Starting phenix.real_space_refine on Fri Jul 3 16:38:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgc_50394/07_2026/9fgc_50394.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgc_50394/07_2026/9fgc_50394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fgc_50394/07_2026/9fgc_50394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgc_50394/07_2026/9fgc_50394.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fgc_50394/07_2026/9fgc_50394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgc_50394/07_2026/9fgc_50394.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 82 5.16 5 C 9732 2.51 5 N 2439 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15032 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2704 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 319} Chain breaks: 1 Chain: "B" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2711 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Chain: "C" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2720 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2780 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 Chain: "E" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2732 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain breaks: 1 Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain breaks: 1 Chain: "a" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.89, per 1000 atoms: 0.19 Number of scatterers: 15032 At special positions: 0 Unit cell: (99.6389, 109.896, 139.201, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 3 15.00 O 2776 8.00 N 2439 7.00 C 9732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS F 429 " - pdb=" SG CYS F 502 " 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 Links applied ALPHA1-2 " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN a 8 " - " MAN a 9 " ALPHA1-3 " BMA G 3 " - " MAN G 6 " " MAN G 4 " - " MAN G 5 " " BMA H 3 " - " MAN H 6 " " MAN H 4 " - " MAN H 5 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 10 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 8 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG C 501 " - " ASN C 208 " " NAG G 1 " - " ASN B 149 " " NAG H 1 " - " ASN E 149 " " NAG a 1 " - " ASN A 111 " " NAG b 1 " - " ASN B 80 " " NAG d 1 " - " ASN D 111 " " NAG e 1 " - " ASN E 80 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 462.4 milliseconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3394 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 20 sheets defined 39.1% alpha, 40.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 removed outlier: 4.104A pdb=" N LEU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.496A pdb=" N ASP A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.727A pdb=" N SER A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 251 through 276 Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.573A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 416 removed outlier: 3.906A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 11 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 237 removed outlier: 3.549A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 246 through 272 removed outlier: 3.654A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 308 removed outlier: 3.571A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 446 removed outlier: 3.546A pdb=" N ILE B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.594A pdb=" N MET C 102 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 196 Processing helix chain 'C' and resid 233 through 240 Processing helix chain 'C' and resid 240 through 252 Processing helix chain 'C' and resid 253 through 257 Processing helix chain 'C' and resid 261 through 281 removed outlier: 3.562A pdb=" N THR C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 294 through 322 Processing helix chain 'C' and resid 409 through 435 removed outlier: 3.840A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'D' and resid 14 through 23 removed outlier: 4.395A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.655A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.481A pdb=" N ASP D 145 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.684A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 277 removed outlier: 3.575A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 309 removed outlier: 3.539A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 417 removed outlier: 4.041A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix removed outlier: 3.676A pdb=" N ASN D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 225 through 237 removed outlier: 3.598A pdb=" N SER E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 246 through 272 Processing helix chain 'E' and resid 279 through 308 removed outlier: 3.510A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 446 removed outlier: 3.825A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing helix chain 'F' and resid 468 through 471 Processing helix chain 'F' and resid 493 through 497 Processing helix chain 'F' and resid 513 through 517 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 86 removed outlier: 4.529A pdb=" N LEU A 119 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASP A 63 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE A 50 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N PHE A 65 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N THR A 48 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ARG A 67 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE A 46 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N SER A 69 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ASP A 44 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N LYS A 71 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N LYS A 42 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.961A pdb=" N ASP A 63 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE A 50 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N PHE A 65 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N THR A 48 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ARG A 67 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE A 46 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N SER A 69 