Starting phenix.real_space_refine on Thu Sep 26 13:43:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp6_36469/09_2024/8jp6_36469.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp6_36469/09_2024/8jp6_36469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp6_36469/09_2024/8jp6_36469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp6_36469/09_2024/8jp6_36469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp6_36469/09_2024/8jp6_36469.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jp6_36469/09_2024/8jp6_36469.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.136 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 36 5.16 5 C 8466 2.51 5 N 2346 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13500 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2619 Classifications: {'peptide': 326} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 309} Chain: "B" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 297} Chain breaks: 1 Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "E" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2619 Classifications: {'peptide': 326} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 309} Chain: "F" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 297} Chain breaks: 1 Chain: "G" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "H" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} 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: "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} 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} Time building chain proxies: 7.01, per 1000 atoms: 0.52 Number of scatterers: 13500 At special positions: 0 Unit cell: (120.516, 118.524, 127.488, 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 36 16.00 O 2632 8.00 N 2346 7.00 C 8466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS E 190 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.5 seconds 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 33.5% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.696A pdb=" N ASP A 181 " --> pdb=" O HIS A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 309 removed outlier: 3.681A pdb=" N LYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.509A pdb=" N ILE A 322 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 338 through 367 Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.628A pdb=" N ASP B 181 " --> pdb=" O HIS B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 311 removed outlier: 3.765A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 365 Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.886A pdb=" N ILE C 52 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 80 removed outlier: 3.582A pdb=" N HIS C 80 " --> pdb=" O TYR C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 Processing helix chain 'C' and resid 113 through 129 Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 48 through 57 removed outlier: 4.129A pdb=" N ILE D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET D 53 " --> pdb=" O GLN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 89 through 98 Processing helix chain 'D' and resid 113 through 129 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'E' and resid 48 through 51 Processing helix chain 'E' and resid 177 through 181 removed outlier: 3.711A pdb=" N ASP E 181 " --> pdb=" O HIS E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 309 removed outlier: 3.682A pdb=" N LYS E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU E 306 " --> pdb=" O LYS E 302 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE E 307 " --> pdb=" O LYS E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 323 removed outlier: 3.510A pdb=" N ILE E 322 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 338 through 367 Processing helix chain 'F' and resid 177 through 181 removed outlier: 3.624A pdb=" N ASP F 181 " --> pdb=" O HIS F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 311 removed outlier: 3.765A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 365 Processing helix chain 'G' and resid 42 through 47 Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.885A pdb=" N ILE G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 80 removed outlier: 3.587A pdb=" N HIS G 80 " --> pdb=" O TYR G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 98 Processing helix chain 'G' and resid 113 through 129 Processing helix chain 'G' and resid 137 through 142 Processing helix chain 'H' and resid 42 through 47 Processing helix chain 'H' and resid 48 through 57 removed outlier: 3.670A pdb=" N ILE H 52 " --> pdb=" O ASP H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 80 Processing helix chain 'H' and resid 89 through 98 Processing helix chain 'H' and resid 113 through 129 Processing helix chain 'H' and resid 137 through 142 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 53 removed outlier: 3.845A pdb=" N HIS A 43 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR A 264 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LYS A 49 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 11.047A pdb=" N PHE A 262 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N SER A 51 