Starting phenix.real_space_refine on Thu Sep 26 05:58:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t90_25749/09_2024/7t90_25749_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t90_25749/09_2024/7t90_25749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t90_25749/09_2024/7t90_25749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t90_25749/09_2024/7t90_25749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t90_25749/09_2024/7t90_25749_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t90_25749/09_2024/7t90_25749_neut.cif" } resolution = 3.32 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= -0.004 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4680 atoms to isotropic. 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 58 5.16 5 C 5384 2.51 5 N 1431 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8451 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2042 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 276, 2028 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 265} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 79 Conformer: "B" Number of residues, atoms: 276, 2028 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 265} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 79 bond proxies already assigned to first conformer: 2063 Chain: "B" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1707 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2541 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 403 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1747 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A 427 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 427 " occ=0.50 Time building chain proxies: 6.57, per 1000 atoms: 0.78 Number of scatterers: 8451 At special positions: 0 Unit cell: (90.95, 122.4, 125.8, 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 58 16.00 O 1578 8.00 N 1431 7.00 C 5384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.5 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 38.3% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 22 through 51 removed outlier: 3.949A pdb=" N ILE A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 30 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS A 49 " --> pdb=" O MET A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 59 through 87 removed outlier: 3.898A pdb=" N SER A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 127 removed outlier: 4.224A pdb=" N VAL A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 136 through 162 Proline residue: A 157 - end of helix removed outlier: 3.629A pdb=" N LEU A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.514A pdb=" N PHE A 181 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 214 removed outlier: 3.693A pdb=" N THR A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Proline residue: A 198 - end of helix removed outlier: 4.037A pdb=" N LYS A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 413 removed outlier: 3.706A pdb=" N ALA A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Proline residue: A 402 - end of helix removed outlier: 3.937A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 431 removed outlier: 4.279A pdb=" N CYS A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.855A pdb=" N LYS A 452 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 removed outlier: 3.543A pdb=" N GLU B 14 " --> pdb=" O LYS B 10 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.749A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.650A pdb=" N LYS B 211 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N HIS B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 256 Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.575A pdb=" N ILE B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 329 through 351 removed outlier: 4.014A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 removed outlier: 4.277A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.874A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.966A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 191 removed outlier: 3.757A pdb=" N ASP B 201 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 190 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU B 38 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N ALA B 221 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 39 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N