Starting phenix.real_space_refine on Sat Mar 16 17:28:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sng_25225/03_2024/7sng_25225_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sng_25225/03_2024/7sng_25225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sng_25225/03_2024/7sng_25225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sng_25225/03_2024/7sng_25225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sng_25225/03_2024/7sng_25225_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sng_25225/03_2024/7sng_25225_neut.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.195 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 9632 2.51 5 N 2616 2.21 5 O 2876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 315": "OE1" <-> "OE2" Residue "C ASP 313": "OD1" <-> "OD2" Residue "C GLU 417": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15204 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLU A 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU A 504 " occ=0.50 residue: pdb=" N GLU B 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU B 504 " occ=0.50 residue: pdb=" N GLU C 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU C 504 " occ=0.50 residue: pdb=" N GLU D 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU D 504 " occ=0.50 Time building chain proxies: 7.92, per 1000 atoms: 0.52 Number of scatterers: 15204 At special positions: 0 Unit cell: (135.29, 96.28, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2876 8.00 N 2616 7.00 C 9632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.72 Conformation dependent library (CDL) restraints added in 2.8 seconds 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 8 sheets defined 43.3% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.793A pdb=" N PHE A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.735A pdb=" N HIS A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.546A pdb=" N GLN A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.746A pdb=" N PHE A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.282A pdb=" N ARG A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.717A pdb=" N GLU A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.645A pdb=" N ASP A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 454 through 476 removed outlier: 3.572A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.891A pdb=" N ASP A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 47 through 58 Processing helix chain 'B' and resid 76 through 89 Proline residue: B 86 - end of helix removed outlier: 3.810A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.585A pdb=" N TYR B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ALA B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 206 through 218 removed outlier: 3.809A pdb=" N ASN B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 3.745A pdb=" N PHE B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.623A pdb=" N GLU B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.531A pdb=" N ASP B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 476 removed outlier: 3.550A pdb=" N PHE B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 489 through 500 removed outlier: 4.080A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 47 through 58 Processing helix chain 'C' and resid 76 through 89 Proline residue: C 86 - end of helix removed outlier: 3.837A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 143 through 157 removed outlier: 3.612A pdb=" N TYR C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ALA C 149 " --> pdb=" O THR C 145 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 191 Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.757A pdb=" N PHE C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.250A pdb=" N ARG C 257 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 273 Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.626A pdb=" N GLU C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 435 through 447 removed outlier: 3.502A pdb=" N ASP C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 476 removed outlier: 3.562A pdb=" N PHE C 465 " --> pdb=" O ALA C 461 " (cutoff:3.500A) Proline residue: C 467 - end of helix Processing helix chain 'C' and resid 489 through 500 removed outlier: 4.042A pdb=" N ASP C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 47 through 58 Processing helix chain 'D' and resid 76 through 89 Proline residue: D 86 - end of helix removed outlier: 3.873A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 94 through 103 removed outlier: 3.534A pdb=" N GLU D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 143 through 157 removed outlier: 3.692A pdb=" N TYR D 147 " --> pdb=" O PRO D 143 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ALA D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'D' and resid 206 through 218 removed outlier: 3.805A pdb=" N ASN D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 removed outlier: 3.541A pdb=" N PHE D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 removed