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 11.705A pdb=" N LEU A 260 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 12.099A pdb=" N LYS A 53 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 14.929A pdb=" N ASP A 258 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N HIS A 257 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 53 removed outlier: 3.845A pdb=" N HIS A 43 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR A 264 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LYS A 49 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 11.047A pdb=" N PHE A 262 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N SER A 51 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 11.705A pdb=" N LEU A 260 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 12.099A pdb=" N LYS A 53 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 14.929A pdb=" N ASP A 258 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS A 257 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N THR A 113 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL A 259 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG A 111 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE A 216 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 5.125A 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: 5.652A pdb=" N PHE A 244 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 53 removed outlier: 4.622A pdb=" N THR B 264 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N LYS B 49 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 10.936A pdb=" N PHE B 262 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 10.983A pdb=" N SER B 51 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 11.580A pdb=" N LEU B 260 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 11.891A pdb=" N LYS B 53 " --> pdb=" O ASP B 258 " (cutoff:3.500A) removed outlier: 14.388A pdb=" N ASP B 258 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N HIS B 257 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 53 removed outlier: 4.622A pdb=" N THR B 264 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N LYS B 49 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 10.936A pdb=" N PHE B 262 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 10.983A pdb=" N SER B 51 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 11.580A pdb=" N LEU B 260 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 11.891A pdb=" N LYS B 53 " --> pdb=" O ASP B 258 " (cutoff:3.500A) removed outlier: 14.388A pdb=" N ASP B 258 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N HIS B 257 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR B 113 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL B 259 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ARG B 111 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE B 216 " --> pdb=" O PHE B 229 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N PHE B 229 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.747A pdb=" N PHE B 244 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 43 through 46 removed outlier: 3.845A pdb=" N HIS E 43 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N HIS E 257 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 43 through 46 removed outlier: 3.845A pdb=" N HIS E 43 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS E 257 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N THR E 113 " --> pdb=" O HIS E 257 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N VAL E 259 " --> pdb=" O ARG E 111 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ARG E 111 " --> pdb=" O VAL E 259 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE E 216 " --> pdb=" O PHE E 229 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE E 229 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.653A pdb=" N PHE E 244 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA E 188 " --> pdb=" O ILE E 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 43 through 53 removed outlier: 4.612A pdb=" N THR F 264 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N LYS F 49 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N PHE F 262 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N SER F 51 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 11.579A pdb=" N LEU F 260 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N LYS F 53 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 14.384A pdb=" N ASP F 258 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N HIS F 257 " --> pdb=" O VAL F 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 43 through 53 removed outlier: 4.612A pdb=" N THR F 264 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N LYS F 49 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N PHE F 262 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N SER F 51 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 11.579A pdb=" N LEU F 260 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N LYS F 53 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 14.384A pdb=" N ASP F 258 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS F 257 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR