Starting phenix.real_space_refine on Thu Jul 31 08:22:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp7_36470/07_2025/8jp7_36470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp7_36470/07_2025/8jp7_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/cci-nas-00/data/ceres_data/8jp7_36470/07_2025/8jp7_36470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp7_36470/07_2025/8jp7_36470.map" model { file = "/net/cci-nas-00/data/ceres_data/8jp7_36470/07_2025/8jp7_36470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp7_36470/07_2025/8jp7_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.76, per 1000 atoms: 0.58 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: 2.97 Conformation dependent library (CDL) restraints added in 1.6 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: 1.67 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: 3.96 Time building geometry restraints manager: 3.55 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: 0.01 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: 0.580 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: 0.110 Process input model: 30.720 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- 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 13774 Z= 0.236 Angle : 0.641 9.927 18606 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 Details of bonding type rmsd hydrogen bonds : bond 0.16722 ( 641) hydrogen bonds : angle 6.88286 ( 1920) SS BOND : bond 0.00183 ( 4) SS BOND : angle 2.30705 ( 8) covalent geometry : bond 0.00537 (13770) covalent geometry : angle 0.63924 (18598) *********************** 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 : 1.638 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: 0.2834 time to fit residues: 133.9598 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 : 1.467 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.164714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106717 restraints weight = 19660.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107891 restraints weight = 17280.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.108386 restraints weight = 13389.190| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 13774 Z= 0.166 Angle : 0.598 8.089 18606 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 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 641) hydrogen bonds : angle 4.64198 ( 1920) SS BOND : bond 0.00208 ( 4) SS BOND : angle 1.69455 ( 8) covalent geometry : bond 0.00377 (13770) covalent geometry : angle 0.59683 (18598) *********************** 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 : 1.535 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 350 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7741 (ptp90) REVERT: A 355 ILE cc_start: 0.8227 (tt) cc_final: 0.7802 (tt) REVERT: B 58 VAL cc_start: 0.8391 (t) cc_final: 0.8093 (p) REVERT: B 230 CYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7817 (t) REVERT: B 289 TYR cc_start: 0.8940 (m-80) cc_final: 0.8677 (m-80) REVERT: B 329 ARG cc_start: 0.7805 (ttp-110) cc_final: 0.7472 (ptp-110) REVERT: B 351 GLN cc_start: 0.8532 (tp40) cc_final: 0.8110 (tt0) REVERT: B 359 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7317 (tp40) REVERT: C 67 MET cc_start: 0.8146 (mmp) cc_final: 0.7941 (mmt) REVERT: C 99 HIS cc_start: 0.6951 (OUTLIER) cc_final: 0.6555 (t70) REVERT: D 119 ASN cc_start: 0.9212 (m110) cc_final: 0.8892 (m-40) REVERT: E 93 VAL cc_start: 0.9312 (t) cc_final: 0.9015 (p) REVERT: E 199 TYR cc_start: 0.8631 (m-80) cc_final: 0.8284 (m-10) REVERT: E 295 HIS cc_start: 0.8443 (m-70) cc_final: 0.8243 (m-70) REVERT: E 350 ARG cc_start: 0.7962 (tmm-80) cc_final: 0.7502 (tmm-80) REVERT: G 73 GLN cc_start: 0.8548 (tt0) cc_final: 0.7733 (mm110) REVERT: G 99 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7837 (t70) REVERT: H 77 PHE cc_start: 0.8098 (t80) cc_final: 0.7695 (t80) REVERT: H 119 ASN cc_start: 0.9347 (m110) cc_final: 0.9028 (m-40) REVERT: F 137 VAL cc_start: 0.8579 (t) cc_final: 0.8192 (p) outliers start: 47 outliers final: 18 residues processed: 306 average time/residue: 0.2624 time to fit residues: 114.8267 Evaluate side-chains 244 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 230 CYS 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 65 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 0.0050 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.164213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.106205 restraints weight = 19688.