outlier: 4.294A pdb=" N ARG D 257 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 273 removed outlier: 3.521A pdb=" N GLN D 266 " --> pdb=" O ASN D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.695A pdb=" N GLU D 287 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 316 through 320 removed outlier: 3.604A pdb=" N THR D 319 " --> pdb=" O GLY D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 447 Processing helix chain 'D' and resid 454 through 476 removed outlier: 3.534A pdb=" N PHE D 465 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Proline residue: D 467 - end of helix Processing helix chain 'D' and resid 489 through 500 removed outlier: 4.046A pdb=" N ASP D 493 " --> pdb=" O PRO D 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 removed outlier: 6.418A pdb=" N ILE A 33 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N TYR A 139 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 35 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 421 removed outlier: 6.449A pdb=" N ALA A 367 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS A 232 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N ILE A 480 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 305 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N TYR A 482 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLN A 307 " --> pdb=" O TYR A 482 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 109 removed outlier: 6.491A pdb=" N ILE B 33 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TYR B 139 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE B 35 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE B 168 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE B 138 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 167 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 415 through 421 removed outlier: 6.699A pdb=" N ALA B 367 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS B 232 " --> pdb=" O GLN B 372 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA B 231 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N ILE B 355 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 233 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ARG B 357 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU B 235 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY B 359 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B 237 " --> pdb=" O GLY B 359 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ILE B 480 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU B 305 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N TYR B 482 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLN B 307 " --> pdb=" O TYR B 482 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 105 through 109 removed outlier: 6.420A pdb=" N ILE C 33 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR C 139 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE C 35 " --> pdb=" O TYR C 139 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG C 136 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE C 168 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE C 138 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 415 through 421 removed outlier: 6.760A pdb=" N ALA C 367 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS C 232 " --> pdb=" O GLN C 372 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA C 231 " --> pdb=" O PRO C 353 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ILE C 355 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C 233 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ARG C 357 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU C 235 " --> pdb=" O ARG C 357 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLY C 359 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE C 237 " --> pdb=" O GLY C 359 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N ILE C 480 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU C 305 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR C 482 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLN C 307 " --> pdb=" O TYR C 482 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 105 through 109 removed outlier: 6.485A pdb=" N ILE D 33 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR D 139 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE D 35 " --> pdb=" O TYR D 139 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG D 136 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE D 168 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE D 138 " --> pdb=" O ILE D 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 415 through 421 removed outlier: 6.719A pdb=" N ALA D 367 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS D 232 " --> pdb=" O GLN D 372 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ILE D 480 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU D 305 " --> pdb=" O ILE D 480 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TYR D 482 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN D 307 " --> pdb=" O TYR D 482 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.90 Time building geometry restraints manager: 6.