Starting phenix.real_space_refine on Sat Aug 23 16:22:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp7_36470/08_2025/8jp7_36470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp7_36470/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jp7_36470/08_2025/8jp7_36470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp7_36470/08_2025/8jp7_36470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jp7_36470/08_2025/8jp7_36470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp7_36470/08_2025/8jp7_36470.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.38, per 1000 atoms: 0.25 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: 0.98 Conformation dependent library (CDL) restraints added in 674.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.51 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: 2.00 Time building geometry restraints manager: 1.39 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 703)) selection = chain 'D' selection = (chain 'G' and (resid 41 through 101 or resid 108 through 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.030 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.910 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG E 192 TYR 0.017 0.002 TYR C 76 PHE 0.027 0.002 PHE A 262 TRP 0.014 0.002 TRP E 67 HIS 0.029 0.002 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00537 (13770) covalent geometry : angle 0.63924 (18598) SS BOND : bond 0.00183 ( 4) SS BOND : angle 2.30705 ( 8) hydrogen bonds : bond 0.16722 ( 641) hydrogen bonds : angle 6.88286 ( 1920) *********************** 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 : 0.428 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 121 ASP cc_start: 0.8854 (t0) cc_final: 0.8640 (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: 0.7922 (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: 0.7031 (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: 0.9206 (p) REVERT: E 105 GLU cc_start: 0.8207 (tt0) cc_final: 0.8003 (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: 0.7856 (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: 0.7918 (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: 0.7935 (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: 0.7249 (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: 0.1405 time to fit residues: 66.9136 Evaluate side-chains 246 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 242 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 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 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 HIS ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 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 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 F 359 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.166910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107087 restraints weight = 19942.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.111486 restraints weight = 14331.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111979 restraints weight = 11216.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112458 restraints weight = 9979.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.112750 restraints weight = 9970.731| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13774 Z= 0.143 Angle : 0.593 8.702 18606 Z= 0.311 Chirality : 0.046 0.247 1912 Planarity : 0.004 0.037 2506 Dihedral : 4.961 56.291 1793 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.32 % Allowed : 21.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.21), residues: 1646 helix: 1.17 (0.24), residues: 492 sheet: 1.58 (0.29), residues: 326 loop : -1.10 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 126 TYR 0.022 0.001 TYR C 138 PHE 0.018 0.001 PHE B 52 TRP 0.010 0.001 TRP E 126 HIS 0.009 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00311 (13770) covalent geometry : angle 0.59184 (18598) SS BOND : bond 0.00209 ( 4) SS BOND : angle 1.55800 ( 8) hydrogen bonds : bond 0.04285 ( 641) hydrogen bonds : angle 4.58607 ( 1920) *********************** 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 325 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 277 time to evaluate : 0.565 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 176 TYR cc_start: 0.7862 (t80) cc_final: 0.7567 (t80) REVERT: A 350 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7773 (ptp90) REVERT: B 58 VAL cc_start: 0.8362 (t) cc_final: 0.8083 (p) REVERT: B 230 CYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7602 (t) REVERT: B 289 TYR cc_start: 0.9043 (m-80) cc_final: 0.8739 (m-80) REVERT: B 351 GLN cc_start: 0.8512 (tp40) cc_final: 0.8078 (tt0) REVERT: C 67 MET cc_start: 0.8213 (mmp) cc_final: 0.7984 (mmt) REVERT: C 140 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6840 (mt-10) REVERT: D 119 ASN cc_start: 0.9144 (m110) cc_final: 0.8881 (m-40) REVERT: E 93 VAL cc_start: 0.9309 (t) cc_final: 0.9036 (p) REVERT: E 199 TYR cc_start: 0.8571 (m-80) cc_final: 0.8268 (m-10) REVERT: E 289 TYR cc_start: 0.8661 (m-10) cc_final: 0.8456 (m-10) REVERT: E 350 ARG cc_start: 0.7937 (tmm-80) cc_final: 0.7422 (tmm-80) REVERT: G 99 HIS cc_start: 0.8070 (OUTLIER) cc_final: 0.7781 (t70) REVERT: H 73 GLN cc_start: 0.7897 (mt0) cc_final: 0.7639 (mm110) REVERT: H 77 PHE cc_start: 0.7928 (t80) cc_final: 0.7591 (t80) REVERT: H 119 ASN cc_start: 0.9379 (m110) cc_final: 0.9048 (m-40) REVERT: F 137 VAL cc_start: 0.8457 (t) cc_final: 0.8007 (p) outliers start: 48 outliers final: 18 residues processed: 313 average time/residue: 0.1263 time to fit residues: 57.0617 Evaluate side-chains 246 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 C residue 55 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 95 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain 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 68 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 347 GLN A 351 GLN B 59 GLN B 243 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS E 79 GLN E 131 GLN ** E 338 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 70 GLN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.160017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.103037 restraints weight = 19848.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103555 restraints weight = 15224.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103766 restraints weight = 13079.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104071 restraints weight = 12232.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104210 restraints weight = 12021.351| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 13774 Z= 0.280 Angle : 0.683 12.460 18606 Z= 0.355 Chirality : 0.049 0.185 1912 Planarity : 0.004 0.041 2506 Dihedral : 4.868 58.474 1788 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.43 % Allowed : 22.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.21), residues: 1646 helix: 1.35 (0.24), residues: 492 sheet: 0.94 (0.27), residues: 350 loop : -1.10 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 126 TYR 0.027 0.002 TYR C 138 PHE 0.035 0.003 PHE A 296 TRP 0.010 0.002 TRP E 67 HIS 0.023 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00660 (13770) covalent geometry : angle 0.68262 (18598) SS BOND : bond 0.00199 ( 4) SS BOND : angle 1.72261 ( 8) hydrogen bonds : bond 0.04584 ( 641) hydrogen bonds : angle 4.62569 ( 1920) *********************** 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 284 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 220 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8532 (tt) REVERT: B 50 TYR cc_start: 0.8778 (m-80) cc_final: 0.8550 (m-80) REVERT: B 289 TYR cc_start: 0.9084 (m-80) cc_final: 0.8674 (m-80) REVERT: B 351 GLN cc_start: 0.8575 (tp40) cc_final: 0.8141 (tt0) REVERT: B 358 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8316 (mm-30) REVERT: D 119 ASN cc_start: 0.9171 (m110) cc_final: 0.8919 (m-40) REVERT: D 124 VAL cc_start: 0.9124 (t) cc_final: 0.8710 (p) REVERT: D 128 ASP cc_start: 0.7931 (t70) cc_final: 0.7348 (m-30) REVERT: E 199 TYR cc_start: 0.8752 (m-80) cc_final: 0.8319 (m-10) REVERT: E 350 ARG cc_start: 0.8061 (tmm-80) cc_final: 0.7480 (tmm-80) REVERT: G 49 GLN cc_start: 0.9160 (tp-100) cc_final: 0.8737 (tp-100) REVERT: G 53 MET cc_start: 0.7662 (mmt) cc_final: 0.7390 (mmt) REVERT: G 73 GLN cc_start: 0.8613 (tt0) cc_final: 0.7874 (mm110) REVERT: G 99 HIS cc_start: 0.8184 (OUTLIER) cc_final: 0.7951 (t70) REVERT: H 119 ASN cc_start: 0.9332 (m110) cc_final: 0.9019 (m-40) REVERT: F 56 HIS cc_start: 0.7837 (m-70) cc_final: 0.7608 (m170) REVERT: F 137 VAL cc_start: 0.8774 (t) cc_final: 0.8329 (p) outliers start: 64 outliers final: 38 residues processed: 266 average time/residue: 0.1052 time to fit residues: 41.0210 Evaluate side-chains 242 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 345 ILE 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 255 ASP Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain C residue 55 HIS 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 75 HIS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 147 VAL 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 G residue 122 ASP Chi-restraints excluded: chain H residue 48 ASP 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 131 GLN Chi-restraints excluded: chain F residue 218 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 55 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 C 80 HIS D 49 GLN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 75 HIS E 79 GLN E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN ** H 73 GLN ** 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 = 0.4083 r_free = 0.4083 target = 0.164240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.108553 restraints weight = 19956.