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.108978 restraints weight = 14487.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.109476 restraints weight = 11898.994| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13774 Z= 0.138 Angle : 0.612 13.810 18606 Z= 0.312 Chirality : 0.046 0.183 1912 Planarity : 0.003 0.044 2506 Dihedral : 4.554 59.089 1788 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.05 % Allowed : 23.13 % Favored : 73.82 % 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: 0.38 (0.21), residues: 1646 helix: 1.45 (0.24), residues: 490 sheet: 1.35 (0.28), residues: 338 loop : -1.01 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 126 HIS 0.016 0.001 HIS G 47 PHE 0.030 0.001 PHE A 296 TYR 0.020 0.002 TYR C 138 ARG 0.007 0.000 ARG G 126 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 641) hydrogen bonds : angle 4.37684 ( 1920) SS BOND : bond 0.01166 ( 4) SS BOND : angle 1.42965 ( 8) covalent geometry : bond 0.00312 (13770) covalent geometry : angle 0.61131 (18598) *********************** 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: 44 poor density : 241 time to evaluate : 1.675 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: A 350 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7786 (ptp90) REVERT: A 362 TYR cc_start: 0.8057 (t80) cc_final: 0.7853 (t80) REVERT: B 58 VAL cc_start: 0.8478 (t) cc_final: 0.8196 (p) REVERT: B 230 CYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7604 (t) REVERT: B 289 TYR cc_start: 0.9131 (m-80) cc_final: 0.8776 (m-80) REVERT: B 351 GLN cc_start: 0.8550 (tp40) cc_final: 0.8108 (tt0) REVERT: B 359 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7272 (tp40) REVERT: D 119 ASN cc_start: 0.9181 (m110) cc_final: 0.8855 (m-40) REVERT: D 124 VAL cc_start: 0.9133 (t) cc_final: 0.8735 (p) REVERT: D 128 ASP cc_start: 0.7821 (t70) cc_final: 0.7400 (m-30) REVERT: E 79 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8396 (pt0) REVERT: E 93 VAL cc_start: 0.9307 (t) cc_final: 0.9042 (p) REVERT: E 199 TYR cc_start: 0.8676 (m-80) cc_final: 0.8343 (m-10) REVERT: E 289 TYR cc_start: 0.8688 (m-10) cc_final: 0.8391 (m-10) REVERT: G 49 GLN cc_start: 0.9098 (tp-100) cc_final: 0.8721 (tp-100) REVERT: G 53 MET cc_start: 0.7608 (mmt) cc_final: 0.7325 (mmt) REVERT: G 73 GLN cc_start: 0.8559 (tt0) cc_final: 0.7725 (mm110) REVERT: G 99 HIS cc_start: 0.8121 (OUTLIER) cc_final: 0.7864 (t70) REVERT: H 119 ASN cc_start: 0.9353 (m110) cc_final: 0.9036 (m-40) REVERT: F 56 HIS cc_start: 0.7655 (m-70) cc_final: 0.7343 (m170) REVERT: F 137 VAL cc_start: 0.8535 (t) cc_final: 0.8150 (p) outliers start: 44 outliers final: 23 residues processed: 275 average time/residue: 0.2481 time to fit residues: 98.4160 Evaluate side-chains 245 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 143 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 230 CYS 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 114 GLU 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 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 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 Chi-restraints excluded: chain F residue 299 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 61 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS B 359 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 75 HIS E 79 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 ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.160627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101123 restraints weight = 19729.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.104165 restraints weight = 14701.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.105058 restraints weight = 11875.687| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 13774 Z= 0.280 Angle : 0.685 10.861 18606 Z= 0.355 Chirality : 0.050 0.168 1912 Planarity : 0.004 0.047 2506 Dihedral : 4.824 57.579 1788 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.57 % Allowed : 22.85 % Favored : 72.58 % 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: 0.17 (0.21), residues: 1646 helix: 1.39 (0.24), residues: 486 sheet: 0.85 (0.27), residues: 350 loop : -1.05 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 67 HIS 0.012 0.001 HIS E 295 PHE 0.028 0.002 PHE A 262 TYR 0.026 0.002 TYR C 138 ARG 0.006 0.001 ARG G 126 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 