Starting phenix.real_space_refine on Sun Jul 21 09:55:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn3_33309/07_2024/7xn3_33309.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn3_33309/07_2024/7xn3_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_33309/07_2024/7xn3_33309.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn3_33309/07_2024/7xn3_33309.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn3_33309/07_2024/7xn3_33309.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn3_33309/07_2024/7xn3_33309.cif" } 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-dev-5388/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: 7.55, per 1000 atoms: 0.54 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: 4.88 Conformation dependent library (CDL) restraints added in 2.8 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: 1.91 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: 4.03 Time building geometry restraints manager: 5.40 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: 0.800 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.900 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.050 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:10.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.710 ------------------------------------------------------------------------------- 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 : 1.551 Fit side-chains REVERT: A 163 ASN cc_start: 0.8022 (t0) cc_final: 0.7618 (t0) REVERT: A 267 ASP cc_start: 0.7801 (m-30) cc_final: 0.7594 (m-30) REVERT: B 163 ASN cc_start: 0.7928 (t0) cc_final: 0.7541 (t0) REVERT: B 238 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7047 (mm-30) REVERT: F 131 HIS cc_start: 0.5516 (m90) cc_final: 0.5174 (m90) REVERT: F 163 ASN cc_start: 0.7967 (t0) cc_final: 0.7552 (t0) REVERT: F 189 MET cc_start: 0.8426 (tpt) cc_final: 0.8145 (tpt) REVERT: E 163 ASN cc_start: 0.7981 (t0) cc_final: 0.7553 (t0) REVERT: C 75 ASP cc_start: 0.8074 (t70) cc_final: 0.7821 (t0) REVERT: C 131 HIS cc_start: 0.5495 (m90) cc_final: 0.5184 (m90) REVERT: C 163 ASN cc_start: 0.7938 (t0) cc_final: 0.7505 (t0) REVERT: C 256 ASN cc_start: 0.7627 (m-40) cc_final: 0.7410 (m-40) REVERT: D 163 ASN cc_start: 0.8190 (t0) cc_final: 0.7827 (t0) outliers start: 36 outliers final: 0 residues processed: 203 average time/residue: 1.3509 time to fit residues: 298.9889 Evaluate side-chains 176 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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: 4.9990 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 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: 1.2146 ------------------------------------------------------------------------------- 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: 0.8105 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14118 Z= 0.228 Angle : 0.534 5.354 19146 Z= 0.279 Chirality : 0.046 0.149 2298 Planarity : 0.005 0.058 2514 Dihedral : 4.837 15.655 1980 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.05 % Allowed : 6.32 % Favored : 92.62 % 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: -0.43 (0.20), residues: 1806 helix: 1.24 (0.21), residues: 660 sheet: 0.11 (0.26), residues: 450 loop : -2.09 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 250 PHE 0.015 0.001 PHE A 116 TYR 0.008 0.001 TYR D 94 ARG 0.006 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 212 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 196 time to evaluate : 1.511 Fit side-chains REVERT: A 154 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7438 (tm-30) REVERT: A 163 ASN cc_start: 0.8020 (t0) cc_final: 0.7596 (t0) REVERT: B 163 ASN cc_start: 0.7935 (t0) cc_final: 0.7520 (t0) REVERT: F 131 HIS cc_start: 0.5561 (m90) cc_final: 0.5231 (m90) REVERT: F 163 ASN cc_start: 0.7972 (t0) cc_final: 0.7537 (t0) REVERT: F 222 MET cc_start: 0.8509 (ptm) cc_final: 0.8248 (ptm) REVERT: E 163 ASN cc_start: 0.8031 (t0) cc_final: 0.7558 (t0) REVERT: E 205 MET cc_start: 0.7036 (mmt) cc_final: 0.6563 (mmt) REVERT: C 131 HIS cc_start: 0.5500 (m90) cc_final: 0.5170 (m90) REVERT: C 154 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7536 (tm-30) REVERT: C 163 ASN cc_start: 0.7916 (t0) cc_final: 0.7439 (t0) REVERT: C 222 MET cc_start: 0.8519 (ptm) cc_final: 0.8261 (ptm) REVERT: D 163 ASN cc_start: 0.8156 (t0) cc_final: 0.7733 (t0) REVERT: D 222 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8121 (ptm) outliers start: 16 outliers final: 4 residues processed: 202 average time/residue: 1.1010 time to fit residues: 246.6283 Evaluate side-chains 188 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 183 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 222 MET 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: 2.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 E 136 GLN C 136 GLN C 256 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14118 Z= 0.214 Angle : 0.528 8.598 19146 Z= 0.270 Chirality : 0.046 0.148 2298 Planarity : 0.005 0.060 2514 Dihedral : 4.689 15.441 1980 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.65 % Allowed : 10.41 % Favored : 87.94 % 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: -0.20 (0.21), residues: 1806 helix: 1.57 (0.21), residues: 660 sheet: 0.12 (0.24), residues: 504 loop : -2.21 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 250 PHE 0.012 0.001 PHE D 116 TYR 0.008 0.001 TYR D 94 ARG 0.006 0.000 ARG D 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 218 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 1.697 Fit side-chains REVERT: A 163 ASN cc_start: 0.8024 (t0) cc_final: 0.7567 (t0) REVERT: B 73 MET cc_start: 0.8557 (ttm) cc_final: 0.8349 (ttm) REVERT: B 163 ASN cc_start: 0.7968 (t0) cc_final: 0.7537 (t0) REVERT: F 43 GLN cc_start: 0.8339 (pt0) cc_final: 0.8127 (tt0) REVERT: F 75 ASP cc_start: 0.8122 (t70) cc_final: 0.7803 (t0) REVERT: F 131 HIS cc_start: 0.5600 (m90) cc_final: 0.5157 (m90) REVERT: F 163 ASN cc_start: 0.7983 (t0) cc_final: 0.7540 (t0) REVERT: F 222 MET cc_start: 0.8564 (ptm) cc_final: 0.7878 (ptp) REVERT: E 43 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: E 163 ASN cc_start: 0.7998 (t0) cc_final: 0.7491 (t0) REVERT: E 205 MET cc_start: 0.6946 (mmt) cc_final: 0.6330 (mmt) REVERT: C 75 ASP cc_start: 0.8135 (t70) cc_final: 0.7850 (t0) REVERT: C 131 HIS cc_start: 0.5371 (m90) cc_final: 0.5105 (m90) REVERT: C 163 ASN cc_start: 0.7958 (t0) cc_final: 0.7496 (t0) REVERT: C 222 MET cc_start: 0.8565 (ptm) cc_final: 0.7890 (ptp) REVERT: D 43 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: D 163 ASN cc_start: 0.8151 (t0) cc_final: 0.7706 (t0) REVERT: D 222 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7903 (ptm) outliers start: 25 outliers final: 10 residues processed: 200 average time/residue: 1.0979 time to fit residues: 243.0099 Evaluate side-chains 204 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8129 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14118 Z= 0.331 Angle : 0.582 9.764 19146 Z= 0.297 Chirality : 0.048 0.159 2298 Planarity : 0.005 0.064 2514 Dihedral : 4.861 15.904 1980 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.57 % Allowed : 11.20 % Favored : 86.23 % 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: -0.30 (0.21), residues: 1806 helix: 1.44 (0.21), residues: 660 sheet: -0.02 (0.26), residues: 450 loop : -1.97 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 250 PHE 0.013 0.001 PHE D 116 TYR 0.012 0.002 TYR D 94 ARG 0.007 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 240 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 201 time to evaluate : 1.534 Fit side-chains REVERT: A 163 ASN cc_start: 0.8034 (t0) cc_final: 0.7566 (t0) REVERT: B 75 ASP cc_start: 0.8219 (t70) cc_final: 0.8006 (t0) REVERT: B 163 ASN cc_start: 0.8004 (t0) cc_final: 0.7551 (t0) REVERT: B 238 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7183 (mm-30) REVERT: F 43 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: F 99 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7287 (ptm160) REVERT: F 131 HIS cc_start: 0.5568 (m90) cc_final: 0.5246 (m90) REVERT: F 163 ASN cc_start: 0.7999 (t0) cc_final: 0.7555 (t0) REVERT: F 222 MET cc_start: 0.8656 (ptm) cc_final: 0.7840 (ptp) REVERT: E 43 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: E 163 ASN cc_start: 0.8051 (t0) cc_final: 0.7555 (t0) REVERT: C 4 MET cc_start: 0.8916 (ttm) cc_final: 0.8627 (ttm) REVERT: C 99 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7203 (ptm160) REVERT: C 131 HIS cc_start: 0.5492 (m90) cc_final: 0.5276 (m90) REVERT: C 163 ASN cc_start: 0.7974 (t0) cc_final: 0.7497 (t0) REVERT: C 205 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6494 (mmt) REVERT: C 222 MET cc_start: 0.8656 (ptm) cc_final: 0.7896 (ptp) REVERT: D 43 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: D 163 ASN cc_start: 0.8137 (t0) cc_final: 0.7684 (t0) REVERT: D 222 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7890 (ptm) outliers start: 39 outliers final: 17 residues processed: 210 average time/residue: 1.2239 time to fit residues: 281.9179 Evaluate side-chains 222 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 222 MET 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: 1.9990 chunk 2 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN E 136 GLN C 45 ASN C 136 GLN C 256 ASN D 136 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14118 Z= 0.228 Angle : 0.533 9.482 19146 Z= 0.274 Chirality : 0.046 0.148 2298 Planarity : 0.005 0.062 2514 Dihedral : 4.674 16.331 1980 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.37 % Allowed : 12.12 % Favored : 85.51 % 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: -0.17 (0.21), residues: 1806 helix: 1.60 (0.21), residues: 660 sheet: -0.06 (0.26), residues: 456 loop : -1.89 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 250 PHE 0.007 0.001 PHE D 116 TYR 0.008 0.001 TYR D 94 ARG 0.007 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 239 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 203 time to evaluate : 1.572 Fit side-chains REVERT: A 43 GLN cc_start: 0.8273 (pt0) cc_final: 0.7879 (tt0) REVERT: A 163 ASN cc_start: 0.7993 (t0) cc_final: 0.7513 (t0) REVERT: B 43 GLN cc_start: 0.8324 (pt0) cc_final: 0.8000 (tt0) REVERT: B 75 ASP cc_start: 0.8200 (t70) cc_final: 0.7994 (t0) REVERT: B 163 ASN cc_start: 0.7949 (t0) cc_final: 0.7478 (t0) REVERT: F 43 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: F 75 ASP cc_start: 0.8135 (t70) cc_final: 0.7843 (t0) REVERT: F 131 HIS cc_start: 0.5462 (m90) cc_final: 0.5142 (m90) REVERT: F 163 ASN cc_start: 0.7993 (t0) cc_final: 0.7545 (t0) REVERT: F 222 MET cc_start: 0.8568 (ptm) cc_final: 0.7871 (ptp) REVERT: E 43 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: E 163 ASN cc_start: 0.7973 (t0) cc_final: 0.7440 (t0) REVERT: C 4 MET cc_start: 0.8913 (ttm) cc_final: 0.8637 (ttm) REVERT: C 75 ASP cc_start: 0.8148 (t70) cc_final: 0.7845 (t0) REVERT: C 163 ASN cc_start: 0.7985 (t0) cc_final: 0.7527 (t0) REVERT: C 222 MET cc_start: 0.8651 (ptm) cc_final: 0.7920 (ptm) REVERT: D 43 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: D 163 ASN cc_start: 0.8112 (t0) cc_final: 0.7631 (t0) REVERT: D 189 MET cc_start: 0.8430 (tmm) cc_final: 0.8163 (tpp) REVERT: D 222 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7913 (ptm) outliers start: 36 outliers final: 21 residues processed: 211 average time/residue: 1.1714 time to fit residues: 272.2778 Evaluate side-chains 224 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 