F 113 " --> pdb=" O HIS F 257 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL F 259 " --> pdb=" O ARG F 111 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG F 111 " --> pdb=" O VAL F 259 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE F 216 " --> pdb=" O PHE F 229 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE F 229 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 71 removed outlier: 5.747A pdb=" N PHE F 244 " --> pdb=" O THR F 95 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1857 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 2.99 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: 4572 1.34 - 1.46: 2472 1.46 - 1.58: 6686 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 13794 Sorted by residual: bond pdb=" CA GLN F 173 " pdb=" CB GLN F 173 " ideal model delta sigma weight residual 1.527 1.570 -0.042 2.48e-02 1.63e+03 2.93e+00 bond pdb=" CA GLN B 173 " pdb=" CB GLN B 173 " ideal model delta sigma weight residual 1.527 1.570 -0.042 2.48e-02 1.63e+03 2.90e+00 bond pdb=" N TYR A 127 " pdb=" CA TYR A 127 " ideal model delta sigma weight residual 1.464 1.444 0.020 1.36e-02 5.41e+03 2.07e+00 bond pdb=" C ASN E 162 " pdb=" N PRO E 163 " ideal model delta sigma weight residual 1.338 1.362 -0.024 1.90e-02 2.77e+03 1.65e+00 bond pdb=" CB GLN A 290 " pdb=" CG GLN A 290 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 ... (remaining 13789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 18366 2.09 - 4.18: 230 4.18 - 6.26: 27 6.26 - 8.35: 5 8.35 - 10.44: 2 Bond angle restraints: 18630 Sorted by residual: angle pdb=" CA GLU F 292 " pdb=" CB GLU F 292 " pdb=" CG GLU F 292 " ideal model delta sigma weight residual 114.10 120.79 -6.69 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CA GLU B 292 " pdb=" CB GLU B 292 " pdb=" CG GLU B 292 " ideal model delta sigma weight residual 114.10 120.73 -6.63 2.00e+00 2.50e-01 1.10e+01 angle pdb=" CA LEU G 72 " pdb=" CB LEU G 72 " pdb=" CG LEU G 72 " ideal model delta sigma weight residual 116.30 126.74 -10.44 3.50e+00 8.16e-02 8.89e+00 angle pdb=" CA LEU C 72 " pdb=" CB LEU C 72 " pdb=" CG LEU C 72 " ideal model delta sigma weight residual 116.30 126.73 -10.43 3.50e+00 8.16e-02 8.88e+00 angle pdb=" C GLY B 132 " pdb=" N LEU B 133 " pdb=" CA LEU B 133 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.53e+00 ... (remaining 18625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7148 17.79 - 35.59: 815 35.59 - 53.38: 200 53.38 - 71.18: 78 71.18 - 88.97: 7 Dihedral angle restraints: 8248 sinusoidal: 3432 harmonic: 4816 Sorted by residual: dihedral pdb=" CA ASN E 162 " pdb=" C ASN E 162 " pdb=" N PRO E 163 " pdb=" CA PRO E 163 " ideal model delta harmonic sigma weight residual 0.00 23.75 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TRP B 126 " pdb=" C TRP B 126 " pdb=" N TYR B 127 " pdb=" CA TYR B 127 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+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 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 8245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1203 0.035 - 0.070: 476 0.070 - 0.104: 158 0.104 - 0.139: 72 0.139 - 0.174: 7 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CA VAL G 100 " pdb=" N VAL G 100 " pdb=" C VAL G 100 " pdb=" CB VAL G 100 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CA VAL C 100 " pdb=" N VAL C 100 " pdb=" C VAL C 100 " pdb=" CB VAL C 100 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA VAL F 93 " pdb=" N VAL F 93 " pdb=" C VAL F 93 " pdb=" CB VAL F 93 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1913 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 162 " -0.017 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C ASN E 162 " 0.057 2.00e-02 2.50e+03 pdb=" O ASN E 162 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO E 163 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 135 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO A 136 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 135 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO E 136 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 136 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 136 " 0.024 5.00e-02 4.00e+02 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 76 2.36 - 2.99: 6501 2.99 - 3.63: 20026 3.63 - 4.26: 31129 4.26 - 4.90: 53204 Nonbonded interactions: 110936 Sorted by model distance: nonbonded pdb=" OD1 ASP B 155 " pdb=" OD1 ASN B 162 " model vdw 1.720 3.040 nonbonded pdb=" OD1 ASP F 155 " pdb=" OD1 ASN F 162 " model vdw 1.723 3.040 nonbonded pdb=" CE1 HIS D 51 " pdb="ZN ZN D 703 " model vdw 1.915 2.450 nonbonded pdb=" CE1 HIS H 51 " pdb="ZN ZN H 703 " model vdw 1.950 2.450 nonbonded pdb=" NE2 HIS H 101 " pdb="ZN ZN H 703 " model vdw 2.004 2.310 ... (remaining 110931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 42 through 312 or resid 324 through 365 or resid 601 throu \ gh 602)) selection = chain 'B' selection = (chain 'E' and (resid 42 through 312 or resid 324 through 365 or resid 601 throu \ gh 602)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.080 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.003 0.042 