641) hydrogen bonds : angle 4.55625 ( 1920) SS BOND : bond 0.00321 ( 4) SS BOND : angle 1.92963 ( 8) covalent geometry : bond 0.00660 (13770) covalent geometry : angle 0.68439 (18598) *********************** 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 285 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 219 time to evaluate : 2.090 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 79 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8516 (pt0) REVERT: B 50 TYR cc_start: 0.8766 (m-80) cc_final: 0.8538 (m-80) REVERT: B 230 CYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7945 (t) REVERT: B 289 TYR cc_start: 0.9238 (m-80) cc_final: 0.8835 (m-80) REVERT: B 293 PHE cc_start: 0.8311 (t80) cc_final: 0.7963 (t80) REVERT: B 351 GLN cc_start: 0.8476 (tp40) cc_final: 0.8093 (tt0) REVERT: B 359 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7192 (tp40) REVERT: C 99 HIS cc_start: 0.7178 (OUTLIER) cc_final: 0.6786 (t70) REVERT: D 119 ASN cc_start: 0.9177 (m110) cc_final: 0.8851 (m-40) REVERT: D 124 VAL cc_start: 0.9135 (t) cc_final: 0.8758 (p) REVERT: D 143 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8631 (mmmm) REVERT: E 199 TYR cc_start: 0.8740 (m-80) cc_final: 0.8312 (m-10) REVERT: E 289 TYR cc_start: 0.8788 (m-10) cc_final: 0.8476 (m-10) REVERT: E 295 HIS cc_start: 0.8313 (m-70) cc_final: 0.8009 (m-70) REVERT: G 49 GLN cc_start: 0.9106 (tp-100) cc_final: 0.8682 (tp-100) REVERT: G 53 MET cc_start: 0.7710 (mmt) cc_final: 0.7384 (mmt) REVERT: G 70 GLN cc_start: 0.8431 (pm20) cc_final: 0.8064 (pm20) REVERT: G 73 GLN cc_start: 0.8547 (tt0) cc_final: 0.7725 (mm110) REVERT: G 99 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7924 (t70) REVERT: H 119 ASN cc_start: 0.9357 (m110) cc_final: 0.9025 (m-40) REVERT: F 137 VAL cc_start: 0.8762 (t) cc_final: 0.8340 (p) outliers start: 66 outliers final: 36 residues processed: 267 average time/residue: 0.2950 time to fit residues: 116.5769 Evaluate side-chains 246 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 1.866 ------------------------------------------------------------------------------- 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 221 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 213 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain C residue 55 HIS 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 97 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 143 LYS 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 253 LEU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 64 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 347 GLN B 342 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS D 49 GLN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN E 257 HIS E 295 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN H 73 GLN ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.173485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120658 restraints weight = 19644.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120466 restraints weight = 13137.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120942 restraints weight = 10565.996| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13774 Z= 0.133 Angle : 0.611 10.004 18606 Z= 0.314 Chirality : 0.046 0.162 1912 Planarity : 0.003 0.049 2506 Dihedral : 4.597 58.092 1788 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.67 % Allowed : 23.96 % Favored : 72.37 % 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: 1.46 (0.24), residues: 484 sheet: 0.94 (0.28), residues: 338 loop : -1.01 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 126 HIS 0.010 0.001 HIS C 75 PHE 0.024 0.001 PHE E 296 TYR 0.029 0.002 TYR F 289 ARG 0.007 0.000 ARG G 126 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 641) hydrogen bonds : angle 4.26536 ( 1920) SS BOND : bond 0.00255 ( 4) SS BOND : angle 1.64405 ( 8) covalent geometry : bond 0.00302 (13770) covalent geometry : angle 0.61021 (18598) *********************** 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 283 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 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: B 230 CYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7519 (t) REVERT: B 351 GLN cc_start: 0.8373 (tp40) cc_final: 0.8098 (tt0) REVERT: D 119 ASN cc_start: 0.9079 (m110) cc_final: 0.8779 (m-40) REVERT: D 143 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8664 (mmmm) REVERT: E 93 VAL cc_start: 0.9265 (t) cc_final: 0.9020 (p) REVERT: E 199 TYR cc_start: 0.8698 (m-80) cc_final: 0.8269 (m-10) REVERT: G 41 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7617 (mp) REVERT: G 49 GLN cc_start: 0.9026 (tp-100) cc_final: 0.8636 (tp-100) REVERT: G 53 MET cc_start: 0.7507 (mmt) cc_final: 0.7222 (mmt) REVERT: G 73 GLN cc_start: 0.8435 (tt0) cc_final: 0.7688 (mm110) REVERT: G 99 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.7900 (t70) REVERT: H 119 ASN cc_start: 0.9230 (m110) cc_final: 0.8910 (m-40) REVERT: F 137 VAL cc_start: 0.8649 (t) cc_final: 0.8251 (p) outliers start: 53 outliers final: 26 residues processed: 270 average time/residue: 0.2767 time to fit residues: 107.9603 Evaluate side-chains 249 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 114 GLU 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 218 ASN 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 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 H residue 122 ASP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN C 80 HIS ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** 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** ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.170839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.113521 restraints weight = 19933.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116579 restraints weight = 13587.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.117829 restraints weight = 11147.691| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13774 Z= 0.215 Angle : 0.670 15.419 18606 Z= 0.344 Chirality : 0.048 0.171 1912 Planarity : 0.004 0.049 2506 Dihedral : 4.757 58.326 1788 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.60 % Allowed : 24.72 % Favored : 71.68 % 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: 0.10 (0.21), residues: 1646 helix: 1.39 (0.24), residues: 482 sheet: 0.60 (0.27), residues: 362 loop : -1.03 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 67 HIS 0.015 0.001 HIS B 342 PHE 0.039 0.002 PHE E 323 TYR 0.042 0.002 TYR F 289 ARG 0.007 0.001 ARG E 350 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 641) hydrogen bonds : angle 4.44631 ( 1920) SS BOND : bond 0.00143 ( 4) SS BOND : angle 2.07287 ( 8) covalent geometry : bond 0.00508 (13770) covalent geometry : angle 0.66887 (18598) *********************** 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 283 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 1.582 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: A 79 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8408 (pt0) REVERT: A 292 GLU cc_start: 0.8647 (pt0) cc_final: 0.8331 (pt0) REVERT: B 230 CYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7776 (t) REVERT: B 289 TYR cc_start: 0.9234 (m-80) cc_final: 0.8830 (m-80) REVERT: B 351 GLN cc_start: 0.8351 (tp40) cc_final: 0.8043 (tt0) REVERT: D 119 ASN cc_start: 0.9083 (m110) cc_final: 0.8755 (m-40) REVERT: D 128 ASP cc_start: 0.7873 (t0) cc_final: 0.7326 (t0) REVERT: D 143 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8675 (mmmm) REVERT: E 79 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7957 (pt0) REVERT: E 199 TYR cc_start: 0.8669 (m-80) cc_final: 0.8269 (m-10) REVERT: E 347 GLN cc_start: 0.7612 (tp-100) cc_final: 0.7088 (tm-30) REVERT: G 41 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7615 (mp) REVERT: G 49 GLN cc_start: 0.9077 (tp-100) cc_final: 0.8701 (tp-100) REVERT: G 53 MET cc_start: 0.7697 (mmt) cc_final: 0.7440 (mmt) REVERT: G 73 GLN cc_start: 0.8444 (tt0) cc_final: 0.7663 (mm110) REVERT: H 119 ASN cc_start: 0.9258 (m110) cc_final: 0.8944 (m-40) REVERT: F 137 VAL cc_start: 0.8757 (t) cc_final: 0.8350 (p) outliers start: 52 outliers final: 35 residues processed: 272 average time/residue: 0.3416 time to fit residues: 134.2916 Evaluate side-chains 257 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 2.350 ------------------------------------------------------------------------------- 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 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 230 CYS Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 GLU 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 218 ASN 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 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 95 THR 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 289 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 0 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN C 80 HIS D 55 HIS D 75 HIS 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.166097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110615 restraints weight = 19302.