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ASP A 44 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N LYS A 71 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N LYS A 42 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.366A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.326A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.989A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.172A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 95 through 98 removed outlier: 3.560A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS C 118 " --> pdb=" O ASP C 148 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU C 150 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N SER C 116 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 95 through 98 removed outlier: 3.560A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLU C 71 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N THR C 51 " --> pdb=" O TYR C 181 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N TRP C 183 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N ILE C 53 " --> pdb=" O TRP C 183 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N ARG C 185 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N THR C 55 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER C 187 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.713A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.713A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.718A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP D 63 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N PHE D 50 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N PHE D 65 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N THR D 48 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ARG D 67 " --> pdb=" O PHE D 46 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE D 46 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N SER D 69 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP D 44 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N LYS D 71 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N LYS D 42 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 109 removed outlier: 6.877A pdb=" N ASP D 63 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N PHE D 50 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N PHE D 65 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N THR D 48 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ARG D 67 " --> pdb=" O PHE D 46 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE D 46 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N SER D 69 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP D 44 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N LYS D 71 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N LYS D 42 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.293A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.452A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.938A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.172A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.172A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR E 205 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN E 197 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG E 207 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER E 195 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER E 209 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU E 193 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER E 211 " --> pdb=" O HIS E 191 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS E 191 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG E 213 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.511A pdb=" N ALA F 498 " --> pdb=" O VAL F 526 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N MET F 441 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA F 457 " --> pdb=" O MET F 441 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TRP F 443 " --> pdb=" O LEU F 455 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.511A pdb=" N ALA F 498 " --> pdb=" O VAL F 526 " (cutoff:3.500A) 827 hydrogen bonds defined for protein. 2319 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: 1.93 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2437 1.32 - 1.45: 4484 1.45 - 1.57: 8343 1.57 - 1.69: 4 1.69 - 1.81: 141 Bond restraints: 15409 Sorted by residual: bond pdb=" O4 PIO D 501 " pdb=" P4 PIO D 501 " ideal model delta sigma weight residual 1.710 1.626 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" O5 PIO D 501 " pdb=" P5 PIO D 501 " ideal model delta sigma weight residual 1.699 1.626 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" O13 PIO D 501 " pdb=" P1 PIO D 501 " ideal model delta sigma weight residual 1.651 1.595 0.056 2.00e-02 2.50e+03 7.86e+00 bond pdb=" C5 PIO D 501 " pdb=" O5 PIO D 501 " ideal model delta sigma weight residual 1.388 1.443 -0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" C4 PIO D 501 " pdb=" O4 PIO D 501 " ideal model delta sigma weight residual 1.389 1.442 -0.053 2.00e-02 2.50e+03 7.11e+00 ... (remaining 15404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 20395 1.61 - 3.23: 468 3.23 - 4.84: 63 4.84 - 6.46: 14 6.46 - 8.07: 1 Bond angle restraints: 20941 Sorted by residual: angle pdb=" C1 MAN a 5 " pdb=" C2 MAN a 5 " pdb=" O2 MAN a 5 " ideal model delta sigma weight residual 106.80 114.87 -8.07 3.00e+00 1.11e-01 7.24e+00 angle pdb=" CA TYR B 299 " pdb=" CB TYR B 299 " pdb=" CG TYR B 299 " ideal model delta sigma weight residual 113.90 109.23 4.67 1.80e+00 3.09e-01 6.74e+00 angle pdb=" N VAL E 87 " pdb=" CA VAL E 87 " pdb=" C VAL E 87 " ideal model delta sigma weight residual 113.00 109.74 3.26 1.30e+00 5.92e-01 6.30e+00 angle pdb=" C VAL F 427 " pdb=" N SER F 428 " pdb=" CA SER F 428 " ideal model delta sigma weight residual 123.05 118.61 4.44 1.79e+00 3.12e-01 6.16e+00 angle pdb=" C ILE D 271 " pdb=" N SER D 272 " pdb=" CA SER D 272 " ideal model delta sigma weight residual 120.31 116.57 3.74 1.52e+00 4.33e-01 6.05e+00 ... (remaining 20936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 9151 21.17 - 42.34: 214 42.34 - 63.50: 17 63.50 - 84.67: 29 84.67 - 105.84: 17 Dihedral angle restraints: 9428 