144 optimal weight: 0.3980 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 0.0170 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- 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 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN E 136 GLN C 136 GLN C 256 ASN D 136 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14118 Z= 0.177 Angle : 0.516 10.104 19146 Z= 0.262 Chirality : 0.045 0.143 2298 Planarity : 0.004 0.060 2514 Dihedral : 4.481 16.026 1980 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.91 % Allowed : 13.57 % Favored : 84.52 % 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: -0.00 (0.21), residues: 1806 helix: 1.83 (0.21), residues: 660 sheet: 0.01 (0.24), residues: 510 loop : -2.04 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 250 PHE 0.009 0.001 PHE B 116 TYR 0.006 0.001 TYR D 94 ARG 0.008 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 238 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 1.560 Fit side-chains REVERT: A 43 GLN cc_start: 0.8237 (pt0) cc_final: 0.7780 (tt0) REVERT: A 163 ASN cc_start: 0.7884 (t0) cc_final: 0.7407 (t0) REVERT: B 43 GLN cc_start: 0.8294 (pt0) cc_final: 0.7925 (tt0) REVERT: B 163 ASN cc_start: 0.7866 (t0) cc_final: 0.7421 (t0) REVERT: F 43 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: F 75 ASP cc_start: 0.8141 (t70) cc_final: 0.7823 (t0) REVERT: F 131 HIS cc_start: 0.5445 (m90) cc_final: 0.5145 (m90) REVERT: F 163 ASN cc_start: 0.7950 (t0) cc_final: 0.7522 (t0) REVERT: F 222 MET cc_start: 0.8548 (ptm) cc_final: 0.7857 (ptp) REVERT: E 163 ASN cc_start: 0.7915 (t0) cc_final: 0.7405 (t0) REVERT: C 4 MET cc_start: 0.8922 (ttm) cc_final: 0.8654 (ttm) REVERT: C 75 ASP cc_start: 0.8155 (t70) cc_final: 0.7855 (t0) REVERT: C 163 ASN cc_start: 0.7972 (t0) cc_final: 0.7513 (t0) REVERT: C 222 MET cc_start: 0.8571 (ptm) cc_final: 0.7867 (ptm) REVERT: D 43 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: D 163 ASN cc_start: 0.8103 (t0) cc_final: 0.7594 (t0) REVERT: D 222 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7867 (ptm) outliers start: 29 outliers final: 10 residues processed: 215 average time/residue: 1.1541 time to fit residues: 273.9878 Evaluate side-chains 217 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 204 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 C 256 ASN D 136 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1738 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= 0.190 Angle : 0.524 10.191 19146 Z= 0.265 Chirality : 0.045 0.146 2298 Planarity : 0.004 0.060 2514 Dihedral : 4.455 16.142 1980 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.38 % Allowed : 15.02 % Favored : 83.60 % 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: 1.91 (0.21), residues: 660 sheet: 0.05 (0.24), residues: 510 loop : -1.98 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 250 PHE 0.009 0.001 PHE A 116 TYR 0.007 0.001 TYR D 94 ARG 0.008 0.000 ARG E 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 224 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 1.626 Fit side-chains REVERT: A 163 ASN cc_start: 0.7826 (t0) cc_final: 0.7360 (t0) REVERT: B 43 GLN cc_start: 0.8282 (pt0) cc_final: 0.7858 (tt0) REVERT: B 163 ASN cc_start: 0.7896 (t0) cc_final: 0.7440 (t0) REVERT: F 43 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: F 75 ASP cc_start: 0.8141 (t70) cc_final: 0.7825 (t0) REVERT: F 131 HIS cc_start: 0.5425 (m90) cc_final: 0.5142 (m90) REVERT: F 163 ASN cc_start: 0.7869 (t0) cc_final: 0.7436 (t0) REVERT: F 222 MET cc_start: 0.8560 (ptm) cc_final: 0.7862 (ptp) REVERT: E 163 ASN cc_start: 0.7889 (t0) cc_final: 0.7369 (t0) REVERT: E 189 MET cc_start: 0.8289 (tmm) cc_final: 0.7982 (tpp) REVERT: C 4 MET cc_start: 0.8925 (ttm) cc_final: 0.8654 (ttm) REVERT: C 75 ASP cc_start: 0.8161 (t70) cc_final: 