Starting phenix.real_space_refine on Wed Jun 11 02:23:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t90_25749/06_2025/7t90_25749_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t90_25749/06_2025/7t90_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/cci-nas-00/data/ceres_data/7t90_25749/06_2025/7t90_25749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t90_25749/06_2025/7t90_25749.map" model { file = "/net/cci-nas-00/data/ceres_data/7t90_25749/06_2025/7t90_25749_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t90_25749/06_2025/7t90_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.76, per 1000 atoms: 0.80 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: 2.32 Conformation dependent library (CDL) restraints added in 1.7 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: 0.91 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: 2.21 Time building geometry restraints manager: 2.71 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.900 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.780 ------------------------------------------------------------------------------- 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 8632 Z= 0.355 Angle : 0.945 13.621 11750 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 Details of bonding type rmsd hydrogen bonds : bond 0.21072 ( 382) hydrogen bonds : angle 7.41985 ( 1075) SS BOND : bond 0.00341 ( 3) SS BOND : angle 1.03421 ( 6) covalent geometry : bond 0.00551 ( 8629) covalent geometry : angle 0.94539 (11744) *********************** 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 to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.926 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: 0.1990 time to fit residues: 50.0100 Evaluate side-chains 130 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 436 ASN C 119 ASN E 35 HIS E 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.133003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102885 restraints weight = 28804.635| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 4.03 r_work: 0.3258 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 8632 Z= 0.210 Angle : 0.665 9.420 11750 Z= 0.359 Chirality : 0.046 0.223 1364 Planarity : 0.004 0.037 1483 Dihedral : 4.963 32.813 1205 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.96 % Allowed : 9.70 % Favored : 88.34 % 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: -0.58 (0.25), residues: 1107 helix: 1.95 (0.28), residues: 352 sheet: -1.30 (0.32), residues: 265 loop : -1.61 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.007 0.001 HIS C 225 PHE 0.014 0.001 PHE C 235 TYR 0.023 0.002 TYR E 94 ARG 0.004 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.05526 ( 382) hydrogen bonds : angle 5.33731 ( 1075) SS BOND : bond 0.00620 ( 3) SS BOND : angle 1.11968 ( 6) covalent geometry : bond 0.00496 ( 8629) covalent geometry : angle 0.66457 (11744) *********************** 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 151 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7864 (tm-30) REVERT: B 246 GLU cc_start: 0.8016 (tt0) cc_final: 0.7382 (mt-10) REVERT: E 82 GLN cc_start: 0.6477 (mm110) cc_final: 0.5946 (mp10) outliers start: 17 outliers final: 10 residues processed: 147 average time/residue: 0.1850 time to fit residues: 39.3294 Evaluate side-chains 134 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 69 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 13 optimal weight: 0.0040 chunk 72 optimal weight: 0.1980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.137176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.108785 restraints weight = 27669.657| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 4.49 r_work: 0.3290 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 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 = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 8632 Z= 0.120 Angle : 0.563 8.818 11750 Z= 0.302 Chirality : 0.043 0.174 1364 Planarity : 0.004 0.037 1483 Dihedral : 4.398 19.468 1205 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.50 % Allowed : 13.28 % Favored : 85.22 % 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: -0.19 (0.26), residues: 1107 helix: 2.23 (0.28), residues: 354 sheet: -0.97 (0.32), residues: 263 loop : -1.44 (0.27), residues: 490 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 0.016 0.001 TYR E 190 ARG 0.005 0.000 ARG C 251 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 382) hydrogen bonds : angle 4.72343 ( 1075) SS BOND : bond 0.00413 ( 3) SS BOND : angle 0.88579 ( 6) covalent geometry : bond 0.00270 ( 8629) covalent geometry : angle 0.56241 (11744) *********************** 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 152 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: B 246 GLU cc_start: 0.8056 (tt0) cc_final: 0.7445 (mt-10) REVERT: C 76 ASP cc_start: 0.7670 (p0) cc_final: 0.7254 (t0) REVERT: D 47 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: E 82 GLN cc_start: 0.6146 (mm110) cc_final: 0.5785 (mp10) outliers start: 13 outliers final: 6 residues processed: 145 average time/residue: 0.1643 time to fit residues: 34.8412 Evaluate side-chains 133 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain C residue 243 THR 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 48 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 99 optimal weight: 0.0970 chunk 68 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 62 optimal weight: 0.1980 chunk 102 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.138409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.110754 restraints weight = 24766.233| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 4.00 r_work: 0.3328 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 