13794 Z= 0.224 Angle : 0.593 10.438 18630 Z= 0.316 Chirality : 0.046 0.174 1916 Planarity : 0.004 0.044 2510 Dihedral : 16.633 88.970 5140 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.14 % Allowed : 14.38 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1650 helix: 1.65 (0.23), residues: 512 sheet: 1.00 (0.31), residues: 324 loop : -1.41 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 104 HIS 0.008 0.001 HIS G 55 PHE 0.015 0.001 PHE F 52 TYR 0.014 0.001 TYR A 127 ARG 0.004 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 312 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8281 (t0) cc_final: 0.7938 (t0) REVERT: A 226 ASP cc_start: 0.8577 (t70) cc_final: 0.8350 (t70) REVERT: A 354 MET cc_start: 0.8114 (tpp) cc_final: 0.7729 (ttm) REVERT: B 48 TYR cc_start: 0.8787 (p90) cc_final: 0.8574 (p90) REVERT: B 215 MET cc_start: 0.8706 (mtp) cc_final: 0.8317 (mtp) REVERT: B 225 ASN cc_start: 0.7582 (m110) cc_final: 0.7224 (p0) REVERT: B 354 MET cc_start: 0.7829 (ttm) cc_final: 0.7577 (tmm) REVERT: C 73 GLN cc_start: 0.8321 (tt0) cc_final: 0.8009 (pp30) REVERT: D 122 ASP cc_start: 0.8444 (m-30) cc_final: 0.8056 (m-30) REVERT: D 144 SER cc_start: 0.8733 (m) cc_final: 0.8484 (t) REVERT: E 49 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8725 (ttpp) REVERT: E 218 ASN cc_start: 0.8246 (t0) cc_final: 0.7903 (t0) REVERT: E 226 ASP cc_start: 0.8590 (t70) cc_final: 0.8359 (t70) REVERT: E 295 HIS cc_start: 0.8947 (t-90) cc_final: 0.7928 (t-90) REVERT: E 354 MET cc_start: 0.8085 (tpp) cc_final: 0.7700 (ttm) REVERT: F 215 MET cc_start: 0.8647 (mtp) cc_final: 0.8292 (mtp) REVERT: F 225 ASN cc_start: 0.7584 (m110) cc_final: 0.7261 (p0) REVERT: F 354 MET cc_start: 0.7831 (ttm) cc_final: 0.7620 (tmm) REVERT: G 71 GLU cc_start: 0.8631 (tp30) cc_final: 0.8428 (tp30) REVERT: G 73 GLN cc_start: 0.8310 (tt0) cc_final: 0.7965 (pp30) REVERT: H 48 ASP cc_start: 0.7937 (m-30) cc_final: 0.7416 (t0) REVERT: H 122 ASP cc_start: 0.8419 (m-30) cc_final: 0.8133 (m-30) REVERT: H 144 SER cc_start: 0.8782 (m) cc_final: 0.8537 (t) outliers start: 2 outliers final: 2 residues processed: 314 average time/residue: 0.2533 time to fit residues: 114.3818 Evaluate side-chains 220 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 218 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain H residue 101 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 30.0000 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 40.0000 chunk 96 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 185 GLN A 235 ASN A 243 HIS B 333 GLN B 339 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS C 86 ASN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN E 185 GLN E 235 ASN E 243 HIS F 333 GLN F 339 ASN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS G 86 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13794 Z= 0.323 Angle : 0.594 9.355 18630 Z= 0.316 Chirality : 0.046 0.155 1916 Planarity : 0.004 0.038 2510 Dihedral : 5.294 59.798 1792 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.66 % Allowed : 15.91 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1650 helix: 1.88 (0.23), residues: 520 sheet: 0.45 (0.30), residues: 340 loop : -1.32 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 126 HIS 0.007 0.001 HIS B 342 PHE 0.024 0.002 PHE F 307 TYR 0.020 0.002 TYR H 138 ARG 0.004 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 239 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8301 (mt0) REVERT: A 218 ASN cc_start: 0.8317 (t0) cc_final: 0.7995 (t0) REVERT: A 354 MET cc_start: 0.8049 (tpp) cc_final: 0.7766 (ttm) REVERT: B 48 TYR cc_start: 0.8880 (p90) cc_final: 0.8615 (p90) REVERT: B 215 MET cc_start: 0.8721 (mtp) cc_final: 0.8305 (mtp) REVERT: B 223 ASP cc_start: 0.8235 (t0) cc_final: 0.7998 (t0) REVERT: B 225 ASN cc_start: 0.7641 (m110) cc_final: 0.7352 (p0) REVERT: B 354 MET cc_start: 0.8113 (ttm) cc_final: 0.7742 (tmm) REVERT: C 73 GLN cc_start: 0.8483 (tt0) cc_final: 0.8081 (pp30) REVERT: C 126 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7987 (ptp90) REVERT: C 132 ASN cc_start: 0.8787 (t0) cc_final: 0.8533 (t0) REVERT: D 49 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7652 (tm-30) REVERT: D 67 MET cc_start: 0.8169 (mpp) cc_final: 0.7750 (mpp) REVERT: D 75 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.8259 (t70) REVERT: D 101 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7796 (t-90) REVERT: D 131 ASN cc_start: 0.7833 (p0) cc_final: 0.7547 (t0) REVERT: E 185 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8283 (mt0) REVERT: E 218 ASN cc_start: 0.8310 (t0) cc_final: 0.7986 (t0) REVERT: E 295 HIS cc_start: 0.8802 (t-90) cc_final: 0.8367 (t-90) REVERT: E 354 MET cc_start: 0.8043 (tpp) cc_final: 0.7754 (ttm) REVERT: F 215 MET cc_start: 0.8671 (mtp) cc_final: 0.8252 (mtp) REVERT: F 223 ASP cc_start: 0.8191 (t0) cc_final: 0.7982 (t0) REVERT: F 225 ASN cc_start: 0.7630 (m110) cc_final: 0.7367 (p0) REVERT: G 73 GLN cc_start: 0.8442 (tt0) cc_final: 0.8042 (pp30) REVERT: G 126 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7884 (ptp90) REVERT: H 75 HIS cc_start: 0.8836 (OUTLIER) cc_final: 0.8267 (t-90) REVERT: H 101 