Starting phenix.real_space_refine on Sun Nov 17 08:20:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp7_36470/11_2024/8jp7_36470.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp7_36470/11_2024/8jp7_36470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp7_36470/11_2024/8jp7_36470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp7_36470/11_2024/8jp7_36470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp7_36470/11_2024/8jp7_36470.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp7_36470/11_2024/8jp7_36470.cif" } resolution = 3.51 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= 0.012 sd= 0.116 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: 6 Type Number sf(0) Gaussians Ca 16 9.91 5 Zn 4 6.06 5 S 38 5.16 5 C 8452 2.51 5 N 2340 2.21 5 O 2626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13476 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2612 Classifications: {'peptide': 325} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 307} Chain: "B" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 810 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 1 Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Chain: "E" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2612 Classifications: {'peptide': 325} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 307} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 810 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 1 Chain: "H" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Chain: "F" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.62, per 1000 atoms: 0.64 Number of scatterers: 13476 At special positions: 0 Unit cell: (120.516, 116.532, 128.484, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 16 19.99 S 38 16.00 O 2626 8.00 N 2340 7.00 C 8452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS E 190 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.8 seconds 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3092 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 16 sheets defined 33.6% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.550A pdb=" N SER A 51 " --> pdb=" O TYR A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 283 through 308 removed outlier: 3.620A pdb=" N GLU A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 325 through 365 removed outlier: 3.823A pdb=" N VAL A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.578A pdb=" N ASN B 180 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B 181 " --> pdb=" O HIS B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 284 through 308 removed outlier: 4.392A pdb=" N GLU B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 365 removed outlier: 3.662A pdb=" N SER B 365 " --> pdb=" O ARG B 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 70 through 80 Processing helix chain 'C' and resid 89 through 99 Processing helix chain 'C' and resid 113 through 129 Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.579A pdb=" N SER C 144 " --> pdb=" O GLU C 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 47 removed outlier: 3.609A pdb=" N VAL D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 removed outlier: 4.583A pdb=" N ILE D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 80 removed outlier: 3.604A pdb=" N GLN D 73 " --> pdb=" O PRO D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 99 Processing helix chain 'D' and resid 113 through 129 removed outlier: 3.714A pdb=" N ASP D 127 " --> pdb=" O GLY D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'E' and resid 48 through 51 removed outlier: 3.501A pdb=" N SER E 51 " --> pdb=" O TYR E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 283 through 308 removed outlier: 3.625A pdb=" N GLU E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 322 Processing helix chain 'E' and resid 325 through 365 removed outlier: 3.801A pdb=" N VAL E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE E 341 " --> pdb=" O GLY E 337 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU E 348 " --> pdb=" O GLU E 344 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER E 365 " --> pdb=" O ARG E 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 47 Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 70 through 80 Processing helix chain 'G' and resid 89 through 99 Processing helix chain 'G' and resid 113 through 129 Processing helix chain 'G' and resid 137 through 144 removed outlier: 3.567A pdb=" N SER G 144 " --> pdb=" O GLU G 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 47 removed outlier: 3.633A pdb=" N VAL H 46 " --> pdb=" O ASP H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 57 removed outlier: 4.477A pdb=" N ILE H 52 " --> pdb=" O ASP H 48 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU H 57 " --> pdb=" O MET H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 80 removed outlier: 3.610A pdb=" N GLN H 73 " --> pdb=" O PRO H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 99 Processing helix chain 'H' and resid 113 through 129 removed outlier: 3.566A pdb=" N ASP H 127 " --> pdb=" O GLY H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 144 Processing helix chain 'F' and resid 177 through 181 removed outlier: 3.681A pdb=" N ASN F 180 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP F 181 " --> pdb=" O HIS F 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 177 through 181' Processing helix chain 'F' and resid 280 through 283 Processing helix chain 'F' and resid 284 through 308 removed outlier: 4.400A pdb=" N GLU F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 365 removed outlier: 4.024A pdb=" N SER F 365 " --> pdb=" O ARG F 361 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.954A pdb=" N HIS A 257 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 removed outlier: 5.602A pdb=" N HIS A 257 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR A 113 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL A 259 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG A 111 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 261 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 103 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 202 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE A 216 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N PHE A 229 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 71 removed outlier: 5.804A pdb=" N PHE A 244 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 71 removed outlier: 5.804A pdb=" N PHE A 244 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 52 removed outlier: 11.127A pdb=" N PHE B 46 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N THR B 268 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N TYR B 48 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N GLN B 266 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR B 50 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 264 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N HIS B 257 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 52 removed outlier: 11.127A pdb=" N PHE B 46 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N THR B 268 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N TYR B 48 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N GLN B 266 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR B 50 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 264 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N HIS B 257 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N THR B 113 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL B 259 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ARG B 111 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B 261 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE B 216 " --> pdb=" O PHE B 229 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE B 229 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.505A pdb=" N GLN B 89 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N PHE B 244 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.505A pdb=" N GLN B 89 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N PHE B 244 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 123 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 188 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 43 through 46 removed outlier: 6.865A pdb=" N HIS E 257 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 43 through 46 removed outlier: 5.619A pdb=" N HIS E 257 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N THR E 113 " --> pdb=" O HIS E 257 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL E 259 " --> pdb=" O ARG E 111 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG E 111 " --> pdb=" O VAL E 259 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 261 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG E 202 " --> pdb=" O ASN E 217 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE E 216 " --> pdb=" O PHE E 229 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE E 229 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.758A pdb=" N PHE E 244 " --> pdb=" O THR E 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.758A pdb=" N PHE E 244 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA E 188 " --> pdb=" O ILE E 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 43 through 52 removed outlier: 4.582A pdb=" N THR F 264 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LYS F 49 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N PHE F 262 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N SER F 51 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 11.510A pdb=" N LEU F 260 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N HIS F 257 " --> pdb=" O VAL F 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 43 through 52 removed outlier: 4.582A pdb=" N THR F 264 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LYS F 49 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N PHE F 262 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N SER F 51 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 11.510A pdb=" N LEU F 260 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS F 257 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR F 113 " --> pdb=" O HIS F 257 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL F 259 " --> pdb=" O ARG F 111 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARG F 111 " --> pdb=" O VAL F 259 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER F 261 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE F 216 " --> pdb=" O PHE F 229 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE F 229 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 67 through 71 removed outlier: 5.845A pdb=" N PHE F 244 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 67 through 71 removed outlier: 5.845A pdb=" N PHE F 244 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU F 123 " --> pdb=" O PHE F 151 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 1920 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: 4.31 Time building geometry restraints manager: 3.65 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: 4616 1.34 - 1.47: 3129 1.47 - 1.59: 5957 1.59 - 1.71: 0 1.71 - 1.83: 68 Bond restraints: 13770 Sorted by residual: bond pdb=" N LEU C 74 " pdb=" CA LEU C 74 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.29e+00 bond pdb=" N LEU D 111 " pdb=" CA LEU D 111 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.25e-02 6.40e+03 4.76e+00 bond pdb=" N PHE E 296 " pdb=" CA PHE E 296 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.19e-02 7.06e+03 3.40e+00 bond pdb=" N LEU G 74 " pdb=" CA LEU G 74 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.83e+00 bond pdb=" CG LEU