8632 Z= 0.114 Angle : 0.534 9.143 11750 Z= 0.286 Chirality : 0.042 0.167 1364 Planarity : 0.003 0.038 1483 Dihedral : 4.155 17.269 1205 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.73 % Allowed : 14.78 % Favored : 83.49 % 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: 0.06 (0.26), residues: 1107 helix: 2.44 (0.28), residues: 353 sheet: -0.81 (0.32), residues: 264 loop : -1.27 (0.27), residues: 490 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 0.010 0.001 PHE B 251 TYR 0.016 0.001 TYR E 190 ARG 0.004 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 382) hydrogen bonds : angle 4.46401 ( 1075) SS BOND : bond 0.00414 ( 3) SS BOND : angle 0.80920 ( 6) covalent geometry : bond 0.00262 ( 8629) covalent geometry : angle 0.53344 (11744) *********************** 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 152 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 436 ASN cc_start: 0.6982 (OUTLIER) cc_final: 0.6641 (m-40) REVERT: B 246 GLU cc_start: 0.8057 (tt0) cc_final: 0.7462 (mt-10) REVERT: C 76 ASP cc_start: 0.7651 (p0) cc_final: 0.7290 (t0) REVERT: E 82 GLN cc_start: 0.6035 (mm110) cc_final: 0.5727 (mp10) outliers start: 15 outliers final: 11 residues processed: 146 average time/residue: 0.1670 time to fit residues: 35.6555 Evaluate side-chains 139 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 226 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 E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP 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 77 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.135054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.107557 restraints weight = 24395.613| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.90 r_work: 0.3292 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8632 Z= 0.138 Angle : 0.563 9.313 11750 Z= 0.301 Chirality : 0.043 0.165 1364 Planarity : 0.003 0.037 1483 Dihedral : 4.242 17.678 1205 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.73 % Allowed : 15.24 % Favored : 83.03 % 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: 0.09 (0.26), residues: 1107 helix: 2.45 (0.28), residues: 354 sheet: -0.91 (0.32), residues: 262 loop : -1.18 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.007 0.001 HIS B 196 PHE 0.009 0.001 PHE C 235 TYR 0.017 0.002 TYR E 190 ARG 0.002 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 382) hydrogen bonds : angle 4.49170 ( 1075) SS BOND : bond 0.00408 ( 3) SS BOND : angle 0.88259 ( 6) covalent geometry : bond 0.00319 ( 8629) covalent geometry : angle 0.56281 (11744) *********************** 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 146 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: B 246 GLU cc_start: 0.8091 (tt0) cc_final: 0.7485 (mt-10) REVERT: C 76 ASP cc_start: 0.7772 (p0) cc_final: 0.7332 (t0) REVERT: C 220 GLN cc_start: 0.8051 (mt0) cc_final: 0.7720 (mt0) REVERT: E 82 GLN cc_start: 0.6190 (mm110) cc_final: 0.5847 (mp10) outliers start: 15 outliers final: 13 residues processed: 140 average time/residue: 0.1716 time to fit residues: 35.1630 Evaluate side-chains 140 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 B residue 308 PHE 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 99 SER Chi-restraints excluded: chain E residue 140 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 52 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 66 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 82 optimal weight: 0.0670 chunk 81 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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** ** 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 = 0.3860 r_free = 0.3860 target = 0.137765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107186 restraints weight = 32847.869| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 4.67 r_work: 0.3306 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 8632 Z= 0.110 Angle : 0.530 9.767 11750 Z= 0.282 Chirality : 0.042 0.167 1364 Planarity : 0.003 0.035 1483 Dihedral : 4.019 17.420 1205 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.96 % Allowed : 16.40 % Favored : 81.64 % 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: 0.30 (0.26), residues: 1107 helix: 2.56 (0.28), residues: 355 sheet: -0.63 (0.32), residues: 255 loop : -1.11 (0.27), residues: 497 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 0.010 0.001 PHE C 335 TYR 0.014 0.001 TYR E 190 ARG 0.003 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 382) hydrogen bonds : angle 4.30199 ( 1075) SS BOND : bond 0.00381 ( 3) SS BOND : angle 0.62124 ( 6) covalent geometry : bond 0.00261 ( 8629) covalent geometry : angle 0.52946 (11744) *********************** 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 152 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8487 (tp) cc_final: 0.8062 (mt) REVERT: A 436 ASN cc_start: 0.7025 (OUTLIER) cc_final: 0.6614 (m-40) REVERT: B 246 GLU cc_start: 0.8103 (tt0) cc_final: 0.7501 (mt-10) REVERT: C 76 ASP cc_start: 0.7698 (p0) cc_final: 0.7331 (t0) REVERT: C 220 GLN cc_start: 0.8063 (mt0) cc_final: 0.7748 (mt0) REVERT: E 82 GLN cc_start: 0.6096 (mm110) cc_final: 0.5732 (mp10) outliers start: 17 outliers final: 14 residues processed: 145 average time/residue: 0.1701 time to fit residues: 35.7393 Evaluate side-chains 144 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 308 PHE Chi-restraints excluded: chain C residue 156 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** E 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.129724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.102142 restraints weight = 25721.574| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 4.10 r_work: 0.3191 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 