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7791 (t-90) REVERT: H 131 ASN cc_start: 0.7827 (p0) cc_final: 0.7507 (t0) outliers start: 24 outliers final: 13 residues processed: 255 average time/residue: 0.2415 time to fit residues: 92.5003 Evaluate side-chains 222 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 203 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 101 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 102 optimal weight: 0.0050 chunk 41 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 51 optimal weight: 0.0670 chunk 121 optimal weight: 3.9990 overall best weight: 0.9936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 185 GLN A 297 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 290 GLN C 49 GLN C 75 HIS ** D 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS E 185 GLN E 297 GLN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 HIS F 290 GLN G 49 GLN G 75 HIS ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13794 Z= 0.177 Angle : 0.547 8.558 18630 Z= 0.290 Chirality : 0.043 0.152 1916 Planarity : 0.003 0.036 2510 Dihedral : 5.004 56.764 1792 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.97 % Allowed : 16.67 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1650 helix: 1.96 (0.23), residues: 520 sheet: 0.80 (0.31), residues: 322 loop : -1.32 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 126 HIS 0.003 0.001 HIS F 342 PHE 0.011 0.001 PHE E 52 TYR 0.021 0.001 TYR G 138 ARG 0.004 0.000 ARG E 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 249 time to evaluate : 1.594 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 185 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8202 (mt0) REVERT: A 218 ASN cc_start: 0.8223 (t0) cc_final: 0.7894 (t0) REVERT: A 354 MET cc_start: 0.8067 (tpp) cc_final: 0.7745 (ttm) REVERT: B 48 TYR cc_start: 0.8848 (p90) cc_final: 0.8640 (p90) REVERT: B 215 MET cc_start: 0.8703 (mtp) cc_final: 0.8302 (mtp) REVERT: B 225 ASN cc_start: 0.7635 (m110) cc_final: 0.7364 (p0) REVERT: B 354 MET cc_start: 0.8101 (ttm) cc_final: 0.7799 (tmm) REVERT: C 73 GLN cc_start: 0.8429 (tt0) cc_final: 0.8025 (pp30) REVERT: C 116 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: C 132 ASN cc_start: 0.8746 (t0) cc_final: 0.8491 (t0) REVERT: D 48 ASP cc_start: 0.7775 (t0) cc_final: 0.7524 (t0) REVERT: D 53 MET cc_start: 0.8676 (mmm) cc_final: 0.8403 (mmm) REVERT: D 75 HIS cc_start: 0.8708 (OUTLIER) cc_final: 0.8386 (t70) REVERT: D 101 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7941 (t-90) REVERT: D 122 ASP cc_start: 0.8633 (m-30) cc_final: 0.7956 (m-30) REVERT: D 131 ASN cc_start: 0.7878 (p0) cc_final: 0.7440 (t0) REVERT: E 185 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8202 (mt0) REVERT: E 218 ASN cc_start: 0.8188 (t0) cc_final: 0.7871 (t0) REVERT: E 295 HIS cc_start: 0.8767 (t-90) cc_final: 0.8506 (t-90) REVERT: E 354 MET cc_start: 0.8099 (tpp) cc_final: 0.7792 (ttm) REVERT: F 215 MET cc_start: 0.8649 (mtp) cc_final: 0.8272 (mtp) REVERT: G 73 GLN cc_start: 0.8442 (tt0) cc_final: 0.8006 (pp30) REVERT: G 116 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: H 48 ASP cc_start: 0.7976 (m-30) cc_final: 0.7369 (t0) REVERT: H 56 LEU cc_start: 0.9407 (tp) cc_final: 0.9174 (tt) REVERT: H 75 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.8487 (t70) REVERT: H 131 ASN cc_start: 0.7817 (p0) cc_final: 0.7357 (t0) outliers start: 43 outliers final: 18 residues processed: 280 average time/residue: 0.2471 time to fit residues: 100.5834 Evaluate side-chains 222 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 79 optimal weight: 30.0000 chunk 143 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN C 75 HIS C 86 ASN D 70 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN E 298 GLN F 79 GLN F 290 GLN F 349 ASN G 75 HIS H 70 GLN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13794 Z= 0.420 Angle : 0.638 8.188 18630 Z= 0.341 Chirality : 0.047 0.174 1916 Planarity : 0.004 0.044 2510 Dihedral : 5.069 53.694 1790 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.32 % Allowed : 17.63 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1650 helix: 1.79 (0.23), residues: 516 sheet: 0.24 (0.30), residues: 330 loop : -1.41 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 126 HIS 0.008 0.001 HIS F 342 PHE 0.024 0.002 PHE B 52 TYR 0.026 0.002 TYR G 138 ARG 0.005 0.000 ARG E 350 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 212 time to evaluate : 1.503 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 185 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8207 (mt0) REVERT: A 218 ASN cc_start: 0.8445 (t0) cc_final: 0.8117 (t0) REVERT: A 342 HIS cc_start: 0.8217 (m90) cc_final: 0.7991 (m-70) REVERT: A 352 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7808 (tt) REVERT: A 354 MET cc_start: 0.8050 (tpp) cc_final: 0.7678 (ttm) REVERT: B 48 TYR cc_start: 0.8895 (p90) cc_final: 0.8657 (p90) REVERT: B 354 MET cc_start: 0.8119 (ttm) cc_final: 0.7821 (tmm) REVERT: C 73 GLN cc_start: 0.8440 (tt0) cc_final: 0.8046 (pp30) REVERT: C 132 ASN cc_start: 0.8836 (t0) cc_final: 0.8590 (t0) REVERT: D 53 MET cc_start: 0.8675 (mmm) cc_final: 0.8428 (mmm) REVERT: D 75 HIS cc_start: 