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2534 1.32 - 1.44: 4163 1.44 - 1.57: 8623 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 15452 Sorted by residual: bond pdb=" CA LYS D 171 " pdb=" C LYS D 171 " ideal model delta sigma weight residual 1.528 1.477 0.051 1.11e-02 8.12e+03 2.11e+01 bond pdb=" N VAL A 169 " pdb=" CA VAL A 169 " ideal model delta sigma weight residual 1.458 1.406 0.052 1.17e-02 7.31e+03 1.97e+01 bond pdb=" N VAL D 169 " pdb=" CA VAL D 169 " ideal model delta sigma weight residual 1.458 1.407 0.051 1.20e-02 6.94e+03 1.81e+01 bond pdb=" C VAL A 169 " pdb=" O VAL A 169 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.07e-02 8.73e+03 1.75e+01 bond pdb=" C VAL D 169 " pdb=" O VAL D 169 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.13e-02 7.83e+03 1.47e+01 ... (remaining 15447 not shown) Histogram of bond angle deviations from ideal: 99.25 - 106.25: 449 106.25 - 113.25: 8097 113.25 - 120.26: 5744 120.26 - 127.26: 6431 127.26 - 134.26: 175 Bond angle restraints: 20896 Sorted by residual: angle pdb=" N GLY B 314 " pdb=" CA GLY B 314 " pdb=" C GLY B 314 " ideal model delta sigma weight residual 111.85 117.84 -5.99 1.06e+00 8.90e-01 3.19e+01 angle pdb=" C ASN B 311 " pdb=" N PRO B 312 " pdb=" CA PRO B 312 " ideal model delta sigma weight residual 119.24 113.54 5.70 1.04e+00 9.25e-01 3.00e+01 angle pdb=" N GLU D 170 " pdb=" CA GLU D 170 " pdb=" CB GLU D 170 " ideal model delta sigma weight residual 110.85 102.56 8.29 1.60e+00 3.91e-01 2.69e+01 angle pdb=" N GLY B 316 " pdb=" CA GLY B 316 " pdb=" C GLY B 316 " ideal model delta sigma weight residual 113.18 102.16 11.02 2.37e+00 1.78e-01 2.16e+01 angle pdb=" N GLU D 170 " pdb=" CA GLU D 170 " pdb=" C GLU D 170 " ideal model delta sigma weight residual 109.95 116.96 -7.01 1.59e+00 3.96e-01 1.94e+01 ... (remaining 20891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8413 17.98 - 35.97: 700 35.97 - 53.95: 135 53.95 - 71.93: 39 71.93 - 89.91: 17 Dihedral angle restraints: 9304 sinusoidal: 3868 harmonic: 5436 Sorted by residual: dihedral pdb=" CA MET D 411 " pdb=" C MET D 411 " pdb=" N PHE D 412 " pdb=" CA PHE D 412 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA MET A 411 " pdb=" C MET A 411 " pdb=" N PHE A 412 " pdb=" CA PHE A 412 " ideal model delta harmonic sigma weight residual 180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA MET C 411 " pdb=" C MET C 411 " pdb=" N PHE C 412 " pdb=" CA PHE C 412 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 9301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1539 0.040 - 0.080: 496 0.080 - 0.120: 168 0.120 - 0.159: 35 0.159 - 0.199: 2 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA VAL B 309 " pdb=" N VAL B 309 " pdb=" C VAL B 309 " pdb=" CB VAL B 309 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CB VAL D 169 " pdb=" CA VAL D 169 " pdb=" CG1 VAL D 169 " pdb=" CG2 VAL D 169 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA VAL A 369 " pdb=" N VAL A 369 " pdb=" C VAL A 369 " pdb=" CB VAL A 369 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 2237 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 311 " -0.066 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A 312 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 311 " 0.063 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO D 312 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO D 312 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 312 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 225 " -0.017 2.00e-02 2.50e+03 1.96e-02 9.65e+00 pdb=" CG TRP D 225 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP D 225 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP D 225 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 225 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 225 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 225 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 225 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 225 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 225 " -0.002 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1341 2.74 - 3.28: 15171 3.28 - 3.82: 26513 3.82 - 4.36: 34513 4.36 - 4.90: 56961 Nonbonded interactions: 134499 Sorted by model distance: nonbonded pdb=" O LYS A 47 " pdb=" OG1 THR A 51 " model vdw 2.201 2.440 nonbonded pdb=" O LYS C 47 " pdb=" OG1 THR C 51 " model vdw 2.205 2.440 nonbonded pdb=" O ILE B 196 " pdb=" NE2 GLN B 449 " model vdw 2.208 2.520 nonbonded pdb=" O LYS D 47 " pdb=" OG1 THR D 51 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR B 139 " pdb=" OE2 GLU B 170 " model vdw 2.218 2.440 ... (remaining 134494 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.50 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.310 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 41.510 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 0.066 15452 Z= 0.264 Angle : 0.634 11.017 20896 Z= 0.341 Chirality : 0.045 