sinusoidal: 4153 harmonic: 5275 Sorted by residual: dihedral pdb=" O4 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.13 105.84 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.60 105.31 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.54 105.25 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 9425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.930: 2454 0.930 - 1.860: 0 1.860 - 2.789: 0 2.789 - 3.719: 0 3.719 - 4.649: 2 Chirality restraints: 2456 Sorted by residual: chirality pdb=" C1 MAN a 5 " pdb=" O2 MAN a 4 " pdb=" C2 MAN a 5 " pdb=" O5 MAN a 5 " both_signs ideal model delta sigma weight residual False 2.40 -2.25 4.65 2.00e-02 2.50e+03 5.40e+04 chirality pdb=" C1 MAN a 6 " pdb=" O2 MAN a 5 " pdb=" C2 MAN a 6 " pdb=" O5 MAN a 6 " both_signs ideal model delta sigma weight residual False 2.40 -2.24 4.64 2.00e-02 2.50e+03 5.38e+04 chirality pdb=" C2 MAN a 5 " pdb=" C1 MAN a 5 " pdb=" C3 MAN a 5 " pdb=" O2 MAN a 5 " both_signs ideal model delta sigma weight residual False 2.52 2.09 0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 2453 not shown) Planarity restraints: 2548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 205 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C SER A 205 " -0.055 2.00e-02 2.50e+03 pdb=" O SER A 205 " 0.021 2.00e-02 2.50e+03 pdb=" N SER A 206 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 396 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.62e+00 pdb=" C SER D 396 " 0.054 2.00e-02 2.50e+03 pdb=" O SER D 396 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG D 397 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 300 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C ALA A 300 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA A 300 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU A 301 " 0.016 2.00e-02 2.50e+03 ... (remaining 2545 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3083 2.78 - 3.31: 13364 3.31 - 3.84: 25140 3.84 - 4.37: 30310 4.37 - 4.90: 51867 Nonbonded interactions: 123764 Sorted by model distance: nonbonded pdb=" O PHE E 221 " pdb=" OG1 THR E 225 " model vdw 2.247 3.040 nonbonded pdb=" O SER C 267 " pdb=" OG1 THR C 271 " model vdw 2.273 3.040 nonbonded pdb=" O HIS C 318 " pdb=" OG SER C 322 " model vdw 2.279 3.040 nonbonded pdb=" O6 MAN a 5 " pdb=" O4 MAN a 8 " model vdw 2.279 3.040 nonbonded pdb=" O PHE F 436 " pdb=" NH2 ARG F 478 " model vdw 2.296 3.120 ... (remaining 123759 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 13 through 418) selection = (chain 'D' and (resid 13 through 312 or resid 386 through 418)) } ncs_group { reference = (chain 'B' and (resid 10 through 309 or resid 420 through 447)) selection = (chain 'E' and (resid 10 through 309 or resid 420 through 447)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'b' selection = chain 'e' } 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: 0.400 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.290 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 0.004 0.084 15447 Z= 0.195 Angle : 0.611 13.642 21049 Z= 0.311 Chirality : 0.140 4.649 2456 Planarity : 0.005 0.033 2541 Dihedral : 11.361 105.841 6016 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.63 % Allowed : 2.56 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1766 helix: 0.86 (0.21), residues: 575 sheet: 0.69 (0.25), residues: 428 loop : 0.41 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 265 TYR 0.020 0.001 TYR B 299 PHE 0.013 0.001 PHE D 66 TRP 0.021 0.001 TRP A 70 HIS 0.005 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (15409) covalent geometry : angle 0.58920 / 0.31 (20941) SS BOND : bond 0.00184 / 0.10 ( 6) SS BOND : angle 0.70087 / 0.43 ( 12) hydrogen bonds : bond 0.11813 / 7.70 ( 735) hydrogen bonds : angle 5.84416 / 4.08 ( 2319) link_ALPHA1-2 : bond 0.00797 / 0.33 ( 3) link_ALPHA1-2 : angle 6.49264 / 4.05 ( 9) link_ALPHA1-3 : bond 0.00420 / 0.20 ( 7) link_ALPHA1-3 : angle 1.34391 / 0.84 ( 21) link_ALPHA1-6 : bond 0.00535 / 0.27 ( 5) link_ALPHA1-6 : angle 1.31870 / 0.76 ( 15) link_BETA1-4 : bond 0.00471 / 0.27 ( 10) link_BETA1-4 : angle 1.81469 / 1.18 ( 30) link_NAG-ASN : bond 0.00155 / 0.09 ( 7) link_NAG-ASN : angle 1.49727 / 0.93 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.9089 (tpp) cc_final: 0.8583 (tpp) REVERT: A 213 MET cc_start: 0.9473 (mmm) cc_final: 0.9246 (mmm) REVERT: A 242 GLN cc_start: 0.9053 (mt0) cc_final: 0.8741 (mt0) REVERT: C 70 MET cc_start: 0.9241 (mmt) cc_final: 0.8689 (mmm) REVERT: C 71 GLU cc_start: 0.9074 (pt0) cc_final: 0.8710 (pm20) REVERT: D 213 MET cc_start: 0.8960 (mmm) cc_final: 0.8586 (mmm) REVERT: D 229 GLN cc_start: 0.9138 (mm110) cc_final: 0.8760 (tp40) REVERT: D 258 PHE cc_start: 0.8726 (t80) cc_final: 0.8403 (t80) REVERT: D 266 MET cc_start: 0.9380 (mmm) cc_final: 0.9117 (tpp) REVERT: E 9 MET cc_start: 0.9009 (ttt) cc_final: 0.8730 (ttm) REVERT: E 147 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8464 (tt0) REVERT: E 153 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8295 (mm-30) REVERT: E 155 GLU cc_start: 0.8793 (tt0) cc_final: 0.8525 (tp30) REVERT: E 165 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7978 (mt-10) REVERT: E 224 GLN cc_start: 0.9346 (mm-40) cc_final: 0.8875 (tt0) REVERT: E 433 PHE cc_start: 0.9044 (t80) cc_final: 0.8803 (t80) REVERT: F 439 TYR cc_start: 0.7211 (m-80) cc_final: 0.6942 (m-80) REVERT: F 462 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7916 (ttm110) REVERT: F 475 THR cc_start: 0.8802 (m) cc_final: 0.8515 (p) REVERT: F 479 ASP cc_start: 0.8754 (t0) cc_final: 0.8179 (t0) REVERT: F 488 GLN cc_start: 0.8462 (tp40) cc_final: 0.7944 (tm-30) REVERT: F 500 TYR cc_start: 0.8223 (m-80) cc_final: 0.7928 (m-80) outliers start: 10 outliers final: 4 residues processed: 197 average time/residue: 0.1110 time to fit residues: 32.0393 Evaluate side-chains 125 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 HIS A 229 GLN B 41 ASN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN C 69 ASN C 80 GLN C 122 HIS C 128 ASN C 163 HIS D 102 HIS D 110 HIS D 229 GLN E 312 GLN F 6 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.068469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.050409 restraints weight = 51497.968| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.79 