D 74 " pdb=" CD1 LEU D 74 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.73e+00 ... (remaining 13765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 18253 1.99 - 3.97: 299 3.97 - 5.96: 33 5.96 - 7.94: 9 7.94 - 9.93: 4 Bond angle restraints: 18598 Sorted by residual: angle pdb=" C ALA E 120 " pdb=" N ASP E 121 " pdb=" CA ASP E 121 " ideal model delta sigma weight residual 121.70 129.44 -7.74 1.80e+00 3.09e-01 1.85e+01 angle pdb=" C ALA A 120 " pdb=" N ASP A 121 " pdb=" CA ASP A 121 " ideal model delta sigma weight residual 121.70 129.43 -7.73 1.80e+00 3.09e-01 1.84e+01 angle pdb=" C ALA B 120 " pdb=" N ASP B 121 " pdb=" CA ASP B 121 " ideal model delta sigma weight residual 121.70 128.63 -6.93 1.80e+00 3.09e-01 1.48e+01 angle pdb=" C ALA F 120 " pdb=" N ASP F 121 " pdb=" CA ASP F 121 " ideal model delta sigma weight residual 121.70 127.37 -5.67 1.80e+00 3.09e-01 9.93e+00 angle pdb=" CA ILE H 52 " pdb=" CB ILE H 52 " pdb=" CG1 ILE H 52 " ideal model delta sigma weight residual 110.40 115.54 -5.14 1.70e+00 3.46e-01 9.15e+00 ... (remaining 18593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 7004 17.46 - 34.92: 894 34.92 - 52.38: 252 52.38 - 69.84: 68 69.84 - 87.30: 18 Dihedral angle restraints: 8236 sinusoidal: 3428 harmonic: 4808 Sorted by residual: dihedral pdb=" CA THR C 98 " pdb=" C THR C 98 " pdb=" N HIS C 99 " pdb=" CA HIS C 99 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA THR G 98 " pdb=" C THR G 98 " pdb=" N HIS G 99 " pdb=" CA HIS G 99 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TRP F 126 " pdb=" C TRP F 126 " pdb=" N TYR F 127 " pdb=" CA TYR F 127 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 8233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1387 0.049 - 0.099: 398 0.099 - 0.148: 117 0.148 - 0.197: 8 0.197 - 0.246: 2 Chirality restraints: 1912 Sorted by residual: chirality pdb=" CG LEU D 56 " pdb=" CB LEU D 56 " pdb=" CD1 LEU D 56 " pdb=" CD2 LEU D 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE D 60 " pdb=" CA ILE D 60 " pdb=" CG1 ILE D 60 " pdb=" CG2 ILE D 60 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA LEU C 74 " pdb=" N LEU C 74 " pdb=" C LEU C 74 " pdb=" CB LEU C 74 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 1909 not shown) Planarity restraints: 2506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS H 99 " 0.017 2.00e-02 2.50e+03 2.25e-02 7.58e+00 pdb=" CG HIS H 99 " -0.042 2.00e-02 2.50e+03 pdb=" ND1 HIS H 99 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 HIS H 99 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS H 99 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS H 99 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 99 " -0.018 2.00e-02 2.50e+03 1.50e-02 3.39e+00 pdb=" CG HIS D 99 " 0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS D 99 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS D 99 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS D 99 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS D 99 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 61 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C ASN D 61 " -0.028 2.00e-02 2.50e+03 pdb=" O ASN D 61 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS D 62 " 0.009 2.00e-02 2.50e+03 ... (remaining 2503 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.26: 47 2.26 - 2.92: 5760 2.92 - 3.58: 19254 3.58 - 4.24: 31090 4.24 - 4.90: 53322 Nonbonded interactions: 109473 Sorted by model distance: nonbonded pdb=" CE1 HIS H 51 " pdb="ZN ZN H 703 " model vdw 1.606 2.450 nonbonded pdb=" OD1 ASP A 155 " pdb=" OD1 ASN A 161 " model vdw 1.765 3.040 nonbonded pdb=" OD1 ASP B 155 " pdb=" OD1 ASN B 162 " model vdw 1.774 3.040 nonbonded pdb=" OD1 ASP E 155 " pdb=" OD1 ASN E 161 " model vdw 1.797 3.040 nonbonded pdb=" ND2 ASN F 161 " pdb="CA CA F 602 " model vdw 1.817 2.590 ... (remaining 109468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 42 through 312 or resid 324 through 365 or resid 601 throu \ gh 602)) selection = chain 'B' selection = (chain 'E' and (resid 42 through 312 or resid 324 through 365 or resid 601 throu \ gh 602)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 41 through 101 or resid 108 through 144 or resid 701 throu \ gh 703)) selection = chain 'D' selection = (chain 'G' and (resid 41 through 101 or resid 108 through 144 or resid 701 throu \ gh 703)) selection = chain 'H' } 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 group one per residue 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: 1.070 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.580 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.005 0.043 13770 Z= 0.347 Angle : 0.639 9.927 18598 Z= 0.346 Chirality : 0.049 0.246 1912 Planarity : 0.004 0.039 2506 Dihedral : 17.386 87.297 5132 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.62 % Allowed : 20.71 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % 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: -0.06 (0.21), residues: 1646 helix: 0.42 (0.23), residues: 482 sheet: 1.10 (0.28), residues: 378 loop : -0.89 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 67 HIS 0.029 0.002 HIS H 99 PHE 0.027 0.002 PHE A 262 TYR 0.017 0.002 TYR C 76 ARG 0.004 0.000 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 331 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASP cc_start: 0.8854 (t0) cc_final: 0.8639 (t0) REVERT: A 160 LYS cc_start: 0.8792 (mppt) cc_final: 0.8560 (mmtp) REVERT: A 207 TYR cc_start: 0.8812 (t80) cc_final: 0.8561 (t80) REVERT: B 58 VAL cc_start: 0.8659 (t) cc_final: 0.8361 (p) REVERT: B 107 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7920 (mp0) REVERT: B 178 HIS cc_start: 0.7260 (t-90) cc_final: 0.6950 (t-90) REVERT: B 351 GLN cc_start: 0.8558 (tp40) cc_final: 0.8131 (tt0) REVERT: D 74 LEU cc_start: 0.7632 (tp) cc_final: 0.7032 (tp) REVERT: D 119 ASN cc_start: 0.9248 (m110) cc_final: 