0.7856 (t0) REVERT: C 163 ASN cc_start: 0.7969 (t0) cc_final: 0.7548 (t0) REVERT: C 222 MET cc_start: 0.8531 (ptm) cc_final: 0.7884 (ptm) REVERT: D 163 ASN cc_start: 0.8052 (t0) cc_final: 0.7574 (t0) REVERT: D 222 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7849 (ptm) outliers start: 21 outliers final: 16 residues processed: 207 average time/residue: 1.1061 time to fit residues: 253.8058 Evaluate side-chains 218 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 200 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 110 optimal weight: 0.9980 chunk 118 optimal weight: 0.0270 chunk 85 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN E 136 GLN C 136 GLN D 45 ASN D 136 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14118 Z= 0.157 Angle : 0.503 10.144 19146 Z= 0.256 Chirality : 0.045 0.139 2298 Planarity : 0.004 0.058 2514 Dihedral : 4.327 15.337 1980 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.58 % Allowed : 15.55 % Favored : 82.87 % 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: 0.22 (0.21), residues: 1806 helix: 2.04 (0.21), residues: 660 sheet: 0.21 (0.23), residues: 504 loop : -1.99 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 250 PHE 0.009 0.001 PHE A 116 TYR 0.005 0.001 TYR C 91 ARG 0.008 0.000 ARG E 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 231 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 1.604 Fit side-chains REVERT: A 163 ASN cc_start: 0.7831 (t0) cc_final: 0.7327 (t0) REVERT: A 222 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7662 (pp-130) REVERT: B 43 GLN cc_start: 0.8255 (pt0) cc_final: 0.7900 (tt0) REVERT: B 163 ASN cc_start: 0.7819 (t0) cc_final: 0.7346 (t0) REVERT: F 43 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: F 75 ASP cc_start: 0.8139 (t70) cc_final: 0.7800 (t0) REVERT: F 163 ASN cc_start: 0.7760 (t0) cc_final: 0.7334 (t0) REVERT: F 222 MET cc_start: 0.8515 (ptm) cc_final: 0.7863 (ptp) REVERT: E 163 ASN cc_start: 0.7873 (t0) cc_final: 0.7367 (t0) REVERT: C 4 MET cc_start: 0.8936 (ttm) cc_final: 0.8662 (ttm) REVERT: C 75 ASP cc_start: 0.8155 (t70) cc_final: 0.7830 (t0) REVERT: C 163 ASN cc_start: 0.7905 (t0) cc_final: 0.7524 (t0) REVERT: C 222 MET cc_start: 0.8496 (ptm) cc_final: 0.7858 (ptm) REVERT: D 163 ASN cc_start: 0.7924 (t0) cc_final: 0.7420 (t0) REVERT: D 222 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7833 (ptm) outliers start: 24 outliers final: 12 residues processed: 217 average time/residue: 1.0210 time to fit residues: 247.8201 Evaluate side-chains 212 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.7980 chunk 166 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 0.0000 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN E 45 ASN 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: 0.8064 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14118 Z= 0.159 Angle : 0.521 10.812 19146 Z= 0.259 Chirality : 0.045 0.139 2298 Planarity : 0.004 0.058 2514 Dihedral : 4.280 15.116 1980 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.52 % Allowed : 15.81 % Favored : 82.67 % 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: 0.30 (0.21), residues: 1806 helix: 2.11 (0.21), residues: 660 sheet: 0.20 (0.24), residues: 510 loop : -1.92 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 250 PHE 0.015 0.001 PHE A 116 TYR 0.005 0.001 TYR D 94 ARG 0.007 0.000 ARG E 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 224 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 201 time to evaluate : 1.441 Fit side-chains REVERT: A 163 ASN cc_start: 0.7752 (t0) cc_final: 0.7294 (t0) REVERT: A 222 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7685 (pp-130) REVERT: B 43 GLN cc_start: 0.8226 (pt0) cc_final: 0.7791 (tt0) REVERT: B 163 ASN cc_start: 0.7806 (t0) cc_final: 0.7130 (t0) REVERT: F 75 ASP cc_start: 0.8138 (t70) cc_final: 