r_work: 0.2658 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15447 Z= 0.135 Angle : 0.543 8.274 21049 Z= 0.277 Chirality : 0.042 0.170 2456 Planarity : 0.004 0.038 2541 Dihedral : 10.455 103.386 2664 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.94 % Allowed : 5.69 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.20), residues: 1766 helix: 1.90 (0.21), residues: 579 sheet: 0.78 (0.25), residues: 429 loop : 0.50 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 136 TYR 0.020 0.001 TYR B 299 PHE 0.013 0.001 PHE F 454 TRP 0.011 0.001 TRP A 70 HIS 0.007 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (15409) covalent geometry : angle 0.52932 / 0.27 (20941) SS BOND : bond 0.00156 / 0.08 ( 6) SS BOND : angle 0.52014 / 0.30 ( 12) hydrogen bonds : bond 0.03988 / 2.57 ( 735) hydrogen bonds : angle 4.60704 / 3.22 ( 2319) link_ALPHA1-2 : bond 0.01446 / 0.67 ( 3) link_ALPHA1-2 : angle 3.01950 / 1.76 ( 9) link_ALPHA1-3 : bond 0.00775 / 0.43 ( 7) link_ALPHA1-3 : angle 1.85336 / 1.16 ( 21) link_ALPHA1-6 : bond 0.00465 / 0.23 ( 5) link_ALPHA1-6 : angle 1.65643 / 0.95 ( 15) link_BETA1-4 : bond 0.00366 / 0.20 ( 10) link_BETA1-4 : angle 1.74405 / 1.18 ( 30) link_NAG-ASN : bond 0.00132 / 0.08 ( 7) link_NAG-ASN : angle 1.41910 / 0.93 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9327 (mtt) cc_final: 0.9018 (ttm) REVERT: A 204 GLN cc_start: 0.7292 (tm-30) cc_final: 0.6974 (tm-30) REVERT: B 261 MET cc_start: 0.9243 (mmm) cc_final: 0.8931 (mmm) REVERT: C 70 MET cc_start: 0.9134 (mmt) cc_final: 0.8425 (mmm) REVERT: C 71 GLU cc_start: 0.9250 (pt0) cc_final: 0.8465 (pm20) REVERT: C 130 MET cc_start: 0.8342 (ttm) cc_final: 0.7928 (tmm) REVERT: D 213 MET cc_start: 0.9158 (mmm) cc_final: 0.8908 (mmm) REVERT: D 232 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9101 (tp) REVERT: D 236 MET cc_start: 0.9439 (mtm) cc_final: 0.8917 (mtm) REVERT: D 258 PHE cc_start: 0.8747 (t80) cc_final: 0.8354 (t80) REVERT: D 266 MET cc_start: 0.9521 (mmm) cc_final: 0.9288 (tpp) REVERT: E 9 MET cc_start: 0.8924 (ttt) cc_final: 0.8642 (ttm) REVERT: E 182 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8247 (mm-30) REVERT: E 224 GLN cc_start: 0.9554 (mm-40) cc_final: 0.9340 (mm-40) REVERT: E 433 PHE cc_start: 0.9236 (t80) cc_final: 0.9026 (t80) REVERT: F 439 TYR cc_start: 0.7870 (m-80) cc_final: 0.7281 (m-80) REVERT: F 462 ARG cc_start: 0.7336 (mtp85) cc_final: 0.6908 (ttm110) REVERT: F 475 THR cc_start: 0.9166 (m) cc_final: 0.8854 (p) REVERT: F 479 ASP cc_start: 0.8931 (t0) cc_final: 0.8666 (t0) REVERT: F 488 GLN cc_start: 0.8799 (tp40) cc_final: 0.8143 (tm-30) REVERT: F 500 TYR cc_start: 0.8331 (m-80) cc_final: 0.8086 (m-80) REVERT: F 518 HIS cc_start: 0.8012 (m-70) cc_final: 0.7801 (m90) outliers start: 15 outliers final: 7 residues processed: 133 average time/residue: 0.1173 time to fit residues: 23.2761 Evaluate side-chains 120 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 182 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 143 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 148 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.069594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.051407 restraints weight = 51458.767| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.74 r_work: 0.2660 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15447 Z= 0.145 Angle : 0.524 7.850 21049 Z= 0.264 Chirality : 0.042 0.190 2456 Planarity : 0.004 0.041 2541 Dihedral : 9.237 86.256 2661 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.81 % Allowed : 6.44 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.20), residues: 1766 helix: 2.18 (0.21), residues: 579 sheet: 0.73 (0.25), residues: 428 loop : 0.51 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 17 TYR 0.022 0.001 TYR B 299 PHE 0.012 0.001 PHE A 15 TRP 0.010 0.001 TRP C 430 HIS 0.012 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (15409) covalent geometry : angle 0.51123 / 0.26 (20941) SS BOND : bond 0.00122 / 0.07 ( 6) SS BOND : angle 0.54961 / 0.34 ( 12) hydrogen bonds : bond 0.03610 / 2.32 ( 735) hydrogen bonds : angle 4.27954 / 2.98 ( 2319) link_ALPHA1-2 : bond 0.00984 / 0.46 ( 3) link_ALPHA1-2 : angle 2.85389 / 1.59 ( 9) link_ALPHA1-3 : bond 0.00763 / 0.43 ( 7) link_ALPHA1-3 : angle 1.89116 / 1.16 ( 21) link_ALPHA1-6 : bond 0.00590 / 0.29 ( 5) link_ALPHA1-6 : angle 1.63605 / 0.94 ( 15) link_BETA1-4 : bond 0.00372 / 0.20 ( 10) link_BETA1-4 : angle 1.55019 / 1.04 ( 30) link_NAG-ASN : bond 0.00119 / 0.06 ( 7) link_NAG-ASN : angle 1.36984 / 0.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9331 (mtt) cc_final: 0.8972 (ttm) REVERT: A 112 MET cc_start: 0.9104 (tpp) cc_final: 0.8226 (tpp) REVERT: B 40 MET cc_start: 0.9010 (mtp) cc_final: 0.8801 (mtm) REVERT: C 70 MET cc_start: 0.9323 (mmt) cc_final: 0.8495 (mmm) REVERT: C 71 GLU cc_start: 0.9252 (pt0) cc_final: 0.8470 (pm20) REVERT: C 130 MET cc_start: 0.8480 (ttm) cc_final: 0.8005 (tmm) REVERT: C 177 GLU cc_start: 0.9048 (mp0) cc_final: 0.8799 (mp0) REVERT: C 197 ARG cc_start: 0.8748 (mtp180) cc_final: 0.8421 (mtp-110) REVERT: C 223 MET cc_start: 0.9034 (mmm) cc_final: 0.8624 (mmt) REVERT: D 58 MET cc_start: 0.9042 (mtp) cc_final: 0.8718 (mmm) REVERT: D 236 MET cc_start: 0.9497 (mtm) cc_final: 0.8951 (mtm) REVERT: D 258 PHE cc_start: 0.8810 (t80) cc_final: 0.8412 (t80) REVERT: D 266 MET cc_start: 0.9592 (mmm) cc_final: 0.9369 (tpp) REVERT: E 9 MET cc_start: 0.8870 (ttt) cc_final: 0.8583 (ttm) REVERT: E 224 GLN cc_start: 0.9558 (mm-40) cc_final: 0.9332 (mm-40) REVERT: F 436 PHE cc_start: 0.7985 (m-80) cc_final: 0.7768 (m-10) REVERT: F 441 MET cc_start: 0.6411 (ttm) cc_final: 0.5807 (ttm) REVERT: F 462 ARG cc_start: 0.7275 (mtp85) cc_final: 0.6814 (ttm110) REVERT: F 475 THR cc_start: 0.9162 (m) cc_final: 0.8838 (p) REVERT: F 479 ASP cc_start: 0.8943 (t0) cc_final: 0.8620 (t0) REVERT: F 488 GLN cc_start: 0.8816 (tp40) cc_final: 0.8305 (tm-30) REVERT: F 518 HIS cc_start: 0.8148 (m-70) cc_final: 0.7879 (m90) outliers start: 13 outliers final: 9 residues processed: 131 average time/residue: 0.1165 time to fit residues: 23.2342 Evaluate side-chains 120 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 132 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 107 