0.199 2240 Planarity : 0.006 0.098 2732 Dihedral : 14.539 89.913 5800 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.29 % Favored : 96.49 % Rotamer: Outliers : 0.25 % Allowed : 0.31 % Favored : 99.45 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.20), residues: 1852 helix: -0.33 (0.21), residues: 684 sheet: -0.80 (0.24), residues: 412 loop : -0.09 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP D 225 HIS 0.002 0.001 HIS D 451 PHE 0.017 0.001 PHE D 413 TYR 0.038 0.001 TYR D 139 ARG 0.004 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 237 time to evaluate : 1.799 Fit side-chains REVERT: C 37 MET cc_start: 0.9070 (mmm) cc_final: 0.8834 (mmt) REVERT: D 244 GLU cc_start: 0.7737 (mp0) cc_final: 0.7516 (mp0) outliers start: 4 outliers final: 2 residues processed: 241 average time/residue: 1.4351 time to fit residues: 377.7213 Evaluate side-chains 197 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain D residue 171 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN B 83 GLN C 83 GLN C 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 15452 Z= 0.549 Angle : 0.733 14.696 20896 Z= 0.372 Chirality : 0.050 0.163 2240 Planarity : 0.006 0.079 2732 Dihedral : 5.324 37.979 2061 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.67 % Favored : 96.22 % Rotamer: Outliers : 1.53 % Allowed : 9.01 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.19), residues: 1852 helix: -0.12 (0.20), residues: 716 sheet: -0.87 (0.24), residues: 408 loop : -0.24 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 225 HIS 0.007 0.001 HIS C 470 PHE 0.030 0.002 PHE D 413 TYR 0.030 0.002 TYR D 139 ARG 0.007 0.001 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 1.839 Fit side-chains REVERT: A 258 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7197 (t70) REVERT: A 345 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: A 503 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6829 (t80) REVERT: C 99 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7189 (mm-30) REVERT: D 389 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7464 (mt-10) outliers start: 25 outliers final: 11 residues processed: 227 average time/residue: 1.3190 time to fit residues: 328.4859 Evaluate side-chains 213 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 180 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 384 GLN A 414 ASN B 83 GLN C 83 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15452 Z= 0.220 Angle : 0.543 6.136 20896 Z= 0.282 Chirality : 0.043 0.151 2240 Planarity : 0.004 0.059 2732 Dihedral : 4.653 28.774 2057 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 1.04 % Allowed : 13.05 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1852 helix: 0.32 (0.20), residues: 712 sheet: -0.86 (0.24), residues: 408 loop : -0.20 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 164 HIS 0.003 0.001 HIS C 451 PHE 0.012 0.001 PHE D 413 TYR 0.016 0.001 TYR D 139 ARG 0.004 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 228 time to evaluate : 1.877 Fit side-chains REVERT: A 81 ARG cc_start: 0.7916 (ttt90) cc_final: 0.7585 (ttp80) REVERT: A 99 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7202 (mm-30) REVERT: A 258 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.6950 (t70) REVERT: A 503 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.6804 (t80) REVERT: C 99 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7149 (mm-30) REVERT: D 389 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7471 (mt-10) outliers start: 17 outliers final: 6 residues processed: 235 average time/residue: 1.3357 time to fit residues: 344.3086 Evaluate side-chains 219 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 210 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 177 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN B 83 GLN C 83 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15452 Z= 0.199 Angle : 0.522 5.908 20896 Z= 0.269 Chirality : 0.043 0.145 2240 Planarity : 0.004 0.055 2732 Dihedral : 4.439 20.985 2057 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 1.53 % Allowed : 15.13 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1852 helix: 0.55 (0.20), residues: 712 sheet: -0.82 (0.24), residues: 408 loop : -0.11 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 53 HIS 0.003 0.001 HIS D 451 PHE 0.018 0.001 PHE C 88 TYR 0.012 0.001 TYR A 249 ARG 0.005 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 228 time to evaluate : 1.719 Fit side-chains REVERT: A 37 MET cc_start: 0.9041 (mmt) cc_final: 0.8353 (mmt) REVERT: A 81 ARG cc_start: 0.7975 (ttt90) cc_final: 0.7603 (ttp80) REVERT: A 99 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7269 (mm-30) REVERT: A 258 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6921 (t70) REVERT: A 503 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6839 (t80) REVERT: C 99 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7216 (mm-30) REVERT: D 389 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7423 (mt-10) outliers start: 25 outliers final: 