0.8797 (OUTLIER) cc_final: 0.8292 (t70) REVERT: E 185 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8196 (mt0) REVERT: E 218 ASN cc_start: 0.8423 (t0) cc_final: 0.8080 (t0) REVERT: E 226 ASP cc_start: 0.8724 (t70) cc_final: 0.8517 (t70) REVERT: E 342 HIS cc_start: 0.8155 (m90) cc_final: 0.7929 (m-70) REVERT: E 352 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7754 (tt) REVERT: E 354 MET cc_start: 0.8145 (tpp) cc_final: 0.7825 (ttm) REVERT: G 132 ASN cc_start: 0.8834 (t0) cc_final: 0.8263 (t0) REVERT: H 75 HIS cc_start: 0.8835 (OUTLIER) cc_final: 0.8593 (t70) outliers start: 48 outliers final: 22 residues processed: 249 average time/residue: 0.2357 time to fit residues: 87.5777 Evaluate side-chains 225 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 298 GLN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 144 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 298 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS E 185 GLN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13794 Z= 0.224 Angle : 0.589 10.249 18630 Z= 0.309 Chirality : 0.044 0.144 1916 Planarity : 0.004 0.043 2510 Dihedral : 4.591 24.191 1788 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.84 % Allowed : 18.46 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1650 helix: 1.76 (0.23), residues: 516 sheet: 0.46 (0.30), residues: 326 loop : -1.38 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 126 HIS 0.009 0.001 HIS D 80 PHE 0.014 0.001 PHE H 141 TYR 0.022 0.001 TYR C 138 ARG 0.004 0.000 ARG E 350 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 226 time to evaluate : 1.371 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 185 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: A 218 ASN cc_start: 0.8311 (t0) cc_final: 0.7993 (t0) REVERT: A 352 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7756 (tt) REVERT: A 354 MET cc_start: 0.8173 (tpp) cc_final: 0.7705 (ttm) REVERT: B 215 MET cc_start: 0.8722 (mtp) cc_final: 0.8306 (mtp) REVERT: B 226 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8141 (m-30) REVERT: B 354 MET cc_start: 0.8090 (ttm) cc_final: 0.7791 (tmm) REVERT: C 67 MET cc_start: 0.6890 (ptp) cc_final: 0.6608 (ptp) REVERT: C 73 GLN cc_start: 0.8368 (tt0) cc_final: 0.8024 (pp30) REVERT: C 132 ASN cc_start: 0.8772 (t0) cc_final: 0.8513 (t0) REVERT: D 75 HIS cc_start: 0.8819 (OUTLIER) cc_final: 0.8363 (t70) REVERT: E 185 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8288 (mt0) REVERT: E 218 ASN cc_start: 0.8279 (t0) cc_final: 0.7972 (t0) REVERT: E 226 ASP cc_start: 0.8637 (t70) cc_final: 0.8420 (t70) REVERT: E 352 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7690 (tt) REVERT: E 354 MET cc_start: 0.8189 (tpp) cc_final: 0.7815 (ttm) REVERT: F 215 MET cc_start: 0.8660 (mtp) cc_final: 0.8262 (mtp) REVERT: G 132 ASN cc_start: 0.8797 (t0) cc_final: 0.8231 (t0) REVERT: H 41 LEU cc_start: 0.7198 (tp) cc_final: 0.6899 (mm) REVERT: H 75 HIS cc_start: 0.8747 (OUTLIER) cc_final: 0.8497 (t70) outliers start: 41 outliers final: 23 residues processed: 256 average time/residue: 0.2177 time to fit residues: 83.6021 Evaluate side-chains 228 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 198 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 298 GLN B 173 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13794 Z= 0.306 Angle : 0.618 9.426 18630 Z= 0.328 Chirality : 0.045 0.149 1916 Planarity : 0.004 0.040 2510 Dihedral : 4.680 24.711 1788 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.67 % Allowed : 18.74 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1650 helix: 1.66 (0.23), residues: 516 sheet: 0.29 (0.30), residues: 330 loop : -1.38 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 126 HIS 0.009 0.001 HIS D 80 PHE 0.018 0.002 PHE B 52 TYR 0.026 0.002 TYR G 138 ARG 0.005 0.000 ARG F 350 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 219 time to evaluate : 1.627 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: A 218 ASN cc_start: 0.8420 (t0) cc_final: 0.8086 (t0) REVERT: A 342 HIS cc_start: 0.8171 (m90) cc_final: 0.7937 (m-70) REVERT: A 352 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7770 (tt) REVERT: A 354 MET cc_start: 0.8196 (tpp) cc_final: 0.7716 (ttm) REVERT: B 223 ASP cc_start: 0.8167 (t0) cc_final: 0.7624 (t0) REVERT: B 226 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: B 354 MET cc_start: 0.8074 (ttm) cc_final: 0.7804 (tmm) REVERT: C 73 GLN cc_start: 0.8370 (tt0) cc_final: 0.8033 (pp30) REVERT: C 132 ASN cc_start: 0.8775 (t0) cc_final: 0.8525 (t0) REVERT: D 75 HIS cc_start: 0.8847 (OUTLIER) cc_final: 0.8383 (t70) REVERT: E 218 ASN cc_start: 0.8392 (t0) cc_final: 0.8058 (t0) REVERT: E 226 ASP cc_start: 0.8680 (t70) cc_final: 0.8457 (t70) REVERT: E 342 HIS cc_start: 0.8121 (m90) cc_final: 0.7879 (m-70) REVERT: E 352 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7709 (tt) REVERT: E 354 MET cc_start: 0.8200 (tpp) cc_final: 0.7805 (ttm) REVERT: F 226 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: G 132 ASN cc_start: 0.8783 (t0) cc_final: 0.8208 (t0) REVERT: H 75 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8438 (t70) outliers start: 53 outliers final: 29 