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.108486 restraints weight = 15045.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.108727 restraints weight = 12459.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.109388 restraints weight = 12648.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109364 restraints weight = 11875.099| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13774 Z= 0.131 Angle : 0.614 11.825 18606 Z= 0.314 Chirality : 0.046 0.229 1912 Planarity : 0.003 0.046 2506 Dihedral : 4.632 59.448 1788 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.46 % Allowed : 23.82 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.21), residues: 1646 helix: 1.46 (0.24), residues: 484 sheet: 0.94 (0.28), residues: 350 loop : -0.99 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 126 TYR 0.021 0.001 TYR D 138 PHE 0.033 0.001 PHE A 296 TRP 0.012 0.001 TRP E 126 HIS 0.020 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00297 (13770) covalent geometry : angle 0.61265 (18598) SS BOND : bond 0.00687 ( 4) SS BOND : angle 1.72318 ( 8) hydrogen bonds : bond 0.03793 ( 641) hydrogen bonds : angle 4.30603 ( 1920) *********************** 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 279 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.552 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: A 79 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8205 (pt0) REVERT: B 289 TYR cc_start: 0.9194 (m-80) cc_final: 0.8797 (m-80) REVERT: B 293 PHE cc_start: 0.8315 (t80) cc_final: 0.8025 (t80) REVERT: B 351 GLN cc_start: 0.8529 (tp40) cc_final: 0.8083 (tt0) REVERT: B 358 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8316 (mm-30) REVERT: D 75 HIS cc_start: 0.8001 (OUTLIER) cc_final: 0.7791 (t70) REVERT: D 119 ASN cc_start: 0.9217 (m110) cc_final: 0.8922 (m-40) REVERT: D 124 VAL cc_start: 0.9119 (t) cc_final: 0.8794 (p) REVERT: E 79 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8265 (pt0) REVERT: E 93 VAL cc_start: 0.9297 (t) cc_final: 0.9009 (p) REVERT: E 199 TYR cc_start: 0.8726 (m-80) cc_final: 0.8265 (m-10) REVERT: E 289 TYR cc_start: 0.8729 (m-10) cc_final: 0.8460 (m-10) REVERT: E 350 ARG cc_start: 0.7960 (tmm-80) cc_final: 0.7418 (tmm-80) REVERT: G 73 GLN cc_start: 0.8484 (tt0) cc_final: 0.7761 (mm110) REVERT: G 99 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7889 (t70) REVERT: H 119 ASN cc_start: 0.9354 (m110) cc_final: 0.9021 (m-40) REVERT: F 137 VAL cc_start: 0.8606 (t) cc_final: 0.8221 (p) outliers start: 50 outliers final: 20 residues processed: 270 average time/residue: 0.1052 time to fit residues: 41.6759 Evaluate side-chains 232 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 B residue 92 SER Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 345 ILE 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 75 HIS Chi-restraints excluded: chain D residue 94 SER 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 60 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 299 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 33 optimal weight: 0.6980 chunk 160 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 122 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 137 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 GLN C 80 HIS D 49 GLN D 55 HIS ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN E 342 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.173593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117531 restraints weight = 19738.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120082 restraints weight = 13271.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122409 restraints weight = 10651.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122412 restraints weight = 9278.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122566 restraints weight = 9283.468| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13774 Z= 0.133 Angle : 0.632 12.912 18606 Z= 0.322 Chirality : 0.047 0.282 1912 Planarity : 0.003 0.047 2506 Dihedral : 4.617 58.236 1788 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.81 % Allowed : 24.24 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.21), residues: 1646 helix: 1.55 (0.24), residues: 478 sheet: 1.14 (0.29), residues: 326 loop : -1.07 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 126 TYR 0.021 0.001 TYR F 50 PHE 0.022 0.001 PHE E 296 TRP 0.011 0.001 TRP F 126 HIS 0.019 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00303 (13770) covalent geometry : angle 0.63158 (18598) SS BOND : bond 0.00229 ( 4) SS BOND : angle 1.41436 ( 8) hydrogen