ALA B 227 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.527A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 331 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.699A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 103 through 105 removed outlier: 3.550A pdb=" N ALA C 113 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 112 " --> pdb=" O TYR C 124 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.918A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.559A pdb=" N SER C 191 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 200 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.529A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.159A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.549A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.125A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 34 through 39 removed outlier: 6.887A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.993A pdb=" N PHE E 212 " --> pdb=" O CYS E 159 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.076A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.822A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1366 1.31 - 1.43: 2406 1.43 - 1.56: 4775 1.56 - 1.69: 0 1.69 - 1.82: 82 Bond restraints: 8629 Sorted by residual: bond pdb=" C2 ACH A 501 " pdb=" N1 ACH A 501 " ideal model delta sigma weight residual 1.506 1.421 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" CA ILE A 165 " pdb=" CB ILE A 165 " ideal model delta sigma weight residual 1.540 1.486 0.054 1.36e-02 5.41e+03 1.60e+01 bond pdb=" CA SER A 433 " pdb=" CB SER A 433 " ideal model delta sigma weight residual 1.528 1.470 0.059 1.56e-02 4.11e+03 1.41e+01 bond pdb=" C TRP A 422 " pdb=" O TRP A 422 " ideal model delta sigma weight residual 1.236 1.279 -0.042 1.15e-02 7.56e+03 1.36e+01 bond pdb=" N ILE A 217 " pdb=" CA ILE A 217 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.22e-02 6.72e+03 1.29e+01 ... (remaining 8624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 11471 2.72 - 5.45: 233 5.45 - 8.17: 27 8.17 - 10.90: 9 10.90 - 13.62: 4 Bond angle restraints: 11744 Sorted by residual: angle pdb=" N THR A 170 " pdb=" CA THR A 170 " pdb=" C THR A 170 " ideal model delta sigma weight residual 112.90 99.28 13.62 1.31e+00 5.83e-01 1.08e+02 angle pdb=" N ASN A 419 " pdb=" CA ASN A 419 " pdb=" C ASN A 419 " ideal model delta sigma weight residual 113.19 101.58 11.61 1.19e+00 7.06e-01 9.52e+01 angle pdb=" N LEU A 82 " pdb=" CA LEU A 82 " pdb=" C LEU A 82 " ideal model delta sigma weight residual 111.28 102.19 9.09 1.09e+00 8.42e-01 6.95e+01 angle pdb=" N SER A 182 " pdb=" CA SER A 182 " pdb=" C SER A 182 " ideal model delta sigma weight residual 112.88 104.64 8.24 1.29e+00 6.01e-01 4.08e+01 angle pdb=" C PRO A 437 " pdb=" CA PRO A 437 " pdb=" CB PRO A 437 " ideal model delta sigma weight residual 113.06 103.26 9.80 1.59e+00 3.96e-01 3.80e+01 ... (remaining 11739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4640 17.93 - 35.86: 343 35.86 - 53.80: 65 53.80 - 71.73: 4 71.73 - 89.66: 1 Dihedral angle restraints: 5053 sinusoidal: 1795 harmonic: 3258 Sorted by residual: dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 176 " pdb=" CB CYS A 176 " ideal model delta sinusoidal sigma weight residual 93.00 43.05 49.95 1 1.00e+01 1.00e-02 3.42e+01 dihedral pdb=" CA HIS C 225 " pdb=" C HIS C 225 " pdb=" N GLU C 226 " pdb=" CA GLU C 226 " ideal model delta harmonic sigma weight residual -180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 5050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1188 0.083 - 0.166: 144 0.166 - 0.249: 15 0.249 - 0.332: 11 0.332 - 0.415: 6 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CA ASN A 183 " pdb=" N ASN A 183 " pdb=" C ASN A 183 " pdb=" CB ASN A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CB ILE A 72 " pdb=" CA ILE A 72 " pdb=" CG1 ILE A 72 " pdb=" CG2 ILE A 72 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA LEU A 82 " pdb=" N LEU A 82 " pdb=" C LEU A 82 " pdb=" CB LEU A 82 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.47e+00 ... (remaining 1361 not shown) Planarity restraints: 1483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BTRP A 427 " -0.024 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C BTRP A 427 " 0.087 2.00e-02 2.50e+03 pdb=" O BTRP A 427 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU A 