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN C 69 ASN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.067054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.048958 restraints weight = 52464.199| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.68 r_work: 0.2590 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15447 Z= 0.293 Angle : 0.635 9.839 21049 Z= 0.318 Chirality : 0.044 0.215 2456 Planarity : 0.004 0.046 2541 Dihedral : 8.426 67.264 2661 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.19 % Allowed : 6.94 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.20), residues: 1766 helix: 2.37 (0.21), residues: 575 sheet: 0.57 (0.24), residues: 431 loop : 0.43 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 17 TYR 0.022 0.002 TYR B 299 PHE 0.017 0.002 PHE A 304 TRP 0.011 0.002 TRP C 430 HIS 0.009 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.29 (15409) covalent geometry : angle 0.62300 / 0.32 (20941) SS BOND : bond 0.00256 / 0.15 ( 6) SS BOND : angle 0.65043 / 0.39 ( 12) hydrogen bonds : bond 0.03985 / 2.58 ( 735) hydrogen bonds : angle 4.43777 / 3.08 ( 2319) link_ALPHA1-2 : bond 0.00913 / 0.44 ( 3) link_ALPHA1-2 : angle 3.03578 / 1.65 ( 9) link_ALPHA1-3 : bond 0.00681 / 0.42 ( 7) link_ALPHA1-3 : angle 2.09268 / 1.28 ( 21) link_ALPHA1-6 : bond 0.00566 / 0.27 ( 5) link_ALPHA1-6 : angle 1.85027 / 1.08 ( 15) link_BETA1-4 : bond 0.00395 / 0.20 ( 10) link_BETA1-4 : angle 1.57656 / 1.01 ( 30) link_NAG-ASN : bond 0.00403 / 0.18 ( 7) link_NAG-ASN : angle 1.70430 / 1.13 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9343 (mtt) cc_final: 0.9076 (mtt) REVERT: B 297 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9191 (tt) REVERT: C 70 MET cc_start: 0.9369 (mmt) cc_final: 0.8398 (mmm) REVERT: C 130 MET cc_start: 0.8612 (ttm) cc_final: 0.8139 (tmm) REVERT: C 160 MET cc_start: 0.9335 (mtp) cc_final: 0.9072 (ptp) REVERT: C 177 GLU cc_start: 0.9070 (mp0) cc_final: 0.8711 (mp0) REVERT: C 223 MET cc_start: 0.9115 (mmm) cc_final: 0.8713 (mmt) REVERT: D 232 LEU cc_start: 0.9441 (mt) cc_final: 0.9022 (tp) REVERT: D 236 MET cc_start: 0.9572 (mtm) cc_final: 0.9051 (mtm) REVERT: E 55 MET cc_start: 0.8036 (tpp) cc_final: 0.7481 (mmm) REVERT: E 182 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8704 (mm-30) REVERT: E 224 GLN cc_start: 0.9578 (mm-40) cc_final: 0.9331 (mm-40) REVERT: F 441 MET cc_start: 0.6202 (ttm) cc_final: 0.5500 (ttm) REVERT: F 458 MET cc_start: 0.5396 (ttm) cc_final: 0.4980 (ttp) REVERT: F 462 ARG cc_start: 0.7508 (mtp85) cc_final: 0.6761 (mtm-85) REVERT: F 473 ARG cc_start: 0.6584 (mtp180) cc_final: 0.6199 (mtp180) REVERT: F 475 THR cc_start: 0.9132 (m) cc_final: 0.8734 (p) REVERT: F 479 ASP cc_start: 0.8911 (t0) cc_final: 0.8635 (t0) REVERT: F 488 GLN cc_start: 0.8635 (tp40) cc_final: 0.8400 (tm-30) REVERT: F 518 HIS cc_start: 0.8138 (m-70) cc_final: 0.7888 (m90) outliers start: 19 outliers final: 13 residues processed: 126 average time/residue: 0.1027 time to fit residues: 19.8223 Evaluate side-chains 121 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain F residue 513 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.049559 restraints weight = 52190.559| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.70 r_work: 0.2604 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15447 Z= 0.204 Angle : 0.561 11.209 21049 Z= 0.279 Chirality : 0.043 0.208 2456 Planarity : 0.003 0.045 2541 Dihedral : 7.732 63.203 2661 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.00 % Allowed : 7.69 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.20), residues: 1766 helix: 2.54 (0.21), residues: 571 sheet: 0.56 (0.24), residues: 430 loop : 0.41 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 17 TYR 0.022 0.001 TYR E 299 PHE 0.014 0.001 PHE A 304 TRP 0.010 0.001 TRP E 426 HIS 0.006 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (15409) covalent geometry : angle 0.54836 / 0.28 (20941) SS BOND : bond 0.00167 / 0.09 ( 6) SS BOND : angle 0.43514 / 0.25 ( 12) hydrogen bonds : bond 0.03684 / 2.38 ( 735) hydrogen bonds : angle 4.26166 / 2.95 ( 2319) link_ALPHA1-2 : bond 0.00903 / 0.44 ( 3) link_ALPHA1-2 : angle 2.67972 / 1.47 ( 9) link_ALPHA1-3 : bond 0.00697 / 0.42 ( 7) link_ALPHA1-3 : angle 2.12227 / 1.28 ( 21) link_ALPHA1-6 : bond 0.00616 / 0.30 ( 5) link_ALPHA1-6 : angle 1.80476 / 1.07 ( 15) link_BETA1-4 : bond 0.00327 / 0.16 ( 10) link_BETA1-4 : angle 1.54085 / 1.01 ( 30) link_NAG-ASN : bond 0.00230 / 0.11 ( 7) link_NAG-ASN : angle 1.49110 / 1.00 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9348 (mtt) cc_final: 0.8874 (mmm) REVERT: A 112 MET cc_start: 0.9077 (tpp) cc_final: 0.8321 (tpp) REVERT: A 236 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8972 (mtm) REVERT: A 269 LEU cc_start: 0.9714 (mt) cc_final: 0.9422 (mp) REVERT: B 297 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9167 (tt) REVERT: C 70 MET cc_start: 0.9396 (mmt) cc_final: 0.8658 (mmm) REVERT: C 130 MET cc_start: 0.8555 (ttm) cc_final: 0.8110 (tmm) REVERT: C 160 MET cc_start: 0.9356 (mtp) cc_final: 0.9058 (ptp) REVERT: C 223 MET cc_start: 0.9132 (mmm) cc_final: 0.8732 (mmt) REVERT: D 58 MET cc_start: 0.9135 (mmm) cc_final: 0.8888 (tpp) REVERT: D 232 LEU cc_start: 0.9444 (mt) cc_final: 0.9139 (tp) REVERT: D 236 MET cc_start: 0.9559 (mtm) cc_final: 0.9178 (mtm) REVERT: E 55 MET cc_start: 0.7943 (tpp) cc_final: 0.7254 (mmm) REVERT: E 224 GLN cc_start: 0.9590 (mm-40) cc_final: 0.9343 (mm-40) REVERT: E 286 MET cc_start: 0.9103 (tpp) cc_final: 0.8748 (tpp) REVERT: F 436 PHE cc_start: 0.7750 (m-80) cc_final: 0.7486 (m-10) REVERT: F 441 MET cc_start: 0.6181 (ttm) cc_final: 0.5541 (ttm) REVERT: F 458 MET cc_start: 0.5505 (ttm) cc_final: 0.5014 (ttp) REVERT: F 462 ARG cc_start: 0.7551 (mtp85) cc_final: 0.6926 (mtm-85) REVERT: F 475 THR cc_start: 0.9122 (m) cc_final: 0.8714 (p) REVERT: F 479 ASP cc_start: 0.8908 (t0) cc_final: 0.8658 (t0) REVERT: F 518 HIS cc_start: 0.8069 (m-70) cc_final: 0.7783 (m90) outliers start: 16 outliers final: 13 residues processed: 125 average time/residue: 0.1175 time to fit residues: 22.8077 Evaluate side-chains 123 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 LYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.068736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.050720 