bonds : bond 0.03673 ( 641) hydrogen bonds : angle 4.23168 ( 1920) *********************** 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 281 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 0.544 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: 0.8646 (OUTLIER) cc_final: 0.8375 (pt0) REVERT: B 351 GLN cc_start: 0.8395 (tp40) cc_final: 0.8143 (tt0) REVERT: C 70 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8055 (mm-40) REVERT: D 119 ASN cc_start: 0.9002 (m110) cc_final: 0.8699 (m-40) REVERT: E 93 VAL cc_start: 0.9290 (t) cc_final: 0.9021 (p) REVERT: E 199 TYR cc_start: 0.8665 (m-80) cc_final: 0.8226 (m-10) REVERT: E 289 TYR cc_start: 0.8529 (m-10) cc_final: 0.8310 (m-10) REVERT: G 41 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7548 (mp) REVERT: H 67 MET cc_start: 0.4882 (mmt) cc_final: 0.4574 (mmm) REVERT: H 119 ASN cc_start: 0.9185 (m110) cc_final: 0.8890 (m-40) REVERT: F 56 HIS cc_start: 0.7475 (m-70) cc_final: 0.7272 (m170) REVERT: F 137 VAL cc_start: 0.8568 (t) cc_final: 0.8187 (p) REVERT: F 226 ASP cc_start: 0.7358 (t0) cc_final: 0.7155 (t0) outliers start: 55 outliers final: 29 residues processed: 266 average time/residue: 0.1024 time to fit residues: 40.3081 Evaluate side-chains 248 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 B residue 92 SER Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 345 ILE 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 55 HIS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain 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 97 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 289 TYR Chi-restraints excluded: chain F residue 299 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 152 optimal weight: 0.0030 chunk 123 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- 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 A 351 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS G 75 HIS ** H 47 HIS ** 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** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.170236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113886 restraints weight = 19903.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.114869 restraints weight = 15007.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115975 restraints weight = 12201.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116411 restraints weight = 11140.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116604 restraints weight = 10861.202| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13774 Z= 0.255 Angle : 0.696 14.335 18606 Z= 0.359 Chirality : 0.048 0.177 1912 Planarity : 0.004 0.049 2506 Dihedral : 4.858 58.435 1788 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.22 % Allowed : 24.38 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.21), residues: 1646 helix: 1.25 (0.24), residues: 492 sheet: 0.60 (0.27), residues: 362 loop : -1.01 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 126 TYR 0.020 0.002 TYR A 207 PHE 0.026 0.002 PHE A 262 TRP 0.010 0.001 TRP F 126 HIS 0.010 0.001 HIS D 55 Details of bonding type rmsd covalent geometry : bond 0.00603 (13770) covalent geometry : angle 0.69477 (18598) SS BOND : bond 0.00228 ( 4) SS BOND : angle 2.34713 ( 8) hydrogen bonds : bond 0.04202 ( 641) hydrogen bonds : angle 4.52678 ( 1920) *********************** 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 288 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 227 time to evaluate : 0.480 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: 0.8715 (OUTLIER) cc_final: 0.8324 (pt0) REVERT: B 230 CYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7819 (t) REVERT: B 289 TYR cc_start: 0.9309 (m-80) cc_final: 0.8901 (m-80) REVERT: B 351 GLN cc_start: 0.8367 (tp40) cc_final: 0.8031 (tt0) REVERT: C 74 LEU cc_start: 0.8581 (mm) cc_final: 0.8246 (mm) REVERT: C 92 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7785 (mp0) REVERT: D 75 HIS cc_start: 0.8090 (OUTLIER) cc_final: 0.7761 (t70) REVERT: D 119 ASN cc_start: 0.9188 (m110) cc_final: 0.8853 (m-40) REVERT: E 199 TYR cc_start: 0.8685 (m-80) cc_final: 0.8274 (m-10) REVERT: E 295 HIS cc_start: 0.8645 (m90) cc_final: 0.8402 (m90) REVERT: E 347 GLN cc_start: 0.7688 (tp-100) cc_final: 0.7052 (tm-30) REVERT: G 41 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7720 (mp) REVERT: G 73 GLN cc_start: 0.8507 (tt0) cc_final: 0.7662 (mm110) REVERT: H 119 ASN cc_start: 0.9323 (m110) cc_final: 0.8999 (m-40) REVERT: F 56 HIS cc_start: 0.7609 (m-70) cc_final: 0.7355 (m170) REVERT: F 137 VAL cc_start: 0.8777 (t) cc_final: 0.8371 (p) REVERT: F 226 ASP cc_start: 0.7711 (t0) cc_final: 0.7483 (t0) outliers start: 61 outliers final: 39 residues processed: 272 average time/residue: 0.1176 time to fit residues: 46.9376 Evaluate side-chains 