428 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 163 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C GLN A 163 " 0.064 2.00e-02 2.50e+03 pdb=" O GLN A 163 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE A 164 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 408 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C LEU A 408 " 0.062 2.00e-02 2.50e+03 pdb=" O LEU A 408 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE A 409 " -0.021 2.00e-02 2.50e+03 ... (remaining 1480 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 265 2.70 - 3.25: 8232 3.25 - 3.80: 12611 3.80 - 4.35: 16056 4.35 - 4.90: 27493 Nonbonded interactions: 64657 Sorted by model distance: nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.146 3.040 nonbonded pdb=" O LEU A 43 " pdb=" OG SER A 47 " model vdw 2.162 3.040 nonbonded pdb=" ND2 ASN C 119 " pdb=" O GLY C 144 " model vdw 2.190 3.120 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.226 3.040 nonbonded pdb=" O SER C 67 " pdb=" OG SER C 67 " model vdw 2.228 3.040 ... (remaining 64652 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.950 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.006 0.085 8629 Z= 0.368 Angle : 0.945 13.621 11744 Z= 0.628 Chirality : 0.063 0.415 1364 Planarity : 0.005 0.050 1483 Dihedral : 12.713 89.660 2944 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.23 % Allowed : 0.92 % Favored : 98.85 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 3.12 % 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: -0.77 (0.26), residues: 1107 helix: 1.79 (0.29), residues: 337 sheet: -1.36 (0.33), residues: 262 loop : -1.64 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.006 0.001 HIS C 225 PHE 0.015 0.001 PHE C 235 TYR 0.021 0.002 TYR A 426 ARG 0.004 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.5377 (mmt) cc_final: 0.5110 (mmt) REVERT: A 444 ASN cc_start: 0.8528 (t0) cc_final: 0.8098 (t0) REVERT: B 187 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7979 (tm-30) REVERT: B 246 GLU cc_start: 0.7636 (tt0) cc_final: 0.7152 (mt-10) REVERT: E 38 ARG cc_start: 0.8073 (ptt90) cc_final: 0.7818 (ptt180) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.1984 time to fit residues: 49.6968 Evaluate side-chains 130 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 108 ASN A 436 ASN C 119 ASN E 35 HIS E 113 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8629 Z= 0.275 Angle : 0.639 9.252 11744 Z= 0.344 Chirality : 0.045 0.215 1364 Planarity : 0.004 0.037 1483 Dihedral : 4.847 32.844 1205 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.96 % Allowed : 9.12 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.49 (0.26), residues: 1107 helix: 1.99 (0.28), residues: 354 sheet: -1.25 (0.32), residues: 265 loop : -1.54 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.007 0.001 HIS C 225 PHE 0.011 0.001 PHE C 235 TYR 0.021 0.002 TYR E 94 ARG 0.004 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: B 246 GLU cc_start: 0.7591 (tt0) cc_final: 0.7038 (mt-10) REVERT: E 38 ARG cc_start: 0.8073 (ptt90) cc_final: 0.7740 (ptt180) REVERT: E 82 GLN cc_start: 0.6274 (mm110) cc_final: 0.5817 (mp10) REVERT: E 156 SER cc_start: 0.8335 (t) cc_final: 0.8125 (m) outliers start: 17 outliers final: 10 residues processed: 148 average time/residue: 0.1696 time to fit residues: 36.1784 Evaluate side-chains 130 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 99 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 0.3980 chunk 27 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 8629 Z= 0.193 Angle : 0.568 9.323 11744 Z= 0.305 Chirality : 0.043 0.178 1364 Planarity : 0.004 0.037 1483 Dihedral : 4.381 19.767 1205 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.73 % Allowed : 12.93 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1107 helix: 2.28 (0.28), residues: 352 sheet: -0.99 (0.32), residues: 268 loop : -1.39 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS C 225 PHE 0.011 0.001 PHE A 451 TYR 0.017 0.001 TYR E 190 ARG 0.004 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: B 246 GLU cc_start: 0.7595 (tt0) cc_final: 0.7045 (mt-10) REVERT: E 82 GLN cc_start: 0.6029 (mm110) cc_final: 0.5736 (mp10) outliers start: 15 outliers final: 8 residues processed: 145 average time/residue: 0.1805 time to fit residues: 37.6291 Evaluate side-chains 132 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 99 