restraints weight = 50999.295| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.68 r_work: 0.2642 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15447 Z= 0.121 Angle : 0.512 8.446 21049 Z= 0.255 Chirality : 0.041 0.228 2456 Planarity : 0.003 0.043 2541 Dihedral : 7.131 58.803 2661 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.06 % Allowed : 7.88 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.20), residues: 1766 helix: 2.65 (0.21), residues: 573 sheet: 0.58 (0.25), residues: 430 loop : 0.54 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 17 TYR 0.021 0.001 TYR E 299 PHE 0.012 0.001 PHE F 454 TRP 0.011 0.001 TRP E 426 HIS 0.005 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15409) covalent geometry : angle 0.50016 / 0.25 (20941) SS BOND : bond 0.00103 / 0.05 ( 6) SS BOND : angle 0.42286 / 0.25 ( 12) hydrogen bonds : bond 0.03321 / 2.14 ( 735) hydrogen bonds : angle 4.03579 / 2.79 ( 2319) link_ALPHA1-2 : bond 0.00958 / 0.46 ( 3) link_ALPHA1-2 : angle 2.67884 / 1.49 ( 9) link_ALPHA1-3 : bond 0.00838 / 0.48 ( 7) link_ALPHA1-3 : angle 1.90885 / 1.17 ( 21) link_ALPHA1-6 : bond 0.00713 / 0.35 ( 5) link_ALPHA1-6 : angle 1.71743 / 1.03 ( 15) link_BETA1-4 : bond 0.00387 / 0.19 ( 10) link_BETA1-4 : angle 1.46329 / 0.99 ( 30) link_NAG-ASN : bond 0.00154 / 0.08 ( 7) link_NAG-ASN : angle 1.28527 / 0.86 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9347 (mtt) cc_final: 0.8973 (ttm) REVERT: A 112 MET cc_start: 0.9040 (tpp) cc_final: 0.8458 (tpp) REVERT: A 236 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8931 (mtm) REVERT: A 269 LEU cc_start: 0.9711 (mt) cc_final: 0.9440 (mp) REVERT: B 137 MET cc_start: 0.8962 (tpt) cc_final: 0.8575 (tpt) REVERT: C 70 MET cc_start: 0.9410 (mmt) cc_final: 0.8647 (mmm) REVERT: C 130 MET cc_start: 0.8503 (ttm) cc_final: 0.8089 (tmm) REVERT: C 177 GLU cc_start: 0.9084 (mp0) cc_final: 0.8771 (mp0) REVERT: D 58 MET cc_start: 0.9044 (mmm) cc_final: 0.8839 (tpp) REVERT: D 232 LEU cc_start: 0.9438 (mt) cc_final: 0.9106 (tp) REVERT: D 236 MET cc_start: 0.9540 (mtm) cc_final: 0.9214 (mtm) REVERT: D 258 PHE cc_start: 0.8791 (t80) cc_final: 0.8405 (t80) REVERT: D 396 SER cc_start: 0.9273 (m) cc_final: 0.9049 (p) REVERT: E 9 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8208 (tpt) REVERT: E 55 MET cc_start: 0.7940 (tpp) cc_final: 0.7218 (mmm) REVERT: E 155 GLU cc_start: 0.8986 (tt0) cc_final: 0.8404 (tp30) REVERT: E 224 GLN cc_start: 0.9568 (mm-40) cc_final: 0.9326 (mm-40) REVERT: F 441 MET cc_start: 0.6599 (ttm) cc_final: 0.6007 (ttm) REVERT: F 458 MET cc_start: 0.5650 (ttm) cc_final: 0.5037 (ttp) REVERT: F 462 ARG cc_start: 0.7532 (mtp85) cc_final: 0.6670 (mtt-85) REVERT: F 479 ASP cc_start: 0.8931 (t0) cc_final: 0.8549 (t0) REVERT: F 482 LYS cc_start: 0.9362 (mtpt) cc_final: 0.9063 (mtpt) REVERT: F 489 LEU cc_start: 0.9250 (mp) cc_final: 0.8824 (pp) REVERT: F 518 HIS cc_start: 0.8121 (m-70) cc_final: 0.7797 (m90) outliers start: 17 outliers final: 12 residues processed: 130 average time/residue: 0.0999 time to fit residues: 20.3244 Evaluate side-chains 127 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 LYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 82 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 170 optimal weight: 20.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 HIS ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.049924 restraints weight = 51068.394| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.65 r_work: 0.2616 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15447 Z= 0.198 Angle : 0.549 7.457 21049 Z= 0.274 Chirality : 0.042 0.235 2456 Planarity : 0.003 0.042 2541 Dihedral : 6.961 59.793 2661 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.25 % Allowed : 8.38 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.20), residues: 1766 helix: 2.66 (0.21), residues: 572 sheet: 0.53 (0.25), residues: 431 loop : 0.51 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.022 0.001 TYR B 299 PHE 0.014 0.001 PHE A 304 TRP 0.010 0.001 TRP E 426 HIS 0.005 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (15409) covalent geometry : angle 0.53749 / 0.27 (20941) SS BOND : bond 0.00131 / 0.07 ( 6) SS BOND : angle 0.39990 / 0.23 ( 12) hydrogen bonds : bond 0.03525 / 2.28 ( 735) hydrogen bonds : angle 4.12061 / 2.85 ( 2319) link_ALPHA1-2 : bond 0.00786 / 0.38 ( 3) link_ALPHA1-2 : angle 2.60516 / 1.45 ( 9) link_ALPHA1-3 : bond 0.00766 / 0.45 ( 7) link_ALPHA1-3 : angle 1.94533 / 1.20 ( 21) link_ALPHA1-6 : bond 0.00717 / 0.35 ( 5) link_ALPHA1-6 : angle 1.75599 / 1.07 ( 15) link_BETA1-4 : bond 0.00391 / 0.19 ( 10) link_BETA1-4 : angle 1.49237 / 0.97 ( 30) link_NAG-ASN : bond 0.00245 / 0.11 ( 7) link_NAG-ASN : angle 1.44164 / 0.95 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9351 (mtt) cc_final: 0.8891 (mmm) REVERT: A 112 MET cc_start: 0.9063 (tpp) cc_final: 0.8461 (tpp) REVERT: A 236 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8921 (mtm) REVERT: B 137 MET cc_start: 0.8975 (tpt) cc_final: 0.8578 (tpt) REVERT: C 70 MET cc_start: 0.9422 (mmt) cc_final: 0.8653 (mmm) REVERT: C 130 MET cc_start: 0.8559 (ttm) cc_final: 0.8122 (tmm) REVERT: C 177 GLU cc_start: 0.9048 (mp0) cc_final: 0.8632 (mp0) REVERT: D 90 MET cc_start: 0.9494 (tpp) cc_final: 0.9214 (tpp) REVERT: D 232 LEU cc_start: 0.9467 (mt) cc_final: 0.9178 (tp) REVERT: D 236 MET cc_start: 0.9529 (mtm) cc_final: 0.9261 (mtm) REVERT: E 55 MET cc_start: 0.7992 (tpp) cc_final: 0.7242 (mmm) REVERT: E 182 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8610 (mm-30) REVERT: E 224 GLN cc_start: 0.9581 (mm-40) cc_final: 0.9341 (mm-40) REVERT: F 441 MET cc_start: 0.6656 (ttm) cc_final: 0.6035 (ttm) REVERT: F 462 ARG cc_start: 0.7566 (mtp85) cc_final: 0.7214 (mtp85) REVERT: F 479 ASP cc_start: 0.8908 (t0) cc_final: 0.8523 (t0) REVERT: F 482 LYS cc_start: 0.9359 (mtpt) cc_final: 0.9059 (mtpt) REVERT: F 489 LEU cc_start: 0.9243 (mp) cc_final: 0.8960 (pp) REVERT: F 518 HIS cc_start: 0.8081 (m-70) cc_final: 0.7740 (m90) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 0.1142 time to fit residues: 22.8691 Evaluate side-chains 128 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 279 LYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 