0.7791 (t0) REVERT: F 163 ASN cc_start: 0.7811 (t0) cc_final: 0.7344 (t0) REVERT: F 222 MET cc_start: 0.8499 (ptm) cc_final: 0.7858 (ptp) REVERT: E 163 ASN cc_start: 0.7824 (t0) cc_final: 0.7303 (t0) REVERT: E 205 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6593 (mmt) REVERT: C 4 MET cc_start: 0.8938 (ttm) cc_final: 0.8665 (ttm) REVERT: C 75 ASP cc_start: 0.8159 (t70) cc_final: 0.7821 (t0) REVERT: C 163 ASN cc_start: 0.7836 (t0) cc_final: 0.7461 (t0) REVERT: C 222 MET cc_start: 0.8487 (ptm) cc_final: 0.7844 (ptm) REVERT: D 163 ASN cc_start: 0.7879 (t0) cc_final: 0.7370 (t0) REVERT: D 222 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7800 (ptm) outliers start: 23 outliers final: 15 residues processed: 209 average time/residue: 1.0626 time to fit residues: 246.8957 Evaluate side-chains 215 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 165 optimal weight: 0.0020 chunk 142 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14118 Z= 0.276 Angle : 0.564 10.311 19146 Z= 0.286 Chirality : 0.047 0.154 2298 Planarity : 0.005 0.061 2514 Dihedral : 4.560 15.454 1980 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.84 % Allowed : 15.42 % Favored : 82.74 % 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: 0.18 (0.21), residues: 1806 helix: 1.89 (0.21), residues: 660 sheet: 0.17 (0.23), residues: 510 loop : -1.87 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 250 PHE 0.020 0.001 PHE A 116 TYR 0.011 0.001 TYR D 94 ARG 0.009 0.000 ARG D 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 229 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 1.472 Fit side-chains REVERT: A 163 ASN cc_start: 0.7803 (t0) cc_final: 0.7341 (t0) REVERT: B 43 GLN cc_start: 0.8347 (pt0) cc_final: 0.7872 (tt0) REVERT: B 163 ASN cc_start: 0.7768 (t0) cc_final: 0.7132 (t0) REVERT: F 163 ASN cc_start: 0.7799 (t0) cc_final: 0.7335 (t0) REVERT: F 222 MET cc_start: 0.8523 (ptm) cc_final: 0.7865 (ptp) REVERT: E 163 ASN cc_start: 0.7783 (t0) cc_final: 0.7248 (t0) REVERT: E 205 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6601 (mmt) REVERT: C 4 MET cc_start: 0.8919 (ttm) cc_final: 0.8641 (ttm) REVERT: C 75 ASP cc_start: 0.8157 (t70) cc_final: 0.7867 (t0) REVERT: C 163 ASN cc_start: 0.7845 (t0) cc_final: 0.7472 (t0) REVERT: C 222 MET cc_start: 0.8516 (ptm) cc_final: 0.8001 (ptm) REVERT: D 163 ASN cc_start: 0.7841 (t0) cc_final: 0.7324 (t0) REVERT: D 189 MET cc_start: 0.8300 (mmm) cc_final: 0.7855 (tpp) REVERT: D 222 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7854 (ptm) outliers start: 28 outliers final: 20 residues processed: 211 average time/residue: 1.0749 time to fit residues: 252.1629 Evaluate side-chains 223 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 201 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 45 ASN F 136 GLN E 136 GLN C 136 GLN C 256 ASN D 136 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.156292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107012 restraints weight = 15190.591| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.06 r_work: 0.2896 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1939 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= 0.193 Angle : 0.538 10.319 19146 Z= 0.270 Chirality : 0.045 0.143 2298 Planarity : 0.004 0.059 2514 Dihedral : 4.425 16.711 1980 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.38 % Allowed : 15.88 % Favored : 82.74 % 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: 0.27 (0.21), residues: 1806 helix: 1.99 (0.21), residues: 660 sheet: 0.24 (0.23), residues: 510 loop : -1.88 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 250 PHE 0.015 0.001 PHE A 116 TYR 0.006 0.001 TYR D 94 ARG 0.008 0.000 ARG D 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4909.53 seconds wall clock time: 86 minutes 31.35 seconds (5191.35 seconds total)