10 residues processed: 237 average time/residue: 1.3924 time to fit residues: 361.1137 Evaluate side-chains 226 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 213 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.4980 chunk 100 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 122 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN B 83 GLN C 83 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15452 Z= 0.331 Angle : 0.587 7.378 20896 Z= 0.299 Chirality : 0.045 0.137 2240 Planarity : 0.005 0.052 2732 Dihedral : 4.630 21.474 2056 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 1.59 % Allowed : 16.30 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1852 helix: 0.44 (0.20), residues: 720 sheet: -0.95 (0.24), residues: 420 loop : -0.06 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 53 HIS 0.005 0.001 HIS C 470 PHE 0.017 0.001 PHE D 413 TYR 0.015 0.002 TYR A 401 ARG 0.006 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 216 time to evaluate : 1.621 Fit side-chains REVERT: A 258 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7085 (t70) REVERT: A 503 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6869 (t80) REVERT: B 286 ASP cc_start: 0.8473 (m-30) cc_final: 0.8122 (m-30) REVERT: C 99 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7209 (mm-30) REVERT: D 389 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: D 473 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6720 (mp0) outliers start: 26 outliers final: 12 residues processed: 230 average time/residue: 1.2940 time to fit residues: 326.8362 Evaluate side-chains 225 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.2980 chunk 160 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN C 83 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15452 Z= 0.297 Angle : 0.568 7.432 20896 Z= 0.291 Chirality : 0.044 0.139 2240 Planarity : 0.004 0.050 2732 Dihedral : 4.585 21.510 2056 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.54 % Rotamer: Outliers : 1.53 % Allowed : 17.03 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.20), residues: 1852 helix: 0.51 (0.20), residues: 716 sheet: -0.97 (0.24), residues: 420 loop : -0.09 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 53 HIS 0.004 0.001 HIS C 470 PHE 0.015 0.001 PHE C 102 TYR 0.014 0.001 TYR A 401 ARG 0.007 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 221 time to evaluate : 1.658 Fit side-chains REVERT: A 37 MET cc_start: 0.9008 (mmt) cc_final: 0.8501 (mmt) REVERT: A 258 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7046 (t70) REVERT: A 503 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6894 (t80) REVERT: B 286 ASP cc_start: 0.8472 (m-30) cc_final: 0.8113 (m-30) REVERT: C 99 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7198 (mm-30) REVERT: D 389 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7462 (mt-10) REVERT: D 473 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6741 (mp0) outliers start: 25 outliers final: 13 residues processed: 236 average time/residue: 1.3782 time to fit residues: 355.6364 Evaluate side-chains 231 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 215 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 0.0570 chunk 130 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN D 384 GLN D 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15452 Z= 0.272 Angle : 0.559 6.822 20896 Z= 0.286 Chirality : 0.044 0.139 2240 Planarity : 0.004 0.050 2732 Dihedral : 4.540 21.426 2056 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 1.78 % Allowed : 16.97 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1852 helix: 0.55 (0.20), residues: 716 sheet: -0.97 (0.24), residues: 420 loop : -0.08 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 53 HIS 0.004 0.001 HIS C 470 PHE 0.013 0.001 PHE C 102 TYR 0.013 0.001 TYR B 249 ARG 0.007 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 227 time to evaluate : 1.886 Fit side-chains REVERT: A 37 MET cc_start: 0.8991 (mmt) cc_final: 0.8534 (mmt) REVERT: A 99 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7440 (mm-30) REVERT: A 258 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7051 (t70) REVERT: B 286 ASP cc_start: 0.8454 (m-30) cc_final: 0.8098 (m-30) REVERT: C 320 LYS cc_start: 0.8203 (mppt) cc_final: 0.7948 (mptt) REVERT: D 389 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: D 473 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6761 (mp0) outliers start: 29 outliers final: 14 residues processed: 246 average time/residue: 1.3034 time to fit residues: 352.5309 Evaluate side-chains 229 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 213 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 GLN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15452 Z= 0.308 Angle : 0.584 7.479 20896 Z= 0.298 Chirality : 0.045 0.137 2240 Planarity : 0.004 0.050 2732 Dihedral : 4.603 21.584 2056 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 1.47 % Allowed : 18.26 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1852 helix: 0.52 (0.20), residues: 716 