0.8919 (m-40) REVERT: D 124 VAL cc_start: 0.9474 (t) cc_final: 0.9112 (t) REVERT: E 93 VAL cc_start: 0.9532 (t) cc_final: 0.9205 (p) REVERT: E 105 GLU cc_start: 0.8207 (tt0) cc_final: 0.8004 (tt0) REVERT: E 199 TYR cc_start: 0.8788 (m-80) cc_final: 0.8467 (m-10) REVERT: E 218 ASN cc_start: 0.8138 (m-40) cc_final: 0.7847 (p0) REVERT: G 115 ASP cc_start: 0.8817 (m-30) cc_final: 0.8487 (t0) REVERT: G 124 VAL cc_start: 0.8797 (t) cc_final: 0.8439 (p) REVERT: H 56 LEU cc_start: 0.8773 (pp) cc_final: 0.8115 (pt) REVERT: H 77 PHE cc_start: 0.8124 (t80) cc_final: 0.7914 (t80) REVERT: H 119 ASN cc_start: 0.8981 (m110) cc_final: 0.8771 (m-40) REVERT: F 56 HIS cc_start: 0.8198 (m-70) cc_final: 0.7936 (m-70) REVERT: F 137 VAL cc_start: 0.8326 (t) cc_final: 0.7866 (p) REVERT: F 207 TYR cc_start: 0.7945 (t80) cc_final: 0.7248 (t80) REVERT: F 208 TYR cc_start: 0.7520 (t80) cc_final: 0.7276 (t80) REVERT: F 306 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7817 (pm20) outliers start: 9 outliers final: 3 residues processed: 339 average time/residue: 0.2923 time to fit residues: 138.2162 Evaluate side-chains 247 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 243 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain F residue 306 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 68 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 128 optimal weight: 0.0870 chunk 49 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN B 235 ASN B 359 GLN C 75 HIS C 80 HIS C 86 ASN D 51 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS E 131 GLN E 178 HIS E 191 GLN E 218 ASN E 338 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 80 HIS H 51 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN ** F 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13770 Z= 0.244 Angle : 0.597 8.089 18598 Z= 0.314 Chirality : 0.047 0.245 1912 Planarity : 0.004 0.037 2506 Dihedral : 4.989 55.434 1793 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.25 % Allowed : 21.68 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % 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: 0.24 (0.21), residues: 1646 helix: 1.16 (0.24), residues: 492 sheet: 1.42 (0.28), residues: 338 loop : -1.06 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 126 HIS 0.007 0.001 HIS C 75 PHE 0.020 0.002 PHE B 52 TYR 0.023 0.002 TYR C 138 ARG 0.009 0.001 ARG G 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 271 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.8891 (mppt) cc_final: 0.8685 (mmtp) REVERT: A 343 LEU cc_start: 0.8915 (mm) cc_final: 0.8666 (tp) REVERT: A 350 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7839 (ptp90) REVERT: A 355 ILE cc_start: 0.8242 (tt) cc_final: 0.7807 (tt) REVERT: B 58 VAL cc_start: 0.8734 (t) cc_final: 0.8460 (p) REVERT: B 107 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7636 (tt0) REVERT: B 178 HIS cc_start: 0.7300 (t-90) cc_final: 0.7056 (t-90) REVERT: B 223 ASP cc_start: 0.8659 (m-30) cc_final: 0.8417 (m-30) REVERT: B 289 TYR cc_start: 0.9205 (m-80) cc_final: 0.8875 (m-80) REVERT: B 329 ARG cc_start: 0.8072 (ttp-110) cc_final: 0.7460 (ptp-110) REVERT: B 351 GLN cc_start: 0.8587 (tp40) cc_final: 0.8100 (tt0) REVERT: B 359 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7300 (tp40) REVERT: C 67 MET cc_start: 0.8495 (mmp) cc_final: 0.8213 (mmt) REVERT: C 99 HIS cc_start: 0.6922 (OUTLIER) cc_final: 0.6536 (t70) REVERT: C 116 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8256 (mt-10) REVERT: D 119 ASN cc_start: 0.9303 (m110) cc_final: 0.8988 (m-40) REVERT: E 93 VAL cc_start: 0.9521 (t) cc_final: 0.9196 (p) REVERT: E 105 GLU cc_start: 0.8228 (tt0) cc_final: 0.7992 (tt0) REVERT: E 199 TYR cc_start: 0.8886 (m-80) cc_final: 0.8517 (m-10) REVERT: E 218 ASN cc_start: 0.8183 (m110) cc_final: 0.7764 (p0) REVERT: E 289 TYR cc_start: 0.8948 (m-10) cc_final: 0.8735 (m-10) REVERT: E 295 HIS cc_start: 0.8770 (m-70) cc_final: 0.8542 (m-70) REVERT: E 343 LEU cc_start: 0.8998 (mp) cc_final: 0.8771 (mm) REVERT: E 350 ARG cc_start: 0.8080 (tmm-80) cc_final: 0.7587 (tmm-80) REVERT: G 49 GLN cc_start: 0.9291 (tp40) cc_final: 0.9079 (tp-100) REVERT: G 73 GLN cc_start: 0.8697 (tt0) cc_final: 0.7765 (mm110) REVERT: G 99 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7857 (t70) REVERT: H 77 PHE cc_start: 0.8151 (t80) cc_final: 0.7835 (t80) REVERT: H 119 ASN cc_start: 0.9052 (m110) cc_final: 0.8817 (m-40) REVERT: F 56 HIS cc_start: 0.8206 (m-70) cc_final: 0.7823 (m-70) REVERT: F 137 VAL cc_start: 0.8505 (t) cc_final: 0.8015 (p) REVERT: F 285 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8857 (pm20) outliers start: 47 outliers final: 18 residues processed: 306 average time/residue: 0.2674 time to fit residues: 116.7678 Evaluate side-chains 251 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 285 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 41 optimal weight: 0.0970 chunk 149 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 333 GLN A 338 GLN A 347 GLN B 59 GLN B 243 HIS B 359 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS E 131 GLN G 61 ASN H 47 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13770 Z= 0.251 Angle : 0.618 13.426 18598 Z= 0.316 Chirality : 0.047 0.185 1912 Planarity : 0.004 0.043 2506 Dihedral : 4.616 59.490 1788 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.91 % Allowed : 23.48 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % 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: 0.34 (0.21), residues: 1646 helix: 1.47 (0.24), residues: 490 sheet: 1.04 (0.27), residues: 362 loop : -0.99 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 126 HIS 0.015 0.001 HIS G 47 PHE 0.029 0.002 PHE A 296 TYR 0.021 0.002 TYR C 138 ARG 0.007 0.001 ARG G 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8666 (tt) REVERT: A 160 LYS cc_start: 0.8915 (mppt) cc_final: 0.8672 (mmtp) REVERT: A 350 