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.112653 restraints weight = 15888.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.112691 restraints weight = 12679.836| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13774 Z= 0.140 Angle : 0.637 14.319 18606 Z= 0.330 Chirality : 0.046 0.176 1912 Planarity : 0.003 0.049 2506 Dihedral : 4.455 55.965 1786 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.74 % Allowed : 24.79 % Favored : 71.47 % 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: 0.18 (0.21), residues: 1646 helix: 1.46 (0.24), residues: 484 sheet: 0.71 (0.27), residues: 350 loop : -0.99 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 126 HIS 0.009 0.001 HIS C 75 PHE 0.028 0.001 PHE E 296 TYR 0.037 0.002 TYR F 289 ARG 0.007 0.000 ARG E 350 Details of bonding type rmsd hydrogen bonds : bond 0.03631 ( 641) hydrogen bonds : angle 4.30309 ( 1920) SS BOND : bond 0.00150 ( 4) SS BOND : angle 1.78060 ( 8) covalent geometry : bond 0.00321 (13770) covalent geometry : angle 0.63558 (18598) *********************** 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 286 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 1.819 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 79 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8474 (pt0) REVERT: B 50 TYR cc_start: 0.8668 (m-80) cc_final: 0.8464 (m-80) REVERT: B 230 CYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7501 (t) REVERT: B 289 TYR cc_start: 0.9108 (m-80) cc_final: 0.8714 (m-80) REVERT: B 294 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9090 (mt-10) REVERT: B 351 GLN cc_start: 0.8404 (tp40) cc_final: 0.8157 (tt0) REVERT: D 119 ASN cc_start: 0.9011 (m110) cc_final: 0.8700 (m-40) REVERT: E 79 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7900 (pt0) REVERT: E 93 VAL cc_start: 0.9277 (t) cc_final: 0.8980 (p) REVERT: E 199 TYR cc_start: 0.8685 (m-80) cc_final: 0.8259 (m-10) REVERT: E 273 GLU cc_start: 0.7532 (pp20) cc_final: 0.7128 (pp20) REVERT: E 347 GLN cc_start: 0.7647 (tp-100) cc_final: 0.7155 (tm-30) REVERT: G 41 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7720 (mp) REVERT: G 49 GLN cc_start: 0.8886 (tp-100) cc_final: 0.8544 (tp-100) REVERT: G 53 MET cc_start: 0.7550 (mmt) cc_final: 0.7311 (mmt) REVERT: H 119 ASN cc_start: 0.9214 (m110) cc_final: 0.8904 (m-40) REVERT: F 137 VAL cc_start: 0.8678 (t) cc_final: 0.8289 (p) outliers start: 54 outliers final: 32 residues processed: 274 average time/residue: 0.2876 time to fit residues: 115.9222 Evaluate side-chains 251 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU 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 218 ASN 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 42 ASP 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 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 355 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 61 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 HIS C 80 HIS D 47 HIS D 70 GLN 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.163953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108440 restraints weight = 19252.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109851 restraints weight = 14827.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110015 restraints weight = 12727.732| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13774 Z= 0.195 Angle : 0.685 16.116 18606 Z= 0.353 Chirality : 0.048 0.181 1912 Planarity : 0.004 0.049 2506 Dihedral : 4.617 58.201 1786 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.25 % Allowed : 25.69 % Favored : 71.05 % 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: 1.42 (0.24), residues: 492 sheet: 0.65 (0.27), residues: 350 loop : -1.06 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 126 HIS 0.011 0.001 HIS C 75 PHE 0.042 0.002 PHE E 307 TYR 0.026 0.002 TYR F 50 ARG 0.009 0.000 ARG E 350 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 641) hydrogen bonds : angle 4.44388 ( 1920) SS BOND : bond 0.00133 ( 4) SS BOND : angle 1.88779 ( 8) covalent geometry : bond 0.00458 (13770) covalent geometry : angle 0.68423 (18598) *********************** 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 