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 0.0050 chunk 105 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 8629 Z= 0.191 Angle : 0.548 9.379 11744 Z= 0.294 Chirality : 0.043 0.167 1364 Planarity : 0.003 0.038 1483 Dihedral : 4.236 18.460 1205 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.85 % Allowed : 14.78 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 1107 helix: 2.43 (0.28), residues: 353 sheet: -0.95 (0.31), residues: 272 loop : -1.24 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.005 0.001 HIS B 196 PHE 0.009 0.001 PHE A 451 TYR 0.017 0.001 TYR E 190 ARG 0.004 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 436 ASN cc_start: 0.7150 (OUTLIER) cc_final: 0.6891 (m110) REVERT: B 246 GLU cc_start: 0.7615 (tt0) cc_final: 0.7088 (mt-10) REVERT: E 82 GLN cc_start: 0.6004 (mm110) cc_final: 0.5736 (mp10) outliers start: 16 outliers final: 13 residues processed: 142 average time/residue: 0.1693 time to fit residues: 35.0853 Evaluate side-chains 138 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 140 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8629 Z= 0.342 Angle : 0.644 9.908 11744 Z= 0.345 Chirality : 0.045 0.174 1364 Planarity : 0.004 0.039 1483 Dihedral : 4.761 23.203 1205 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.42 % Allowed : 15.13 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1107 helix: 2.20 (0.28), residues: 352 sheet: -1.02 (0.32), residues: 258 loop : -1.37 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 47 HIS 0.010 0.002 HIS B 196 PHE 0.012 0.001 PHE E 110 TYR 0.021 0.002 TYR B 320 ARG 0.003 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: A 188 PHE cc_start: 0.5881 (OUTLIER) cc_final: 0.5546 (t80) REVERT: B 17 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7815 (mptt) REVERT: B 246 GLU cc_start: 0.7704 (tt0) cc_final: 0.7057 (mt-10) REVERT: E 82 GLN cc_start: 0.6288 (mm110) cc_final: 0.5972 (mp10) REVERT: E 156 SER cc_start: 0.8365 (t) cc_final: 0.8033 (m) outliers start: 21 outliers final: 17 residues processed: 136 average time/residue: 0.1729 time to fit residues: 33.9928 Evaluate side-chains 133 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8629 Z= 0.283 Angle : 0.605 9.974 11744 Z= 0.323 Chirality : 0.044 0.176 1364 Planarity : 0.004 0.038 1483 Dihedral : 4.653 22.673 1205 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.12 % Allowed : 15.59 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.13 (0.26), residues: 1107 helix: 2.29 (0.28), residues: 352 sheet: -1.01 (0.32), residues: 258 loop : -1.34 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.010 0.001 HIS C 225 PHE 0.010 0.001 PHE E 110 TYR 0.017 0.002 TYR E 190 ARG 0.005 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 188 PHE cc_start: 0.5936 (OUTLIER) cc_final: 0.5536 (t80) REVERT: B 17 LYS cc_start: 0.8018 (mmtm) cc_final: 0.7797 (mptt) REVERT: C 220 GLN cc_start: 0.7455 (mt0) cc_final: 0.7164 (mt0) REVERT: E 82 GLN cc_start: 0.6320 (mm110) cc_final: 0.5969 (mp10) REVERT: E 156 SER cc_start: 0.8356 (t) cc_final: 0.8016 (m) outliers start: 27 outliers final: 18 residues processed: 141 average time/residue: 0.1779 time to fit residues: 36.3672 Evaluate side-chains 136 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 77 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.153 8629 Z= 0.218 Angle : 0.561 9.922 11744 Z= 0.298 Chirality : 0.042 0.177 1364 Planarity : 0.003 0.038 1483 Dihedral : 4.339 21.269 1205 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.54 % Allowed : 16.51 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1107 helix: 2.44 (0.28), residues: 355 sheet: -0.82 (0.33), residues: 252 loop : -1.19 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.010 0.001 HIS B 196 PHE 0.009 0.001 PHE C 335 TYR 0.024 0.001 TYR B 303 ARG 0.003 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 188 PHE cc_start: 0.5909 (OUTLIER) cc_final: 0.5493 (t80) REVERT: A 406 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6068 (mpp) REVERT: C 220 GLN cc_start: 0.7405 (mt0) cc_final: 0.7115 (mt0) REVERT: E 156 SER cc_start: 0.8319 (t) cc_final: 0.7977 (m) outliers start: 22 outliers final: 15 residues processed: 144 average time/residue: 0.1850 time to fit residues: 38.0243 Evaluate side-chains 138 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 140 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 8629 Z= 