 2601)) } 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=1.00 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.250 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 39.100 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.090 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:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 0.066 14118 Z= 0.396 Angle : 0.616 7.804 19146 Z= 0.352 Chirality : 0.048 0.148 2298 Planarity : 0.004 0.056 2514 Dihedral : 13.518 85.082 5220 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.37 % Allowed : 2.04 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.76 (0.20), residues: 1806 helix: 0.95 (0.21), residues: 624 sheet: -0.21 (0.26), residues: 456 loop : -2.01 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 250 PHE 0.024 0.002 PHE D 116 TYR 0.006 0.001 TYR D 94 ARG 0.003 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 195 time to evaluate : 1.483 Fit side-chains outliers start: 36 outliers final: 0 residues processed: 203 average time/residue: 1.3417 time to fit residues: 297.0385 Evaluate side-chains 174 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.433 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN F 136 GLN E 136 GLN C 136 GLN D 136 GLN D 256 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 14118 Z= 0.152 Angle : 0.501 4.986 19146 Z= 0.263 Chirality : 0.045 0.138 2298 Planarity : 0.004 0.054 2514 Dihedral : 4.652 15.203 1980 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.79 % Allowed : 7.31 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.32 (0.20), residues: 1806 helix: 1.37 (0.21), residues: 660 sheet: 0.17 (0.24), residues: 504 loop : -2.27 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 250 PHE 0.011 0.001 PHE F 116 TYR 0.006 0.001 TYR E 94 ARG 0.005 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 1.574 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 200 average time/residue: 1.0514 time to fit residues: 234.4256 Evaluate side-chains 184 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 2.2434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN F 136 GLN E 136 GLN C 136 GLN D 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 14118 Z= 0.404 Angle : 0.614 8.756 19146 Z= 0.317 Chirality : 0.049 0.166 2298 Planarity : 0.005 0.066 2514 Dihedral : 5.009 16.349 1980 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.24 % Allowed : 10.21 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.46 (0.21), residues: 1806 helix: 1.27 (0.21), residues: 660 sheet: -0.11 (0.26), residues: 456 loop : -2.03 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 250 PHE 0.019 0.001 PHE D 116 TYR 0.014 0.002 TYR D 94 ARG 0.006 0.001 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 195 time to evaluate : 1.846 Fit side-chains outliers start: 34 outliers final: 13 residues processed: 203 average time/residue: 1.2093 time to fit residues: 270.7251 Evaluate side-chains 205 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 192 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 3 residues processed: 10 average time/residue: 0.8022 time to fit residues: 11.1093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 18 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 173 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN B 256 ASN F 43 GLN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN E 136 GLN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN D 136 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14118 Z= 0.160 Angle : 0.506 9.658 19146 Z= 0.260 Chirality : 0.045 0.140 2298 Planarity : 0.004 0.058 2514 Dihedral : 4.571 15.574 1980 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.58 % Allowed : 12.06 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.16 (0.21), residues: 1806 helix: 1.62 (0.21), residues: 660 sheet: 0.08 (0.24), residues: 504 loop : -2.16 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 250 PHE 0.006 0.001 PHE A 35 TYR 0.005 0.001 TYR C 91 ARG 0.006 0.000 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 1.743 Fit side-chains outliers start: 24 outliers final: 15 residues processed: 209 average time/residue: 1.1659 time to fit residues: 269.6651 Evaluate side-chains 211 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 1.584 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 3 residues processed: 12 average time/residue: 0.7813 time to fit residues: 13.0827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 136 GLN B 45 ASN B 136 GLN F 43 GLN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN C 45 ASN C 136 GLN D 43 GLN D 136 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14118 Z= 0.186 Angle : 0.531 10.566 19146 Z= 0.266 Chirality : 0.045 0.147 2298 Planarity : 0.004 0.059 2514 Dihedral : 4.503 16.307 1980 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.78 % Allowed : 12.91 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.02 (0.21), residues: 1806 helix: 1.80 (0.21), residues: 660 sheet: 0.05 (0.24), residues: 510 loop : -2.08 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 250 PHE 0.006 0.001 PHE E 116 TYR 0.007 0.001 TYR D 94 ARG 0.005 0.000 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 209 time to evaluate : 1.664 Fit side-chains outliers start: 27 outliers final: 12 residues processed: 214 average time/residue: 1.1840 time to fit residues: 279.9720 Evaluate side-chains 210 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 198 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 3 residues processed: 9 average time/residue: 0.8768 time to fit residues: 11.1416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 43 GLN B 45 ASN B 136 GLN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN E 45 ASN E 136 GLN C 136 GLN D 45 ASN D 136 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14118 Z= 0.158 Angle : 0.486 6.162 19146 Z= 0.253 Chirality : 0.045 0.139 2298 Planarity : 0.004 0.057 2514 Dihedral : 4.367 16.196 1980 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.52 % Allowed : 14.10 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.11 (0.21), residues: 1806 helix: 1.97 (0.21), residues: 660 sheet: 0.07 (0.24), residues: 510 loop : -2.03 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 250 PHE 0.010 0.001 PHE A 116 TYR 0.005 0.001 TYR D 94 ARG 0.007 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 1.532 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 205 average time/residue: 1.1504 time to fit residues: 260.9560 Evaluate side-chains 204 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 193 time to evaluate : 1.470 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 3 residues processed: 8 average time/residue: 0.4255 time to fit residues: 6.2316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN B 136 GLN F 45 ASN F 136 GLN E 136 GLN C 136 GLN D 136 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14118 Z= 0.267 Angle : 0.560 9.783 19146 Z= 0.283 Chirality : 0.046 0.155 2298 Planarity : 0.004 0.061 2514 Dihedral : 4.582 16.049 1980 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.52 % Allowed : 15.55 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.03 (0.21), residues: 1806 helix: 1.85 (0.21), residues: 660 sheet: 0.01 (0.23), residues: 510 loop : -1.99 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 250 PHE 0.008 0.001 PHE E 116 TYR 0.011 0.001 TYR D 94 ARG 0.004 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 198 time to evaluate : 1.630 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 205 average time/residue: 1.1520 time to fit residues: 262.3054 Evaluate side-chains 211 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 1.652 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 4 residues processed: 12 average time/residue: 0.9089 time to fit residues: 14.5086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 45 ASN B 136 GLN F 136 GLN E 136 GLN C 136 GLN D 136 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14118 Z= 0.286 Angle : 0.567 9.795 19146 Z= 0.289 Chirality : 0.047 0.156 2298 Planarity : 0.005 0.062 2514 Dihedral : 4.674 16.286 1980 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.58 % Allowed : 15.81 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.09 (0.21), residues: 1806 helix: 1.71 (0.21), residues: 660 sheet: -0.09 (0.23), residues: 516 loop : -1.97 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 250 PHE 0.008 0.001 PHE D 116 TYR 0.011 0.001 TYR D 94 ARG 0.004 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 197 time to evaluate : 1.519 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 205 average time/residue: 1.1306 time to fit residues: 257.5997 Evaluate side-chains 206 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 1.671 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 6 average time/residue: 0.6417 time to fit residues: 7.2151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN F 136 GLN E 136 GLN C 136 GLN D 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14118 Z= 0.316 Angle : 0.599 10.485 19146 Z= 0.302 Chirality : 0.047 0.157 2298 Planarity : 0.005 0.063 2514 Dihedral : 4.755 16.196 1980 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.32 % Allowed : 16.40 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.15 (0.21), residues: 1806 helix: 1.62 (0.21), residues: 660 sheet: -0.13 (0.25), residues: 456 loop : -1.81 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 250 PHE 0.008 0.001 PHE D 116 TYR 0.012 0.002 TYR D 94 ARG 0.006 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 1.600 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 205 average time/residue: 1.1542 time to fit residues: 262.6341 Evaluate side-chains 212 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 199 time to evaluate : 1.426 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 6 residues processed: 9 average time/residue: 0.9924 time to fit residues: 12.1295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 165 optimal weight: 0.0370 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN F 136 GLN E 136 GLN C 136 GLN D 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14118 Z= 0.149 Angle : 0.504 8.542 19146 Z= 0.260 Chirality : 0.045 0.136 2298 Planarity : 0.004 0.058 2514 Dihedral : 4.375 16.037 1980 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.79 % Allowed : 16.67 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.15 (0.21), residues: 1806 helix: 1.98 (0.21), residues: 660 sheet: 0.05 (0.23), residues: 510 loop : -1.95 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 250 PHE 0.008 0.001 PHE B 116 TYR 0.005 0.001 TYR C 91 ARG 0.006 0.000 ARG C 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 203 time to evaluate : 1.749 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 208 average time/residue: 1.0216 time to fit residues: 237.7113 Evaluate side-chains 206 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 198 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 4 average time/residue: 1.0624 time to fit residues: 6.7682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN F 136 GLN E 136 GLN C 136 GLN D 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.156209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.107358 restraints weight = 15265.574| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.03 r_work: 0.2946 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14118 Z= 0.185 Angle : 0.546 10.794 19146 Z= 0.273 Chirality : 0.045 0.143 2298 Planarity : 0.004 0.059 2514 Dihedral : 4.369 16.084 1980 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.72 % Allowed : 17.65 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.25 (0.21), residues: 1806 helix: 2.06 (0.21), residues: 660 sheet: 0.15 (0.23), residues: 510 loop : -1.93 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 250 PHE 0.013 0.001 PHE B 116 TYR 0.006 0.001 TYR D 94 ARG 0.007 0.000 ARG C 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4852.19 seconds wall clock time: 86 minutes 44.28 seconds (5204.28 seconds total)