262 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 1.873 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 79 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8499 (pt0) REVERT: B 230 CYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7744 (t) REVERT: B 289 TYR cc_start: 0.9069 (m-80) cc_final: 0.8660 (m-80) REVERT: C 79 MET cc_start: 0.7976 (ttm) cc_final: 0.7739 (ptt) REVERT: D 49 GLN cc_start: 0.8075 (tp40) cc_final: 0.7711 (tp-100) REVERT: D 52 ILE cc_start: 0.9134 (mp) cc_final: 0.8809 (tt) REVERT: D 53 MET cc_start: 0.8570 (mmm) cc_final: 0.7715 (mmm) REVERT: D 119 ASN cc_start: 0.8965 (m110) cc_final: 0.8644 (m-40) REVERT: E 79 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7728 (pt0) REVERT: E 199 TYR cc_start: 0.8656 (m-80) cc_final: 0.8256 (m-10) REVERT: H 119 ASN cc_start: 0.9170 (m110) cc_final: 0.8880 (m-40) REVERT: F 137 VAL cc_start: 0.8754 (t) cc_final: 0.8369 (p) outliers start: 47 outliers final: 36 residues processed: 250 average time/residue: 0.3677 time to fit residues: 135.8330 Evaluate side-chains 252 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU 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 218 ASN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 42 ASP 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 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 123 LEU 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 355 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 51 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 50.0000 chunk 148 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS D 47 HIS ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN G 75 HIS ** H 55 HIS ** 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 = 0.4084 r_free = 0.4084 target = 0.166541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111950 restraints weight = 19057.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113811 restraints weight = 14365.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114000 restraints weight = 11715.845| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13774 Z= 0.135 Angle : 0.681 16.007 18606 Z= 0.348 Chirality : 0.047 0.180 1912 Planarity : 0.003 0.050 2506 Dihedral : 4.538 57.427 1786 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.22 % Allowed : 27.01 % Favored : 70.78 % 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: 1.47 (0.24), residues: 492 sheet: 0.76 (0.28), residues: 350 loop : -0.98 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 126 HIS 0.014 0.001 HIS C 75 PHE 0.033 0.001 PHE E 307 TYR 0.025 0.002 TYR F 289 ARG 0.010 0.000 ARG E 350 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 641) hydrogen bonds : angle 4.34416 ( 1920) SS BOND : bond 0.00185 ( 4) SS BOND : angle 1.58927 ( 8) covalent geometry : bond 0.00309 (13770) covalent geometry : angle 0.68040 (18598) *********************** 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 257 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 1.477 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: 0.8616 (OUTLIER) cc_final: 0.8375 (pt0) REVERT: B 230 CYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7513 (t) REVERT: B 289 TYR cc_start: 0.9021 (m-80) cc_final: 0.8665 (m-80) REVERT: D 48 ASP cc_start: 0.6675 (p0) cc_final: 0.6404 (p0) REVERT: D 52 ILE cc_start: 0.9098 (mp) cc_final: 0.8848 (tt) REVERT: D 53 MET cc_start: 0.8543 (mmm) cc_final: 0.7884 (mmm) REVERT: D 73 GLN cc_start: 0.7418 (pt0) cc_final: 0.7034 (mp10) REVERT: D 119 ASN cc_start: 0.8931 (m110) cc_final: 0.8667 (m-40) REVERT: E 79 GLN cc_start: 0.8226 (pt0) cc_final: 0.7977 (pt0) REVERT: E 93 VAL cc_start: 0.9256 (t) cc_final: 0.9012 (p) REVERT: E 199 TYR cc_start: 0.8655 (m-80) cc_final: 0.8306 (m-10) REVERT: G 127 ASP cc_start: 0.7562 (t0) cc_final: 0.7315 (t0) REVERT: H 119 ASN cc_start: 0.9101 (m110) cc_final: 0.8852 (m-40) REVERT: H 136 ILE cc_start: 0.8929 (mm) cc_final: 0.8725 (tt) REVERT: F 137 VAL cc_start: 0.8667 (t) cc_final: 0.8291 (p) outliers start: 32 outliers final: 26 residues processed: 247 average time/residue: 0.2480 time to fit residues: 89.6999 Evaluate side-chains 240 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 221 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 GLU 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 215 MET Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 221 THR 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 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 255 ASP Chi-restraints excluded: chain F residue 258 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 151 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 75 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.167316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111454 restraints weight = 19129.