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7855 (ptp90) REVERT: B 58 VAL cc_start: 0.8780 (t) cc_final: 0.8551 (p) REVERT: B 107 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7663 (tt0) REVERT: B 178 HIS cc_start: 0.7343 (t-90) cc_final: 0.7078 (t-90) REVERT: B 223 ASP cc_start: 0.8643 (m-30) cc_final: 0.8368 (m-30) REVERT: B 289 TYR cc_start: 0.9341 (m-80) cc_final: 0.8977 (m-80) REVERT: B 329 ARG cc_start: 0.8062 (ttp-110) cc_final: 0.7486 (ptp-110) REVERT: B 351 GLN cc_start: 0.8627 (tp40) cc_final: 0.8116 (tt0) REVERT: B 359 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7248 (tp40) REVERT: C 116 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8453 (mt-10) REVERT: D 119 ASN cc_start: 0.9282 (m110) cc_final: 0.8970 (m-40) REVERT: D 124 VAL cc_start: 0.9281 (t) cc_final: 0.8850 (p) REVERT: D 128 ASP cc_start: 0.8126 (t70) cc_final: 0.7450 (m-30) REVERT: E 105 GLU cc_start: 0.8290 (tt0) cc_final: 0.8046 (tt0) REVERT: E 199 TYR cc_start: 0.8937 (m-80) cc_final: 0.8595 (m-10) REVERT: E 218 ASN cc_start: 0.8321 (m110) cc_final: 0.7730 (p0) REVERT: E 289 TYR cc_start: 0.8996 (m-10) cc_final: 0.8594 (m-10) REVERT: E 295 HIS cc_start: 0.8781 (m-70) cc_final: 0.8571 (m-70) REVERT: E 343 LEU cc_start: 0.8923 (mp) cc_final: 0.8688 (mm) REVERT: G 49 GLN cc_start: 0.9214 (tp40) cc_final: 0.8889 (tp-100) REVERT: G 53 MET cc_start: 0.8154 (mmt) cc_final: 0.7645 (mmt) REVERT: G 73 GLN cc_start: 0.8715 (tt0) cc_final: 0.7773 (mm110) REVERT: G 99 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7906 (t70) REVERT: G 124 VAL cc_start: 0.8881 (t) cc_final: 0.8650 (p) REVERT: H 119 ASN cc_start: 0.9048 (m110) cc_final: 0.8813 (m-40) REVERT: F 56 HIS cc_start: 0.8192 (m-70) cc_final: 0.7850 (m-70) REVERT: F 137 VAL cc_start: 0.8539 (t) cc_final: 0.8029 (p) outliers start: 42 outliers final: 23 residues processed: 275 average time/residue: 0.2920 time to fit residues: 116.5075 Evaluate side-chains 251 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 258 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 100 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN C 80 HIS D 49 GLN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 75 HIS E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13770 Z= 0.275 Angle : 0.631 11.867 18598 Z= 0.323 Chirality : 0.047 0.235 1912 Planarity : 0.004 0.046 2506 Dihedral : 4.666 59.677 1788 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.64 % Allowed : 21.95 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % 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: 1646 helix: 1.56 (0.24), residues: 482 sheet: 1.09 (0.28), residues: 338 loop : -1.06 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 126 HIS 0.008 0.001 HIS G 47 PHE 0.032 0.002 PHE A 296 TYR 0.021 0.002 TYR D 138 ARG 0.008 0.000 ARG G 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 233 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8695 (tt) REVERT: A 79 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8688 (pt0) REVERT: A 160 LYS cc_start: 0.8933 (mppt) cc_final: 0.8703 (mmtp) REVERT: B 45 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7153 (tpt-90) REVERT: B 50 TYR cc_start: 0.9026 (m-80) cc_final: 0.8750 (m-80) REVERT: B 107 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7638 (tt0) REVERT: B 178 HIS cc_start: 0.7431 (t-90) cc_final: 0.7149 (t-90) REVERT: B 289 TYR cc_start: 0.9415 (m-80) cc_final: 0.8991 (m-80) REVERT: B 293 PHE cc_start: 0.8518 (t80) cc_final: 0.8163 (t80) REVERT: B 329 ARG cc_start: 0.8076 (ttp-110) cc_final: 0.7501 (ptp-110) REVERT: B 351 GLN cc_start: 0.8494 (tp40) cc_final: 0.8061 (tt0) REVERT: B 358 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8434 (mm-30) REVERT: C 92 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8318 (mp0) REVERT: C 116 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8453 (mt-10) REVERT: D 119 ASN cc_start: 0.9268 (m110) cc_final: 0.8945 (m-40) REVERT: D 124 VAL cc_start: 0.9319 (t) cc_final: 0.8890 (p) REVERT: E 79 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8800 (pt0) REVERT: E 105 GLU cc_start: 0.8290 (tt0) cc_final: 0.8014 (tt0) REVERT: E 199 TYR cc_start: 0.8978 (m-80) cc_final: 0.8630 (m-10) REVERT: E 289 TYR cc_start: 0.9054 (m-10) cc_final: 0.8625 (m-10) REVERT: E 295 HIS cc_start: 0.8759 (m-70) cc_final: 0.8524 (m-70) REVERT: E 323 PHE cc_start: 0.8178 (t80) cc_final: 0.7865 (t80) REVERT: E 343 LEU cc_start: 0.8911 (mp) cc_final: 0.8638 (mm) REVERT: G 70 GLN cc_start: 0.8659 (pm20) cc_final: 0.8346 (pm20) REVERT: G 73 GLN cc_start: 0.8654 (tt0) cc_final: 0.7735 (mm110) REVERT: G 99 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.7961 (t70) REVERT: G 124 VAL cc_start: 0.8897 (t) cc_final: 0.8675 (p) REVERT: H 119 ASN cc_start: 0.9017 (m110) cc_final: 0.8794 (m-40) REVERT: H 126 ARG cc_start: 0.8713 (ttp-110) cc_final: 0.8506 (ttp-110) REVERT: F 56 HIS cc_start: 0.8220 (m-70) cc_final: 0.7849 (m-70) REVERT: F 137 VAL cc_start: 0.8643 (t) cc_final: 0.8141 (p) outliers start: 67 outliers final: 34 residues processed: 285 average time/residue: 0.2623 time to fit residues: 108.3738 Evaluate side-chains 264 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 289 TYR Chi-restraints excluded: chain F residue 299 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 65 optimal weight: 0.0970 chunk 135 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 overall best weight: 1.