0.378 Angle : 0.652 10.323 11744 Z= 0.350 Chirality : 0.046 0.181 1364 Planarity : 0.004 0.040 1483 Dihedral : 4.857 26.144 1205 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.00 % Allowed : 16.28 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.17 (0.26), residues: 1107 helix: 2.23 (0.28), residues: 352 sheet: -1.05 (0.32), residues: 263 loop : -1.32 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 47 HIS 0.008 0.001 HIS B 196 PHE 0.012 0.002 PHE C 180 TYR 0.019 0.002 TYR B 303 ARG 0.006 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 188 PHE cc_start: 0.5889 (OUTLIER) cc_final: 0.5351 (t80) REVERT: A 406 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6100 (mpp) REVERT: B 17 LYS cc_start: 0.8039 (mmtm) cc_final: 0.7818 (mptt) REVERT: C 52 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7486 (mtt-85) REVERT: E 82 GLN cc_start: 0.6363 (mm110) cc_final: 0.6024 (mp10) REVERT: E 156 SER cc_start: 0.8431 (t) cc_final: 0.8096 (m) outliers start: 26 outliers final: 19 residues processed: 134 average time/residue: 0.1832 time to fit residues: 34.9596 Evaluate side-chains 133 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 8629 Z= 0.265 Angle : 0.587 10.239 11744 Z= 0.315 Chirality : 0.043 0.178 1364 Planarity : 0.003 0.039 1483 Dihedral : 4.588 23.690 1205 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.31 % Allowed : 18.01 % Favored : 79.68 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % 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: 0.02 (0.26), residues: 1107 helix: 2.30 (0.28), residues: 354 sheet: -0.81 (0.33), residues: 250 loop : -1.24 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.007 0.001 HIS C 225 PHE 0.010 0.001 PHE C 335 TYR 0.018 0.001 TYR B 303 ARG 0.007 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 188 PHE cc_start: 0.5882 (OUTLIER) cc_final: 0.5375 (t80) REVERT: A 406 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6104 (mpp) REVERT: C 52 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7432 (mtt-85) REVERT: C 220 GLN cc_start: 0.7542 (mt0) cc_final: 0.7324 (mt0) REVERT: E 156 SER cc_start: 0.8383 (t) cc_final: 0.8029 (m) outliers start: 20 outliers final: 15 residues processed: 131 average time/residue: 0.1776 time to fit residues: 33.4317 Evaluate side-chains 133 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 8629 Z= 0.284 Angle : 0.610 10.509 11744 Z= 0.325 Chirality : 0.044 0.183 1364 Planarity : 0.004 0.039 1483 Dihedral : 4.608 23.733 1205 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.42 % Allowed : 18.01 % Favored : 79.56 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1107 helix: 2.31 (0.28), residues: 353 sheet: -0.87 (0.32), residues: 258 loop : -1.28 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.007 0.001 HIS C 225 PHE 0.009 0.001 PHE E 110 TYR 0.018 0.001 TYR B 303 ARG 0.007 0.000 ARG C 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 188 PHE cc_start: 0.5837 (OUTLIER) cc_final: 0.5387 (t80) REVERT: A 406 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6107 (mpp) REVERT: C 52 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7444 (mtt-85) REVERT: C 220 GLN cc_start: 0.7543 (mt0) cc_final: 0.7331 (mt0) REVERT: E 82 GLN cc_start: 0.6262 (mm110) cc_final: 0.5913 (mp10) REVERT: E 156 SER cc_start: 0.8398 (t) cc_final: 0.8040 (m) outliers start: 21 outliers final: 17 residues processed: 130 average time/residue: 0.1740 time to fit residues: 32.3608 Evaluate side-chains 134 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.135417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.105658 restraints weight = 28024.255| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 4.16 r_work: 0.3299 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 8629 Z= 0.203 Angle : 0.561 10.123 11744 Z= 0.299 Chirality : 0.043 0.184 1364 Planarity : 0.003 0.037 1483 Dihedral : 4.322 20.223 1205 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.08 % Allowed : 18.48 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.17 (0.26), residues: 1107 helix: 2.35 (0.28), residues: 357 sheet: -0.64 (0.33), residues: 250 loop : -1.15 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS B 196 PHE 0.011 0.001 PHE C 335 TYR 0.016 0.001 TYR B 303 ARG 0.007 0.000 ARG C 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2096.71 seconds wall clock time: 37 minutes 56.44 seconds (2276.44 seconds total)