sheet: -0.97 (0.24), residues: 420 loop : -0.09 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 53 HIS 0.004 0.001 HIS C 470 PHE 0.015 0.001 PHE C 413 TYR 0.014 0.002 TYR B 249 ARG 0.007 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 215 time to evaluate : 1.736 Fit side-chains REVERT: A 37 MET cc_start: 0.8981 (mmt) cc_final: 0.8567 (mmt) REVERT: A 99 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7480 (mm-30) REVERT: A 182 ARG cc_start: 0.7413 (ptp-110) cc_final: 0.7207 (ptp90) REVERT: A 258 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7106 (t70) REVERT: B 286 ASP cc_start: 0.8463 (m-30) cc_final: 0.8169 (m-30) REVERT: D 389 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: D 473 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6799 (mp0) outliers start: 24 outliers final: 15 residues processed: 230 average time/residue: 1.3265 time to fit residues: 334.9111 Evaluate side-chains 227 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 210 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 156 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN D 384 GLN D 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15452 Z= 0.178 Angle : 0.522 6.793 20896 Z= 0.268 Chirality : 0.042 0.142 2240 Planarity : 0.004 0.051 2732 Dihedral : 4.330 20.191 2056 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 1.16 % Allowed : 18.63 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1852 helix: 0.75 (0.20), residues: 708 sheet: -0.87 (0.24), residues: 420 loop : -0.07 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 53 HIS 0.002 0.001 HIS D 451 PHE 0.010 0.001 PHE C 102 TYR 0.015 0.001 TYR B 249 ARG 0.008 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 220 time to evaluate : 1.744 Fit side-chains REVERT: A 37 MET cc_start: 0.8966 (mmt) cc_final: 0.8630 (mmt) REVERT: A 258 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6903 (t70) REVERT: B 286 ASP cc_start: 0.8429 (m-30) cc_final: 0.8145 (m-30) REVERT: B 372 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8433 (tt0) REVERT: C 320 LYS cc_start: 0.8238 (mppt) cc_final: 0.8036 (mptt) REVERT: D 389 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: D 473 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6791 (mp0) outliers start: 19 outliers final: 13 residues processed: 231 average time/residue: 1.3518 time to fit residues: 342.5837 Evaluate side-chains 229 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 213 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 6.9990 chunk 106 optimal weight: 0.4980 chunk 82 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 GLN D 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15452 Z= 0.291 Angle : 0.588 9.965 20896 Z= 0.297 Chirality : 0.044 0.171 2240 Planarity : 0.004 0.050 2732 Dihedral : 4.501 20.358 2056 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 1.16 % Allowed : 19.12 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1852 helix: 0.64 (0.20), residues: 712 sheet: -0.75 (0.25), residues: 412 loop : -0.13 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 53 HIS 0.004 0.001 HIS C 470 PHE 0.018 0.001 PHE A 102 TYR 0.015 0.001 TYR A 401 ARG 0.009 0.000 ARG C 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 209 time to evaluate : 1.608 Fit side-chains REVERT: A 37 MET cc_start: 0.8979 (mmt) cc_final: 0.8562 (mmt) REVERT: A 258 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7043 (t70) REVERT: B 372 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8572 (tt0) REVERT: C 320 LYS cc_start: 0.8206 (mppt) cc_final: 0.8000 (mptt) REVERT: D 389 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: D 473 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6788 (mp0) outliers start: 19 outliers final: 14 residues processed: 221 average time/residue: 1.3096 time to fit residues: 317.9760 Evaluate side-chains 225 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 208 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 21 optimal weight: 0.0010 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN C 383 GLN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 GLN D 414 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.165881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131425 restraints weight = 16076.095| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.00 r_work: 0.3209 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15452 Z= 0.153 Angle : 0.523 10.463 20896 Z= 0.268 Chirality : 0.042 0.143 2240 Planarity : 0.004 0.051 2732 Dihedral : 4.227 19.860 2056 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 0.92 % Allowed : 19.61 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1852 helix: 0.91 (0.20), residues: 704 sheet: -0.69 (0.25), residues: 412 loop : -0.08 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 53 HIS 0.002 0.000 HIS B 186 PHE 0.010 0.001 PHE C 102 TYR 0.016 0.001 TYR A 249 ARG 0.012 0.000 ARG A 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5722.09 seconds wall clock time: 101 minutes 33.74 seconds (6093.74 seconds total)