residues processed: 257 average time/residue: 0.2248 time to fit residues: 86.6582 Evaluate side-chains 236 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 201 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 40.0000 chunk 98 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13794 Z= 0.196 Angle : 0.597 9.572 18630 Z= 0.315 Chirality : 0.044 0.142 1916 Planarity : 0.003 0.038 2510 Dihedral : 4.450 23.659 1788 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.84 % Allowed : 19.57 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1650 helix: 1.60 (0.23), residues: 514 sheet: 0.56 (0.30), residues: 326 loop : -1.31 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 126 HIS 0.013 0.001 HIS H 80 PHE 0.015 0.001 PHE D 141 TYR 0.024 0.002 TYR G 138 ARG 0.004 0.000 ARG E 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 207 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8354 (t0) cc_final: 0.8015 (t0) REVERT: A 352 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7713 (tt) REVERT: A 354 MET cc_start: 0.8215 (tpp) cc_final: 0.7709 (ttm) REVERT: B 223 ASP cc_start: 0.8103 (t0) cc_final: 0.7547 (t0) REVERT: B 226 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8003 (m-30) REVERT: B 354 MET cc_start: 0.8053 (ttm) cc_final: 0.7797 (tmm) REVERT: C 73 GLN cc_start: 0.8328 (tt0) cc_final: 0.7990 (pp30) REVERT: C 132 ASN cc_start: 0.8750 (t0) cc_final: 0.8488 (t0) REVERT: E 218 ASN cc_start: 0.8328 (t0) cc_final: 0.7989 (t0) REVERT: E 226 ASP cc_start: 0.8532 (t70) cc_final: 0.8288 (t70) REVERT: E 352 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7664 (tt) REVERT: E 354 MET cc_start: 0.8296 (tpp) cc_final: 0.7784 (ttm) REVERT: F 223 ASP cc_start: 0.8104 (t0) cc_final: 0.7518 (t0) REVERT: F 226 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: G 71 GLU cc_start: 0.8899 (tp30) cc_final: 0.8464 (tp30) REVERT: H 75 HIS cc_start: 0.8801 (OUTLIER) cc_final: 0.8364 (t-90) outliers start: 41 outliers final: 26 residues processed: 241 average time/residue: 0.2462 time to fit residues: 88.3260 Evaluate side-chains 234 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 203 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 20.0000 chunk 95 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 125 optimal weight: 0.3980 chunk 145 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13794 Z= 0.201 Angle : 0.602 9.736 18630 Z= 0.321 Chirality : 0.044 0.163 1916 Planarity : 0.003 0.037 2510 Dihedral : 4.396 23.494 1788 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.77 % Allowed : 19.64 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1650 helix: 1.59 (0.23), residues: 514 sheet: 0.64 (0.30), residues: 324 loop : -1.29 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 126 HIS 0.004 0.001 HIS D 80 PHE 0.017 0.001 PHE H 141 TYR 0.017 0.002 TYR G 138 ARG 0.006 0.000 ARG F 350 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 217 time to evaluate : 1.564 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 218 ASN cc_start: 0.8413 (t0) cc_final: 0.8047 (t0) REVERT: A 342 HIS cc_start: 0.8083 (m90) cc_final: 0.7819 (m-70) REVERT: A 352 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7754 (tt) REVERT: A 354 MET cc_start: 0.8232 (tpp) cc_final: 0.7666 (ttm) REVERT: B 215 MET cc_start: 0.8690 (mtp) cc_final: 0.8303 (mtp) REVERT: B 223 ASP cc_start: 0.8148 (t0) cc_final: 0.7581 (t0) REVERT: B 226 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: B 354 MET cc_start: 0.8029 (ttm) cc_final: 0.7816 (tmm) REVERT: C 73 GLN cc_start: 0.8327 (tt0) cc_final: 0.7998 (pp30) REVERT: C 132 ASN cc_start: 0.8735 (t0) cc_final: 0.8452 (t0) REVERT: E 218 ASN cc_start: 0.8390 (t0) cc_final: 0.8027 (t0) REVERT: E 226 ASP cc_start: 0.8604 (t70) cc_final: 0.8354 (t70) REVERT: E 352 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7648 (tt) REVERT: E 354 MET cc_start: 0.8302 (tpp) cc_final: 0.7787 (ttm) REVERT: F 223 ASP cc_start: 0.8109 (t0) cc_final: 0.7523 (t0) REVERT: F 226 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8039 (m-30) REVERT: F 289 TYR cc_start: 0.7890 (m-80) cc_final: 0.7688 (m-10) REVERT: G 41 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7019 (tt) REVERT: G 71 GLU cc_start: 0.8889 (tp30) cc_final: 0.8465 (tp30) REVERT: G 132 ASN cc_start: 0.8749 (t0) cc_final: 0.8244 (t0) REVERT: H 75 HIS cc_start: 0.8803 (OUTLIER) cc_final: 0.8279 (t-90) outliers start: 40 outliers final: 24 residues processed: 248 average time/residue: 0.2412 time to fit residues: 89.2479 Evaluate side-chains 243 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 75 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 134 optimal weight: 0.2980 chunk 141 optimal weight: 30.0000 chunk 148 optimal weight: 30.0000 chunk 97 optimal weight: 7.