256 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 303 LYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 LEU 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 255 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 356 LEU 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 55 HIS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 75 HIS 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 339 ASN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain 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 147 VAL Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 255 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 2 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS A 338 GLN B 349 ASN C 49 GLN C 73 GLN C 80 HIS D 55 HIS D 70 GLN D 75 HIS E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 HIS E 342 HIS ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS H 47 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.166650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111930 restraints weight = 19263.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113212 restraints weight = 14830.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113433 restraints weight = 12265.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113586 restraints weight = 11733.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113754 restraints weight = 11469.103| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3965 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= 0.133 Angle : 0.645 14.469 18606 Z= 0.331 Chirality : 0.046 0.175 1912 Planarity : 0.003 0.049 2506 Dihedral : 4.653 54.567 1788 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.98 % Allowed : 25.42 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.21), residues: 1646 helix: 1.49 (0.24), residues: 476 sheet: 0.77 (0.28), residues: 350 loop : -1.06 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 126 TYR 0.029 0.002 TYR F 50 PHE 0.038 0.002 PHE E 323 TRP 0.013 0.001 TRP E 126 HIS 0.006 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00303 (13770) covalent geometry : angle 0.64385 (18598) SS BOND : bond 0.00318 ( 4) SS BOND : angle 1.85534 ( 8) hydrogen bonds : bond 0.03534 ( 641) hydrogen bonds : angle 4.29840 ( 1920) *********************** 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 268 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.502 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: B 230 CYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7555 (t) REVERT: B 289 TYR cc_start: 0.9091 (m-80) cc_final: 0.8729 (m-80) REVERT: B 351 GLN cc_start: 0.8440 (tp40) cc_final: 0.8206 (tt0) REVERT: C 74 LEU cc_start: 0.8506 (mm) cc_final: 0.8110 (mm) REVERT: D 119 ASN cc_start: 0.8978 (m110) cc_final: 0.8644 (m-40) REVERT: E 93 VAL cc_start: 0.9257 (t) cc_final: 0.9008 (p) REVERT: E 199 TYR cc_start: 0.8667 (m-80) cc_final: 0.8243 (m-10) REVERT: E 347 GLN cc_start: 0.7619 (tp-100) cc_final: 0.7164 (tm-30) REVERT: G 41 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7627 (mp) REVERT: G 137 ASP cc_start: 0.7330 (t0) cc_final: 0.6967 (p0) REVERT: H 119 ASN cc_start: 0.9221 (m110) cc_final: 0.8913 (m-40) REVERT: F 56 HIS cc_start: 0.7473 (m-70) cc_final: 0.7265 (m170) REVERT: F 137 VAL cc_start: 0.8652 (t) cc_final: 0.8262 (p) outliers start: 43 outliers final: 30 residues processed: 252 average time/residue: 0.1179 time to fit residues: 43.8014 Evaluate side-chains 244 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 82 VAL 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 72 LEU 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 68 SER Chi-restraints excluded: chain H residue 94 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 145 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 130 optimal weight: 40.0000 chunk 116 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 120 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 HIS D 75 HIS E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.164648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108707 restraints weight = 19169.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111357 restraints weight = 14758.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111802 restraints weight = 11502.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111739 restraints weight = 11052.