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.113981 restraints weight = 14182.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115615 restraints weight = 11885.694| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13774 Z= 0.135 Angle : 0.692 15.741 18606 Z= 0.355 Chirality : 0.047 0.233 1912 Planarity : 0.004 0.049 2506 Dihedral : 4.445 57.592 1786 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.22 % Allowed : 27.63 % Favored : 70.15 % 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: 1.29 (0.24), residues: 502 sheet: 0.96 (0.28), residues: 338 loop : -0.93 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 126 HIS 0.008 0.001 HIS A 295 PHE 0.058 0.002 PHE A 293 TYR 0.036 0.002 TYR C 138 ARG 0.011 0.000 ARG E 350 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 641) hydrogen bonds : angle 4.32773 ( 1920) SS BOND : bond 0.00172 ( 4) SS BOND : angle 1.50635 ( 8) covalent geometry : bond 0.00309 (13770) covalent geometry : angle 0.69177 (18598) ********************** 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 250 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 1.534 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 79 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8401 (pt0) REVERT: B 230 CYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7488 (t) REVERT: B 289 TYR cc_start: 0.9092 (m-80) cc_final: 0.8679 (m-80) REVERT: D 49 GLN cc_start: 0.8289 (tm-30) cc_final: 0.8017 (tm-30) REVERT: D 52 ILE cc_start: 0.9096 (mp) cc_final: 0.8718 (tt) REVERT: D 53 MET cc_start: 0.8474 (mmm) cc_final: 0.7870 (mmm) REVERT: D 119 ASN cc_start: 0.8733 (m110) cc_final: 0.8368 (m-40) REVERT: E 199 TYR cc_start: 0.8682 (m-80) cc_final: 0.8344 (m-10) REVERT: G 127 ASP cc_start: 0.7447 (t0) cc_final: 0.7172 (t0) REVERT: H 119 ASN cc_start: 0.8989 (m110) cc_final: 0.8764 (m-40) REVERT: H 136 ILE cc_start: 0.8820 (mm) cc_final: 0.8598 (tt) REVERT: F 137 VAL cc_start: 0.8647 (t) cc_final: 0.8257 (p) REVERT: F 226 ASP cc_start: 0.7496 (t0) cc_final: 0.7272 (t0) outliers start: 32 outliers final: 26 residues processed: 241 average time/residue: 0.2698 time to fit residues: 94.6838 Evaluate side-chains 241 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU 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 218 ASN Chi-restraints excluded: chain E residue 221 THR 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 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 255 ASP Chi-restraints excluded: chain F residue 258 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 132 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 159 optimal weight: 0.0040 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 134 optimal weight: 0.0980 chunk 67 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.165100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108830 restraints weight = 19293.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110994 restraints weight = 15123.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111566 restraints weight = 12247.737| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13774 Z= 0.189 Angle : 0.724 14.316 18606 Z= 0.373 Chirality : 0.048 0.234 1912 Planarity : 0.004 0.050 2506 Dihedral : 4.601 59.754 1786 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.35 % Allowed : 27.42 % Favored : 70.22 % 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: 0.17 (0.21), residues: 1646 helix: 1.46 (0.24), residues: 486 sheet: 0.73 (0.28), residues: 350 loop : -1.02 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 126 HIS 0.010 0.001 HIS G 75 PHE 0.046 0.002 PHE A 293 TYR 0.050 0.002 TYR C 138 ARG 0.010 0.000 ARG E 350 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 641) hydrogen bonds : angle 4.46753 ( 1920) SS BOND : bond 0.00134 ( 4) SS BOND : angle 1.75114 ( 8) covalent geometry : bond 0.00443 (13770) covalent geometry : angle 0.72331 (18598) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5067.90 seconds wall clock time: 92 minutes 59.70 seconds (5579.70 seconds total)