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN B 79 GLN B 173 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS ** D 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13794 Z= 0.312 Angle : 0.653 10.071 18630 Z= 0.350 Chirality : 0.046 0.160 1916 Planarity : 0.004 0.038 2510 Dihedral : 4.599 24.688 1788 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.56 % Allowed : 20.61 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1650 helix: 1.41 (0.23), residues: 518 sheet: 0.45 (0.30), residues: 328 loop : -1.33 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 126 HIS 0.006 0.001 HIS F 342 PHE 0.019 0.002 PHE D 141 TYR 0.022 0.002 TYR B 48 ARG 0.003 0.000 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 209 time to evaluate : 1.624 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: A 342 HIS cc_start: 0.8157 (m90) cc_final: 0.7879 (m-70) REVERT: A 354 MET cc_start: 0.8237 (tpp) cc_final: 0.7712 (ttm) REVERT: B 223 ASP cc_start: 0.8197 (t0) cc_final: 0.7692 (t0) REVERT: B 226 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: C 73 GLN cc_start: 0.8341 (tt0) cc_final: 0.8005 (pp30) REVERT: C 132 ASN cc_start: 0.8736 (t0) cc_final: 0.8490 (t0) REVERT: E 226 ASP cc_start: 0.8676 (t70) cc_final: 0.8422 (t70) REVERT: E 342 HIS cc_start: 0.8139 (m90) cc_final: 0.7859 (m-70) REVERT: E 352 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7737 (tt) REVERT: E 354 MET cc_start: 0.8302 (tpp) cc_final: 0.7769 (ttm) REVERT: F 223 ASP cc_start: 0.8214 (t0) cc_final: 0.7673 (t0) REVERT: F 226 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: G 41 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7030 (tt) REVERT: G 48 ASP cc_start: 0.7370 (t0) cc_final: 0.7051 (m-30) REVERT: G 71 GLU cc_start: 0.8915 (tp30) cc_final: 0.8494 (tp30) REVERT: G 132 ASN cc_start: 0.8818 (t0) cc_final: 0.8284 (t0) REVERT: H 75 HIS cc_start: 0.8746 (OUTLIER) cc_final: 0.8301 (t-90) outliers start: 37 outliers final: 23 residues processed: 236 average time/residue: 0.2356 time to fit residues: 82.4737 Evaluate side-chains 231 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 80 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 165 optimal weight: 0.9980 chunk 152 optimal weight: 0.0070 chunk 131 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN B 79 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 75 HIS ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13794 Z= 0.195 Angle : 0.660 13.138 18630 Z= 0.353 Chirality : 0.045 0.241 1916 Planarity : 0.003 0.037 2510 Dihedral : 4.454 23.223 1788 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.80 % Allowed : 21.78 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.21), residues: 1650 helix: 1.43 (0.23), residues: 514 sheet: 0.67 (0.30), residues: 324 loop : -1.27 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 126 HIS 0.004 0.001 HIS C 51 PHE 0.022 0.001 PHE D 141 TYR 0.016 0.001 TYR D 76 ARG 0.003 0.000 ARG A 350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 217 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8435 (t0) cc_final: 0.8075 (t0) REVERT: A 354 MET cc_start: 0.8176 (tpp) cc_final: 0.7591 (ttm) REVERT: B 223 ASP cc_start: 0.8123 (t0) cc_final: 0.7554 (t0) REVERT: B 226 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.7992 (m-30) REVERT: B 289 TYR cc_start: 0.8009 (m-80) cc_final: 0.7784 (m-10) REVERT: C 73 GLN cc_start: 0.8280 (tt0) cc_final: 0.7995 (pp30) REVERT: C 132 ASN cc_start: 0.8689 (t0) cc_final: 0.8434 (t0) REVERT: D 41 LEU cc_start: 0.7165 (mm) cc_final: 0.6695 (mm) REVERT: E 218 ASN cc_start: 0.8414 (t0) cc_final: 0.8042 (t0) REVERT: E 226 ASP cc_start: 0.8518 (t70) cc_final: 0.8278 (t70) REVERT: E 295 HIS cc_start: 0.9004 (t-90) cc_final: 0.8691 (t70) REVERT: E 352 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7713 (tt) REVERT: E 354 MET cc_start: 0.8248 (tpp) cc_final: 0.7622 (ttm) REVERT: F 223 ASP cc_start: 0.8126 (t0) cc_final: 0.7523 (t0) REVERT: F 226 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: F 350 ARG cc_start: 0.7685 (ttm-80) cc_final: 0.7480 (ttm110) REVERT: G 41 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7120 (tt) REVERT: G 48 ASP cc_start: 0.7416 (t0) cc_final: 0.6872 (m-30) REVERT: G 71 GLU cc_start: 0.8919 (tp30) cc_final: 0.8518 (tp30) REVERT: G 132 ASN cc_start: 0.8812 (t0) cc_final: 0.8272 (t0) REVERT: H 75 HIS cc_start: 0.8671 (OUTLIER) cc_final: 0.8272 (t-90) outliers start: 26 outliers final: 15 residues processed: 237 average time/residue: 0.2316 time to fit residues: 82.1387 Evaluate side-chains 230 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 210 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 80 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.166602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109952 restraints weight = 16872.319| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.14 r_work: 0.3058 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13794 Z= 0.270 Angle : 0.680 12.699 18630 Z= 0.368 Chirality : 0.046 0.263 1916 Planarity : 0.004 0.037 2510 Dihedral : 4.526 23.976 1788 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.80 % Allowed : 22.06 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1650 helix: 1.40 (0.23), residues: 518 sheet: 0.56 (0.30), residues: 328 loop : -1.29 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 126 HIS 0.005 0.001 HIS F 342 PHE 0.020 0.002 PHE D 141 TYR 0.019 0.002 TYR C 138 ARG 0.003 0.000 ARG E 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3086.93 seconds wall clock time: 55 minutes 32.35 seconds (3332.35 seconds total)