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111861 restraints weight = 11237.603| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13774 Z= 0.173 Angle : 0.682 16.063 18606 Z= 0.350 Chirality : 0.047 0.173 1912 Planarity : 0.004 0.049 2506 Dihedral : 4.755 58.052 1788 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.32 % Allowed : 25.55 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.21), residues: 1646 helix: 1.39 (0.24), residues: 482 sheet: 0.73 (0.28), residues: 350 loop : -0.99 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 350 TYR 0.028 0.002 TYR F 50 PHE 0.031 0.002 PHE E 296 TRP 0.011 0.001 TRP F 126 HIS 0.015 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00403 (13770) covalent geometry : angle 0.68146 (18598) SS BOND : bond 0.00119 ( 4) SS BOND : angle 1.79304 ( 8) hydrogen bonds : bond 0.03863 ( 641) hydrogen bonds : angle 4.40742 ( 1920) *********************** 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 266 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.490 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: 0.8727 (OUTLIER) cc_final: 0.8466 (pt0) REVERT: B 230 CYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7648 (t) REVERT: B 351 GLN cc_start: 0.8481 (tp40) cc_final: 0.8256 (tt0) REVERT: C 74 LEU cc_start: 0.8493 (mm) cc_final: 0.8037 (mm) REVERT: D 49 GLN cc_start: 0.8170 (tp40) cc_final: 0.7667 (tp-100) REVERT: D 52 ILE cc_start: 0.9087 (mp) cc_final: 0.8812 (tt) REVERT: D 53 MET cc_start: 0.8561 (mmm) cc_final: 0.7677 (mmm) REVERT: D 119 ASN cc_start: 0.8897 (m110) cc_final: 0.8571 (m-40) REVERT: E 199 TYR cc_start: 0.8692 (m-80) cc_final: 0.8349 (m-10) REVERT: E 347 GLN cc_start: 0.7685 (tp-100) cc_final: 0.7155 (tm-30) REVERT: G 41 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7708 (mp) REVERT: G 73 GLN cc_start: 0.8301 (tt0) cc_final: 0.7743 (mm110) REVERT: H 119 ASN cc_start: 0.9152 (m110) cc_final: 0.8871 (m-40) REVERT: F 56 HIS cc_start: 0.7496 (m-70) cc_final: 0.7274 (m170) REVERT: F 137 VAL cc_start: 0.8720 (t) cc_final: 0.8317 (p) outliers start: 48 outliers final: 36 residues processed: 251 average time/residue: 0.1160 time to fit residues: 43.0287 Evaluate side-chains 256 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 303 LYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 75 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 75 HIS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 82 VAL 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 55 HIS Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 75 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 94 SER Chi-restraints excluded: chain H residue 118 ILE 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 69 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 148 optimal weight: 0.0060 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN C 73 GLN D 75 HIS E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.163007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107980 restraints weight = 19417.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109165 restraints weight = 15654.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109426 restraints weight = 12643.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109745 restraints weight = 12295.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110014 restraints weight = 11981.205| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13774 Z= 0.230 Angle : 0.715 14.871 18606 Z= 0.370 Chirality : 0.049 0.165 1912 Planarity : 0.004 0.049 2506 Dihedral : 4.952 59.469 1788 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.46 % Allowed : 25.97 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.21), residues: 1646 helix: 1.43 (0.24), residues: 482 sheet: 0.47 (0.27), residues: 362 loop : -1.02 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 350 TYR 0.046 0.002 TYR H 138 PHE 0.027 0.002 PHE E 296 TRP 0.011 0.001 TRP F 126 HIS 0.013 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00543 (13770) covalent geometry : angle 0.71420 (18598) SS BOND : bond 0.00095 ( 4) SS BOND : angle 1.94208 ( 8) hydrogen bonds : bond 0.04115 ( 641) hydrogen bonds : angle 4.56586 ( 1920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 0.553 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: 0.8683 (OUTLIER) cc_final: 0.8435 (pt0) REVERT: B 351 GLN cc_start: 0.8511 (tp40) cc_final: 0.8235 (tt0) REVERT: C 74 LEU cc_start: 0.8507 (mm) cc_final: 0.8051 (mm) REVERT: D 53 MET cc_start: 0.8606 (mmm) cc_final: 0.7835 (mmm) REVERT: D 119 ASN cc_start: 0.8937 (m110) cc_final: 0.8588 (m-40) REVERT: E 199 TYR cc_start: 0.8702 (m-80) cc_final: 0.8361 (m-10) REVERT: G 41 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7715 (mp) REVERT: H 119 ASN cc_start: 0.9170 (m110) cc_final: 0.8886 (m-40) REVERT: H 126 ARG cc_start: 0.8741 (ttm110) cc_final: 0.8340 (ttp-110) REVERT: F 56 HIS cc_start: 0.7552 (m-70) cc_final: 0.7335 (m170) REVERT: F 137 VAL cc_start: 0.8771 (t) cc_final: 0.8389 (p) outliers start: 50 outliers final: 39 residues processed: 254 average time/residue: 0.1194 time to fit residues: 44.7410 Evaluate side-chains 246 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 303 LYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 82 VAL 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 41 LEU Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 72 LEU 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 68 SER 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 355 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 10 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN E 131 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.163425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107285 restraints weight = 19255.