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN C 73 GLN D 49 GLN D 55 HIS D 80 HIS E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN H 73 GLN F 342 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13770 Z= 0.237 Angle : 0.634 14.734 18598 Z= 0.323 Chirality : 0.047 0.287 1912 Planarity : 0.004 0.048 2506 Dihedral : 4.629 57.722 1788 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.16 % Allowed : 22.85 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % 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: 0.29 (0.21), residues: 1646 helix: 1.57 (0.24), residues: 482 sheet: 0.83 (0.27), residues: 362 loop : -0.99 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 126 HIS 0.012 0.001 HIS D 80 PHE 0.024 0.002 PHE E 296 TYR 0.020 0.001 TYR F 50 ARG 0.008 0.000 ARG G 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 230 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8712 (tt) REVERT: A 160 LYS cc_start: 0.8900 (mppt) cc_final: 0.8683 (mmtp) REVERT: A 191 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8606 (tm-30) REVERT: B 50 TYR cc_start: 0.9001 (m-80) cc_final: 0.8750 (m-80) REVERT: B 107 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7631 (tt0) REVERT: B 176 TYR cc_start: 0.8566 (t80) cc_final: 0.8319 (t80) REVERT: B 178 HIS cc_start: 0.7403 (t-90) cc_final: 0.7080 (t-90) REVERT: B 329 ARG cc_start: 0.8050 (ttp-110) cc_final: 0.7501 (ptp-110) REVERT: B 351 GLN cc_start: 0.8453 (tp40) cc_final: 0.8035 (tt0) REVERT: B 358 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8391 (mm-30) REVERT: C 116 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8506 (mt-10) REVERT: D 119 ASN cc_start: 0.9284 (m110) cc_final: 0.8954 (m-40) REVERT: E 79 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8782 (pt0) REVERT: E 105 GLU cc_start: 0.8233 (tt0) cc_final: 0.7982 (tt0) REVERT: E 199 TYR cc_start: 0.9009 (m-80) cc_final: 0.8628 (m-10) REVERT: E 289 TYR cc_start: 0.9056 (m-10) cc_final: 0.8838 (m-10) REVERT: G 41 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7586 (mp) REVERT: G 73 GLN cc_start: 0.8612 (tt0) cc_final: 0.7707 (mm110) REVERT: G 124 VAL cc_start: 0.8912 (t) cc_final: 0.8700 (p) REVERT: H 119 ASN cc_start: 0.9002 (m110) cc_final: 0.8749 (m-40) REVERT: F 56 HIS cc_start: 0.8168 (m-70) cc_final: 0.7843 (m-70) REVERT: F 137 VAL cc_start: 0.8634 (t) cc_final: 0.8115 (p) outliers start: 60 outliers final: 37 residues processed: 274 average time/residue: 0.2732 time to fit residues: 108.3426 Evaluate side-chains 257 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 289 TYR Chi-restraints excluded: chain F residue 299 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 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 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 55 HIS E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13770 Z= 0.256 Angle : 0.645 13.195 18598 Z= 0.330 Chirality : 0.047 0.171 1912 Planarity : 0.004 0.049 2506 Dihedral : 4.673 56.497 1788 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.74 % Allowed : 24.03 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % 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: 0.23 (0.21), residues: 1646 helix: 1.40 (0.24), residues: 490 sheet: 0.74 (0.27), residues: 362 loop : -0.94 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 126 HIS 0.014 0.001 HIS E 295 PHE 0.029 0.002 PHE E 296 TYR 0.024 0.001 TYR F 50 ARG 0.008 0.000 ARG E 350 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8714 (tt) REVERT: A 79 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8691 (pt0) REVERT: A 160 LYS cc_start: 0.8910 (mppt) cc_final: 0.8698 (mmtp) REVERT: A 191 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8663 (tm-30) REVERT: A 292 GLU cc_start: 0.8987 (pt0) cc_final: 0.8613 (pt0) REVERT: B 50 TYR cc_start: 0.9019 (m-80) cc_final: 0.8720 (m-80) REVERT: B 107 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7632 (tt0) REVERT: B 176 TYR cc_start: 0.8578 (t80) cc_final: 0.8361 (t80) REVERT: B 178 HIS cc_start: 0.7414 (t-90) cc_final: 0.7074 (t-90) REVERT: B 289 TYR cc_start: 0.9431 (m-80) cc_final: 0.8973 (m-80) REVERT: B 329 ARG cc_start: 0.8074 (ttp-110) cc_final: 0.7501 (ptp-110) REVERT: B 351 GLN cc_start: 0.8465 (tp40) cc_final: 0.8038 (tt0) REVERT: B 358 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8345 (mm-30) REVERT: C 74 LEU cc_start: 0.8540 (mm) cc_final: 0.8101 (mm) REVERT: D 119 ASN cc_start: 0.9277 (m110) cc_final: 0.8932 (m-40) REVERT: E 79 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8819 (pt0) REVERT: E 105 GLU cc_start: 0.8215 (tt0) cc_final: 0.7958 (tt0) REVERT: E 199 TYR cc_start: 0.9023 (m-80) cc_final: 0.8678 (m-10) REVERT: E 224 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8426 (mtmm) REVERT: E 289 TYR cc_start: 0.9138 (m-10) cc_final: 0.8732 (m-10) REVERT: E 295 HIS cc_start: 0.8644 (m-70) cc_final: 0.8394 (m-70) REVERT: E 323 PHE cc_start: 0.8137 (t80) cc_final: 0.7885 (t80) REVERT: E 347 GLN cc_start: 0.7775 (tp-100) cc_final: 0.7062 (tm-30) REVERT: G 41 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7569 (mp) REVERT: H 119 ASN cc_start: 0.8985 (m110) cc_final: 0.8743 (m-40) REVERT: F 56 HIS cc_start: 0.8151 (m-70) cc_final: 0.7808 (m-70) REVERT: F 137 VAL cc_start: 0.8688 (t) cc_final: 0.8169 (p) outliers start: 54 outliers final: 42 residues processed: 268 average time/residue: 0.2608 time to fit residues: 101.3015 Evaluate side-chains 264 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 299 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 133 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 HIS C 73 GLN D 55 HIS E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN E 257 HIS E 342 HIS ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS G 86 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN H 73 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13770 Z= 0.200 Angle : 0.625 13.641 18598 Z= 0.321 Chirality : 0.046 0.175 1912 Planarity : 0.003 0.049 2506 Dihedral : 4.391 54.929 1786 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.09 % Allowed : 24.17 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % 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: 0.31 (0.21), residues: 1646 helix: 1.63 (0.24), residues: 478 sheet: 0.97 (0.28), residues: 338 loop : -1.02 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 