173 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 137 optimal weight: 0.3980 chunk 175 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 177 optimal weight: 20.0000 chunk 52 optimal weight: 0.0670 chunk 62 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.051195 restraints weight = 51086.529| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.70 r_work: 0.2656 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15447 Z= 0.103 Angle : 0.516 10.828 21049 Z= 0.254 Chirality : 0.041 0.239 2456 Planarity : 0.003 0.043 2541 Dihedral : 6.452 57.061 2660 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.13 % Allowed : 8.76 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.21), residues: 1766 helix: 2.71 (0.21), residues: 572 sheet: 0.59 (0.25), residues: 438 loop : 0.58 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.019 0.001 TYR E 299 PHE 0.011 0.001 PHE B 63 TRP 0.011 0.001 TRP E 426 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (15409) covalent geometry : angle 0.50479 / 0.25 (20941) SS BOND : bond 0.00103 / 0.05 ( 6) SS BOND : angle 0.37139 / 0.22 ( 12) hydrogen bonds : bond 0.03205 / 2.07 ( 735) hydrogen bonds : angle 3.95815 / 2.73 ( 2319) link_ALPHA1-2 : bond 0.00916 / 0.44 ( 3) link_ALPHA1-2 : angle 2.74200 / 1.53 ( 9) link_ALPHA1-3 : bond 0.00873 / 0.48 ( 7) link_ALPHA1-3 : angle 1.78347 / 1.11 ( 21) link_ALPHA1-6 : bond 0.00791 / 0.40 ( 5) link_ALPHA1-6 : angle 1.67242 / 1.02 ( 15) link_BETA1-4 : bond 0.00435 / 0.22 ( 10) link_BETA1-4 : angle 1.44967 / 0.99 ( 30) link_NAG-ASN : bond 0.00160 / 0.09 ( 7) link_NAG-ASN : angle 1.19365 / 0.79 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9341 (mtt) cc_final: 0.9010 (ttm) REVERT: A 112 MET cc_start: 0.9093 (tpp) cc_final: 0.8447 (tpp) REVERT: A 236 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8932 (mtm) REVERT: A 269 LEU cc_start: 0.9708 (mt) cc_final: 0.9459 (mp) REVERT: B 137 MET cc_start: 0.8972 (tpt) cc_final: 0.8592 (tpt) REVERT: B 297 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9094 (tt) REVERT: C 70 MET cc_start: 0.9400 (mmt) cc_final: 0.8616 (mmm) REVERT: C 130 MET cc_start: 0.8466 (ttm) cc_final: 0.8074 (tmm) REVERT: C 223 MET cc_start: 0.9038 (mmm) cc_final: 0.8734 (mmt) REVERT: D 58 MET cc_start: 0.9151 (tpp) cc_final: 0.8658 (tpp) REVERT: D 232 LEU cc_start: 0.9474 (mt) cc_final: 0.9133 (tp) REVERT: D 236 MET cc_start: 0.9505 (mtm) cc_final: 0.9142 (mtm) REVERT: D 258 PHE cc_start: 0.8787 (t80) cc_final: 0.8306 (t80) REVERT: E 9 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8028 (tpt) REVERT: E 155 GLU cc_start: 0.8982 (tt0) cc_final: 0.8400 (tp30) REVERT: E 182 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8736 (mm-30) REVERT: E 224 GLN cc_start: 0.9567 (mm-40) cc_final: 0.9331 (mm-40) REVERT: E 286 MET cc_start: 0.8923 (tpp) cc_final: 0.8536 (tpp) REVERT: F 462 ARG cc_start: 0.7566 (mtp85) cc_final: 0.7188 (mtp85) REVERT: F 479 ASP cc_start: 0.8976 (t0) cc_final: 0.8615 (t0) REVERT: F 482 LYS cc_start: 0.9374 (mtpt) cc_final: 0.9077 (mtpt) REVERT: F 511 LEU cc_start: 0.7820 (pt) cc_final: 0.6867 (tt) REVERT: F 518 HIS cc_start: 0.7968 (m-70) cc_final: 0.7651 (m90) outliers start: 18 outliers final: 11 residues processed: 135 average time/residue: 0.1044 time to fit residues: 21.6271 Evaluate side-chains 129 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 279 LYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain F residue 475 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 143 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 99 optimal weight: 0.0980 chunk 145 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 GLN D 229 GLN E 267 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.069262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.051283 restraints weight = 51123.901| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.70 r_work: 0.2664 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15447 Z= 0.108 Angle : 0.520 9.399 21049 Z= 0.254 Chirality : 0.041 0.241 2456 Planarity : 0.003 0.042 2541 Dihedral : 6.170 51.206 2660 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.19 % Allowed : 9.01 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.21), residues: 1766 helix: 2.70 (0.21), residues: 572 sheet: 0.57 (0.25), residues: 437 loop : 0.63 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.021 0.001 TYR E 299 PHE 0.014 0.001 PHE F 474 TRP 0.011 0.001 TRP E 426 HIS 0.003 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (15409) covalent geometry : angle 0.50910 / 0.25 (20941) SS BOND : bond 0.00101 / 0.05 ( 6) SS BOND : angle 0.34492 / 0.20 ( 12) hydrogen bonds : bond 0.03145 / 2.03 ( 735) hydrogen bonds : angle 3.91481 / 2.70 ( 2319) link_ALPHA1-2 : bond 0.00840 / 0.40 ( 3) link_ALPHA1-2 : angle 2.68226 / 1.49 ( 9) link_ALPHA1-3 : bond 0.00843 / 0.47 ( 7) link_ALPHA1-3 : angle 1.76556 / 1.10 ( 21) link_ALPHA1-6 : bond 0.00812 / 0.41 ( 5) link_ALPHA1-6 : angle 1.69009 / 1.02 ( 15) link_BETA1-4 : bond 0.00443 / 0.22 ( 10) link_BETA1-4 : angle 1.46438 / 0.98 ( 30) link_NAG-ASN : bond 0.00131 / 0.07 ( 7) link_NAG-ASN : angle 1.24630 / 0.82 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9334 (mtt) cc_final: 0.9020 (ttm) REVERT: A 112 MET cc_start: 0.9040 (tpp) cc_final: 0.8458 (tpp) REVERT: A 236 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8928 (mtm) REVERT: A 269 LEU cc_start: 0.9714 (mt) cc_final: 0.9457 (mp) REVERT: B 297 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9089 (tt) REVERT: C 70 MET cc_start: 0.9395 (mmt) cc_final: 0.8614 (mmm) REVERT: C 130 MET cc_start: 0.8494 (ttm) cc_final: 0.8096 (tmm) REVERT: C 177 GLU cc_start: 0.9071 (mp0) cc_final: 0.8702 (mp0) REVERT: C 223 MET cc_start: 0.9052 (mmm) cc_final: 0.8706 (mmt) REVERT: D 58 MET cc_start: 0.9064 (tpp) cc_final: 0.8576 (tpp) REVERT: D 232 LEU cc_start: 0.9473 (mt) cc_final: 0.9097 (tp) REVERT: D 236 MET cc_start: 0.9497 (mtm) cc_final: 0.9157 (mtm) REVERT: D 258 PHE cc_start: 0.8779 (t80) cc_final: 0.8304 (t80) REVERT: E 9 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8024 (tpt) REVERT: E 49 MET cc_start: 0.9080 (tpp) cc_final: 0.8681 (tpp) REVERT: E 155 GLU cc_start: 0.8982 (tt0) cc_final: 0.8411 (tp30) REVERT: E 182 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8675 (mm-30) REVERT: E 224 GLN cc_start: 0.9565 (mm-40) cc_final: 0.9335 (mm-40) REVERT: E 286 MET cc_start: 0.8930 (tpp) cc_final: 0.8547 (tpp) REVERT: F 441 MET cc_start: 0.6814 (ttm) cc_final: 0.6185 (ttm) REVERT: F 462 ARG cc_start: 0.7560 (mtp85) cc_final: 0.7192 (mtp85) REVERT: F 479 ASP cc_start: 0.8947 (t0) cc_final: 0.8554 (t0) REVERT: F 482 LYS cc_start: 0.9365 (mtpt) cc_final: 0.9053 (mtpt) REVERT: F 511 LEU cc_start: 0.7770 (pt) cc_final: 0.6848 (tt) outliers start: 19 outliers final: 14 residues processed: 127 average time/residue: 0.1119 time to fit residues: 21.8745 Evaluate side-chains 128 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 279 LYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain F residue 475 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 18 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 168 optimal weight: 40.0000 chunk 31 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 0.0010 chunk 62 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 229 GLN E 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.069514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.051418 restraints weight = 51300.103| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.76 r_work: 0.2669 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15447 Z= 0.106 Angle : 0.520 9.383 21049 Z= 0.254 Chirality : 0.041 0.240 2456 Planarity : 0.003 0.044 2541 Dihedral : 6.027 48.538 2660 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.06 % Allowed : 9.13 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.21), residues: 1766 helix: 2.69 (0.21), residues: 572 sheet: 0.60 (0.25), residues: 439 loop : 0.66 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.021 0.001 TYR E 299 PHE 0.013 0.001 PHE F 474 TRP 0.010 0.001 TRP E 426 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (15409) covalent geometry : angle 0.50879 / 0.25 (20941) SS BOND : bond 0.00106 / 0.05 ( 6) SS BOND : angle 0.31798 / 0.19 ( 12) hydrogen bonds : bond 0.03108 / 2.01 ( 735) hydrogen bonds : angle 3.90049 / 2.69 ( 2319) link_ALPHA1-2 : bond 0.00830 / 0.40 ( 3) link_ALPHA1-2 : angle 2.68497 / 1.49 ( 9) link_ALPHA1-3 : bond 0.00832 / 0.46 ( 7) link_ALPHA1-3 : angle 1.73473 / 1.08 ( 21) link_ALPHA1-6 : bond 0.00816 / 0.42 ( 5) link_ALPHA1-6 : angle 1.69150 / 1.02 ( 15) link_BETA1-4 : bond 0.00451 / 0.23 ( 10) link_BETA1-4 : angle 1.45757 / 0.98 ( 30) link_NAG-ASN : bond 0.00138 / 0.08 ( 7) link_NAG-ASN : angle 1.22150 / 0.80 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9335 (mtt) cc_final: 0.9039 (ttm) REVERT: A 112 MET cc_start: 0.9027 (tpp) cc_final: 0.8459 (tpp) REVERT: A 236 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8932 (mtm) REVERT: A 269 LEU cc_start: 0.9714 (mt) cc_final: 0.9458 (mp) REVERT: B 137 MET cc_start: 0.8674 (tpp) cc_final: 0.8367 (tpt) REVERT: B 297 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9086 (tt) REVERT: C 70 MET cc_start: 0.9394 (mmt) cc_final: 0.8609 (mmm) REVERT: C 130 MET cc_start: 0.8492 (ttm) cc_final: 0.8096 (tmm) REVERT: C 177 GLU cc_start: 0.9070 (mp0) cc_final: 0.8694 (mp0) REVERT: C 223 MET cc_start: 0.9047 (mmm) cc_final: 0.8702 (mmt) REVERT: D 58 MET cc_start: 0.9061 (tpp) cc_final: 0.8615 (tpp) REVERT: D 232 LEU cc_start: 0.9477 (mt) cc_final: 0.9111 (tp) REVERT: D 236 MET cc_start: 0.9495 (mtm) cc_final: 0.9136 (mtm) REVERT: D 258 PHE cc_start: 0.8749 (t80) cc_final: 0.8351 (t80) REVERT: E 9 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8043 (tpt) REVERT: E 49 MET cc_start: 0.9074 (tpp) cc_final: 0.8653 (tpp) REVERT: E 155 GLU cc_start: 0.8977 (tt0) cc_final: 0.8402 (tp30) REVERT: E 182 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8667 (mm-30) REVERT: E 224 GLN cc_start: 0.9562 (mm-40) cc_final: 0.9332 (mm-40) REVERT: E 286 MET cc_start: 0.8923 (tpp) cc_final: 0.8457 (tpp) REVERT: F 441 MET cc_start: 0.6624 (ttm) cc_final: 0.6202 (ttm) REVERT: F 458 MET cc_start: 0.5895 (ttm) cc_final: 0.5501 (ttp) REVERT: F 462 ARG cc_start: 0.7425 (mtp85) cc_final: 0.7057 (mtp85) REVERT: F 479 ASP cc_start: 0.8938 (t0) cc_final: 0.8550 (t0) REVERT: F 482 LYS cc_start: 0.9366 (mtpt) cc_final: 0.9062 (mtpt) REVERT: F 511 LEU cc_start: 0.7822 (pt) cc_final: 0.6936 (tt) outliers start: 17 outliers final: 12 residues processed: 129 average time/residue: 0.1185 time to fit residues: 23.4841 Evaluate side-chains 129 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 279 LYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain F residue 475 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 24 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 ASN C 239 GLN D 229 GLN E 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.069600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.051614 restraints weight = 50665.766| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.73 r_work: 0.2675 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15447 Z= 0.106 Angle : 0.517 9.050 21049 Z= 0.253 Chirality : 0.041 0.239 2456 Planarity : 0.003 0.044 2541 Dihedral : 5.841 48.170 2660 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.31 % Allowed : 9.07 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.21), residues: 1766 helix: 2.70 (0.21), residues: 573 sheet: 0.69 (0.25), residues: 436 loop : 0.61 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.020 0.001 TYR E 299 PHE 0.015 0.001 PHE C 308 TRP 0.010 0.001 TRP E 426 HIS 0.004 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (15409) covalent geometry : angle 0.50572 / 0.25 (20941) SS BOND : bond 0.00103 / 0.05 ( 6) SS BOND : angle 0.34167 / 0.20 ( 12) hydrogen bonds : bond 0.03084 / 1.99 ( 735) hydrogen bonds : angle 3.87865 / 2.67 ( 2319) link_ALPHA1-2 : bond 0.00817 / 0.39 ( 3) link_ALPHA1-2 : angle 2.67300 / 1.48 ( 9) link_ALPHA1-3 : bond 0.00842 / 0.46 ( 7) link_ALPHA1-3 : angle 1.70606 / 1.07 ( 21) link_ALPHA1-6 : bond 0.00821 / 0.42 ( 5) link_ALPHA1-6 : angle 1.69022 / 1.02 ( 15) link_BETA1-4 : bond 0.00465 / 0.24 ( 10) link_BETA1-4 : angle 1.45530 / 0.97 ( 30) link_NAG-ASN : bond 0.00144 / 0.08 ( 7) link_NAG-ASN : angle 1.20919 / 0.79 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2599.41 seconds wall clock time: 45 minutes 40.02 seconds (2740.02 seconds total)