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109242 restraints weight = 14744.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109736 restraints weight = 12004.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109869 restraints weight = 11679.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109935 restraints weight = 11501.217| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.194 13774 Z= 0.248 Angle : 0.944 59.198 18606 Z= 0.519 Chirality : 0.049 0.460 1912 Planarity : 0.004 0.049 2506 Dihedral : 4.952 59.376 1788 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.46 % Allowed : 25.83 % Favored : 70.71 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.21), residues: 1646 helix: 1.44 (0.24), residues: 482 sheet: 0.44 (0.27), residues: 362 loop : -1.03 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 350 TYR 0.060 0.002 TYR H 138 PHE 0.043 0.002 PHE B 293 TRP 0.010 0.001 TRP F 126 HIS 0.025 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00598 (13770) covalent geometry : angle 0.92736 (18598) SS BOND : bond 0.02343 ( 4) SS BOND : angle 8.44321 ( 8) hydrogen bonds : bond 0.04089 ( 641) hydrogen bonds : angle 4.59272 ( 1920) ********************** 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 259 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 0.546 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: 0.8728 (OUTLIER) cc_final: 0.8467 (pt0) REVERT: B 351 GLN cc_start: 0.8514 (tp40) cc_final: 0.8236 (tt0) REVERT: C 74 LEU cc_start: 0.8541 (mm) cc_final: 0.8095 (mm) REVERT: D 119 ASN cc_start: 0.8935 (m110) cc_final: 0.8594 (m-40) REVERT: E 199 TYR cc_start: 0.8690 (m-80) cc_final: 0.8354 (m-10) REVERT: G 41 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7713 (mp) REVERT: H 119 ASN cc_start: 0.9149 (m110) cc_final: 0.8872 (m-40) REVERT: F 56 HIS cc_start: 0.7549 (m-70) cc_final: 0.7326 (m170) REVERT: F 137 VAL cc_start: 0.8809 (t) cc_final: 0.8436 (p) outliers start: 50 outliers final: 45 residues processed: 247 average time/residue: 0.1134 time to fit residues: 41.3421 Evaluate side-chains 256 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 213 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 355 ILE 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 C residue 120 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 82 VAL 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 41 LEU Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 72 LEU 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 68 SER 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 355 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 99 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 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** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.163456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108205 restraints weight = 19403.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109284 restraints weight = 15631.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109790 restraints weight = 12822.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109946 restraints weight = 12321.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110187 restraints weight = 11928.972| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.194 13774 Z= 0.248 Angle : 0.944 59.198 18606 Z= 0.519 Chirality : 0.049 0.460 1912 Planarity : 0.004 0.049 2506 Dihedral : 4.952 59.376 1788 Min Nonbonded Distance : 1.570 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.32 % Allowed : 26.11 % Favored : 70.57 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.21), residues: 1646 helix: 1.44 (0.24), residues: 482 sheet: 0.44 (0.27), residues: 362 loop : -1.03 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 350 TYR 0.060 0.002 TYR H 138 PHE 0.043 0.002 PHE B 293 TRP 0.010 0.001 TRP F 126 HIS 0.025 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00598 (13770) covalent geometry : angle 0.92736 (18598) SS BOND : bond 0.02343 ( 4) SS BOND : angle 8.44321 ( 8) hydrogen bonds : bond 0.04089 ( 641) hydrogen bonds : angle 4.59272 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2361.16 seconds wall clock time: 41 minutes 30.03 seconds (2490.03 seconds total)