126 HIS 0.012 0.001 HIS D 55 PHE 0.020 0.001 PHE E 296 TYR 0.026 0.001 TYR F 50 ARG 0.008 0.000 ARG E 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 230 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8703 (tt) REVERT: A 79 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8637 (pt0) REVERT: A 160 LYS cc_start: 0.8915 (mppt) cc_final: 0.8697 (mmtp) REVERT: A 191 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8675 (tm-30) REVERT: B 50 TYR cc_start: 0.9036 (m-80) cc_final: 0.8797 (m-80) REVERT: B 107 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7611 (tt0) REVERT: B 176 TYR cc_start: 0.8539 (t80) cc_final: 0.8339 (t80) REVERT: B 178 HIS cc_start: 0.7350 (t-90) cc_final: 0.6991 (t-90) REVERT: B 289 TYR cc_start: 0.9428 (m-80) cc_final: 0.8944 (m-80) REVERT: B 329 ARG cc_start: 0.8058 (ttp-110) cc_final: 0.7492 (ptp-110) REVERT: B 351 GLN cc_start: 0.8424 (tp40) cc_final: 0.8040 (tt0) REVERT: C 71 GLU cc_start: 0.9057 (pm20) cc_final: 0.8668 (pm20) REVERT: C 74 LEU cc_start: 0.8481 (mm) cc_final: 0.8128 (mm) REVERT: C 140 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7221 (mt-10) REVERT: D 119 ASN cc_start: 0.9265 (m110) cc_final: 0.8921 (m-40) REVERT: D 128 ASP cc_start: 0.8194 (t0) cc_final: 0.7341 (m-30) REVERT: E 79 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8513 (pt0) REVERT: E 93 VAL cc_start: 0.9501 (t) cc_final: 0.9178 (p) REVERT: E 105 GLU cc_start: 0.8262 (tt0) cc_final: 0.8001 (tt0) REVERT: E 199 TYR cc_start: 0.9006 (m-80) cc_final: 0.8683 (m-10) REVERT: E 289 TYR cc_start: 0.9130 (m-10) cc_final: 0.8833 (m-10) REVERT: E 291 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8489 (pm20) REVERT: E 295 HIS cc_start: 0.8648 (m-70) cc_final: 0.8381 (m-70) REVERT: E 323 PHE cc_start: 0.8123 (t80) cc_final: 0.7856 (t80) REVERT: E 347 GLN cc_start: 0.7864 (tp-100) cc_final: 0.7130 (tm-30) REVERT: G 41 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7636 (mp) REVERT: H 119 ASN cc_start: 0.8936 (m110) cc_final: 0.8711 (m-40) REVERT: F 56 HIS cc_start: 0.8147 (m-70) cc_final: 0.7760 (m-70) REVERT: F 137 VAL cc_start: 0.8637 (t) cc_final: 0.8126 (p) outliers start: 59 outliers final: 35 residues processed: 279 average time/residue: 0.2593 time to fit residues: 104.8571 Evaluate side-chains 264 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 355 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 HIS D 70 GLN D 75 HIS E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS G 86 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13770 Z= 0.254 Angle : 0.662 16.254 18598 Z= 0.338 Chirality : 0.047 0.171 1912 Planarity : 0.004 0.050 2506 Dihedral : 4.504 57.406 1786 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.46 % Allowed : 25.21 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % 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: 1646 helix: 1.44 (0.24), residues: 490 sheet: 0.93 (0.28), residues: 338 loop : -0.98 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 126 HIS 0.012 0.001 HIS A 295 PHE 0.044 0.002 PHE E 307 TYR 0.026 0.002 TYR F 289 ARG 0.009 0.000 ARG E 350 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8713 (tt) REVERT: A 160 LYS cc_start: 0.8924 (mppt) cc_final: 0.8695 (mmtp) REVERT: A 191 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8693 (tm-30) REVERT: B 50 TYR cc_start: 0.9061 (m-80) cc_final: 0.8811 (m-80) REVERT: B 107 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7628 (tt0) REVERT: B 178 HIS cc_start: 0.7381 (t-90) cc_final: 0.7018 (t-90) REVERT: B 289 TYR cc_start: 0.9442 (m-80) cc_final: 0.8968 (m-80) REVERT: B 329 ARG cc_start: 0.8085 (ttp-110) cc_final: 0.7508 (ptp-110) REVERT: B 351 GLN cc_start: 0.8447 (tp40) cc_final: 0.8087 (tt0) REVERT: C 71 GLU cc_start: 0.9073 (pm20) cc_final: 0.8782 (pm20) REVERT: C 74 LEU cc_start: 0.8534 (mm) cc_final: 0.8073 (mm) REVERT: C 140 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7208 (mt-10) REVERT: D 52 ILE cc_start: 0.9213 (mp) cc_final: 0.8979 (tt) REVERT: D 119 ASN cc_start: 0.9253 (m110) cc_final: 0.8895 (m-40) REVERT: E 79 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8471 (pt0) REVERT: E 105 GLU cc_start: 0.8217 (tt0) cc_final: 0.7952 (tt0) REVERT: E 199 TYR cc_start: 0.9012 (m-80) cc_final: 0.8665 (m-10) REVERT: E 258 ASP cc_start: 0.8731 (m-30) cc_final: 0.8286 (m-30) REVERT: E 289 TYR cc_start: 0.9140 (m-10) cc_final: 0.8836 (m-10) REVERT: E 291 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8471 (pm20) REVERT: E 295 HIS cc_start: 0.8604 (m-70) cc_final: 0.8353 (m90) REVERT: E 347 GLN cc_start: 0.7897 (tp-100) cc_final: 0.7031 (tm-30) REVERT: H 119 ASN cc_start: 0.8926 (m110) cc_final: 0.8706 (m-40) REVERT: F 56 HIS cc_start: 0.8150 (m-70) cc_final: 0.7762 (m-70) REVERT: F 137 VAL cc_start: 0.8696 (t) cc_final: 0.8187 (p) outliers start: 50 outliers final: 36 residues processed: 262 average time/residue: 0.2537 time to fit residues: 97.1745 Evaluate side-chains 257 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 355 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 0.9980 chunk 151 optimal weight: 0.3980 chunk 138 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 HIS E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13770 Z= 0.194 Angle : 0.664 16.199 18598 Z= 0.338 Chirality : 0.046 0.159 1912 Planarity : 0.003 0.050 2506 Dihedral : 4.471 56.013 1786 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.84 % Allowed : 26.18 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % 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: 0.31 (0.21), residues: 1646 helix: 1.53 (0.24), residues: 488 sheet: 1.02 (0.28), residues: 338 loop : -0.99 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 126 HIS 0.014 0.001 HIS D 55 PHE 0.032 0.001 PHE E 307 TYR 0.024 0.001 TYR F 50 ARG 0.007 0.000 ARG G 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8593 (pt0) REVERT: A 160 LYS cc_start: 0.8918 (mppt) cc_final: 0.8709 (mmtp) REVERT: A 191 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8675 (tm-30) REVERT: B 107 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7595 (tt0) REVERT: B 178 HIS cc_start: 0.7337 (t-90) cc_final: 0.6941 (t-90) REVERT: B 289 TYR cc_start: 0.9450 (m-80) cc_final: 0.8992 (m-80) REVERT: B 329 ARG cc_start: 0.8028 (ttp-110) cc_final: 0.7472 (ptp-110) REVERT: B 351 GLN cc_start: 0.8467 (tp40) cc_final: 0.8101 (tt0) REVERT: C 71 GLU cc_start: 0.9067 (pm20) cc_final: 0.8761 (pm20) REVERT: C 74 LEU cc_start: 0.8491 (mm) cc_final: 0.8046 (mm) REVERT: C 140 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7320 (mt-10) REVERT: D 52 ILE cc_start: 0.9271 (mp) cc_final: 0.8804 (tt) REVERT: D 119 ASN cc_start: 0.9251 (m110) cc_final: 0.8872 (m-40) REVERT: D 128 ASP cc_start: 0.8129 (t0) cc_final: 0.7356 (m-30) REVERT: E 79 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8499 (pt0) REVERT: E 93 VAL cc_start: 0.9489 (t) cc_final: 0.9195 (p) REVERT: E 105 GLU cc_start: 0.8216 (tt0) cc_final: 0.7924 (tt0) REVERT: E 199 TYR cc_start: 0.9011 (m-80) cc_final: 0.8697 (m-10) REVERT: E 289 TYR cc_start: 0.9121 (m-10) cc_final: 0.8826 (m-10) REVERT: E 291 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: E 295 HIS cc_start: 0.8603 (m-70) cc_final: 0.8321 (m90) REVERT: E 323 PHE cc_start: 0.8026 (t80) cc_final: 0.7802 (t80) REVERT: G 115 ASP cc_start: 0.8847 (m-30) cc_final: 0.8547 (t0) REVERT: G 140 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7565 (mt-10) REVERT: F 56 HIS cc_start: 0.8128 (m-70) cc_final: 0.7736 (m-70) REVERT: F 137 VAL cc_start: 0.8624 (t) cc_final: 0.8121 (p) outliers start: 41 outliers final: 29 residues processed: 258 average time/residue: 0.2613 time to fit residues: 98.0277 Evaluate side-chains 255 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 355 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 130 optimal weight: 40.0000 chunk 13 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 HIS E 79 GLN E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 HIS E 342 HIS ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13770 Z= 0.392 Angle : 0.734 15.127 18598 Z= 0.378 Chirality : 0.049 0.177 1912 Planarity : 0.004 0.050 2506 Dihedral : 4.816 58.568 1786 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.63 % Allowed : 26.04 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % 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: 0.12 (0.21), residues: 1646 helix: 1.45 (0.24), residues: 490 sheet: 0.61 (0.27), residues: 362 loop : -1.08 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 126 HIS 0.009 0.001 HIS E 295 PHE 0.030 0.002 PHE E 307 TYR 0.026 0.002 TYR H 138 ARG 0.008 0.001 ARG G 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8790 (t0) cc_final: 0.8452 (t0) REVERT: A 160 LYS cc_start: 0.8972 (mppt) cc_final: 0.8747 (mmtp) REVERT: A 346 LYS cc_start: 0.8507 (mttp) cc_final: 0.8227 (mtpp) REVERT: B 107 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7659 (tt0) REVERT: B 178 HIS cc_start: 0.7464 (t-90) cc_final: 0.7081 (t-90) REVERT: B 223 ASP cc_start: 0.8660 (m-30) cc_final: 0.8298 (m-30) REVERT: B 289 TYR cc_start: 0.9532 (m-80) cc_final: 0.8984 (m-80) REVERT: B 304 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7715 (mmmt) REVERT: B 329 ARG cc_start: 0.8060 (ttp-110) cc_final: 0.7511 (ptp-110) REVERT: B 351 GLN cc_start: 0.8501 (tp40) cc_final: 0.8138 (tt0) REVERT: C 71 GLU cc_start: 0.9077 (pm20) cc_final: 0.8781 (pm20) REVERT: C 74 LEU cc_start: 0.8622 (mm) cc_final: 0.8124 (mm) REVERT: C 140 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7259 (mt-10) REVERT: D 49 GLN cc_start: 0.8536 (tm-30) cc_final: 0.7954 (tm-30) REVERT: D 52 ILE cc_start: 0.9221 (mp) cc_final: 0.8903 (tt) REVERT: D 53 MET cc_start: 0.9072 (mmp) cc_final: 0.8828 (mmm) REVERT: D 73 GLN cc_start: 0.7441 (pt0) cc_final: 0.6911 (pp30) REVERT: D 119 ASN cc_start: 0.9249 (m110) cc_final: 0.8873 (m-40) REVERT: E 105 GLU cc_start: 0.8287 (tt0) cc_final: 0.8023 (tt0) REVERT: E 199 TYR cc_start: 0.9040 (m-80) cc_final: 0.8726 (m-10) REVERT: E 289 TYR cc_start: 0.9156 (m-10) cc_final: 0.8856 (m-10) REVERT: E 291 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8508 (pm20) REVERT: E 295 HIS cc_start: 0.8524 (m170) cc_final: 0.8297 (m90) REVERT: H 114 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8011 (tm-30) REVERT: F 50 TYR cc_start: 0.8699 (m-80) cc_final: 0.8463 (m-80) REVERT: F 56 HIS cc_start: 0.8154 (m-70) cc_final: 0.7785 (m-70) REVERT: F 137 VAL cc_start: 0.8821 (t) cc_final: 0.8342 (p) outliers start: 38 outliers final: 29 residues processed: 254 average time/residue: 0.2673 time to fit residues: 99.0967 Evaluate side-chains 246 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 355 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.171241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.114122 restraints weight = 19701.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.117008 restraints weight = 13576.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118296 restraints weight = 10943.008| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13770 Z= 0.300 Angle : 0.711 15.253 18598 Z= 0.364 Chirality : 0.048 0.201 1912 Planarity : 0.004 0.050 2506 Dihedral : 4.776 59.521 1786 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.22 % Allowed : 26.59 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % 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: 1646 helix: 1.46 (0.24), residues: 488 sheet: 0.56 (0.28), residues: 362 loop : -1.08 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 126 HIS 0.006 0.001 HIS D 80 PHE 0.032 0.002 PHE E 323 TYR 0.030 0.002 TYR H 138 ARG 0.008 0.000 ARG G 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2839.64 seconds wall clock time: 52 minutes 32.95 seconds (3152.95 seconds total)