8632 Z= 0.291 Angle : 0.702 10.446 11750 Z= 0.377 Chirality : 0.048 0.185 1364 Planarity : 0.004 0.040 1483 Dihedral : 4.974 25.916 1205 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.46 % Allowed : 15.59 % 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: -0.25 (0.26), residues: 1107 helix: 2.12 (0.28), residues: 354 sheet: -0.95 (0.33), residues: 257 loop : -1.44 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 47 HIS 0.006 0.002 HIS B 196 PHE 0.014 0.002 PHE E 110 TYR 0.024 0.003 TYR B 320 ARG 0.007 0.001 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.05313 ( 382) hydrogen bonds : angle 4.93268 ( 1075) SS BOND : bond 0.00915 ( 3) SS BOND : angle 1.49925 ( 6) covalent geometry : bond 0.00695 ( 8629) covalent geometry : angle 0.70136 (11744) *********************** 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 150 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 188 PHE cc_start: 0.6016 (OUTLIER) cc_final: 0.5796 (t80) REVERT: A 406 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6213 (mpp) REVERT: E 82 GLN cc_start: 0.6596 (mm110) cc_final: 0.6223 (mp10) REVERT: E 156 SER cc_start: 0.8674 (t) cc_final: 0.8372 (m) outliers start: 30 outliers final: 23 residues processed: 141 average time/residue: 0.2538 time to fit residues: 51.4933 Evaluate side-chains 141 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 398 ILE Chi-restraints excluded: chain A residue 406 MET 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 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 C residue 336 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 48 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 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 26 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 0.0170 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.133948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.107001 restraints weight = 20211.424| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.39 r_work: 0.3303 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 8632 Z= 0.133 Angle : 0.579 10.392 11750 Z= 0.309 Chirality : 0.043 0.181 1364 Planarity : 0.003 0.035 1483 Dihedral : 4.476 21.032 1205 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.31 % Allowed : 16.97 % 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: 0.12 (0.26), residues: 1107 helix: 2.40 (0.28), residues: 354 sheet: -0.74 (0.33), residues: 252 loop : -1.20 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.009 0.001 HIS B 196 PHE 0.007 0.001 PHE A 451 TYR 0.027 0.001 TYR B 303 ARG 0.006 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 382) hydrogen bonds : angle 4.50792 ( 1075) SS BOND : bond 0.00500 ( 3) SS BOND : angle 0.77967 ( 6) covalent geometry : bond 0.00320 ( 8629) covalent geometry : angle 0.57917 (11744) *********************** 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 140 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.623 Fit side-chains revert: symmetry clash REVERT: A 406 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6180 (mpp) REVERT: B 17 LYS cc_start: 0.8228 (mmtm) cc_final: 0.8017 (mptt) REVERT: C 52 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7989 (mtt-85) REVERT: E 156 SER cc_start: 0.8558 (t) cc_final: 0.8226 (m) outliers start: 20 outliers final: 17 residues processed: 133 average time/residue: 0.2152 time to fit residues: 41.0934 Evaluate side-chains 136 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU 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 308 PHE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.135191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.105639 restraints weight = 35602.789| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 4.44 r_work: 0.3283 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 8632 Z= 0.125 Angle : 0.565 10.486 11750 Z= 0.299 Chirality : 0.043 0.186 1364 Planarity : 0.003 0.034 1483 Dihedral : 4.230 19.168 1205 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.96 % Allowed : 17.44 % Favored : 80.60 % 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: 0.26 (0.26), residues: 1107 helix: 2.48 (0.28), residues: 354 sheet: -0.63 (0.33), residues: 255 loop : -1.09 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.006 0.001 HIS B 196 PHE 0.011 0.001 PHE C 335 TYR 0.022 0.001 TYR B 303 ARG 0.007 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 382) hydrogen bonds : angle 4.35855 ( 1075) SS BOND : bond 0.00453 ( 3) SS BOND : angle 0.78918 ( 6) covalent geometry : bond 0.00300 ( 8629) covalent geometry : angle 0.56460 (11744) *********************** 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 142 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 406 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6245 (mpp) REVERT: B 316 ASN cc_start: 0.7841 (t0) cc_final: 0.7614 (t0) REVERT: C 52 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8088 (mtt-85) REVERT: C 220 GLN cc_start: 0.7974 (mt0) cc_final: 0.7725 (mt0) REVERT: E 82 GLN cc_start: 0.6278 (mm110) cc_final: 0.5899 (mp10) REVERT: E 156 SER cc_start: 0.8552 (t) cc_final: 0.8223 (m) outliers start: 17 outliers final: 15 residues processed: 135 average time/residue: 0.1998 time to fit residues: 39.2398 Evaluate side-chains 137 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 73 optimal weight: 0.0570 chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 270 ASN ** 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 = 0.3865 r_free = 0.3865 target = 0.137994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108066 restraints weight = 26016.833| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 4.29 r_work: 0.3322 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 8632 Z= 0.112 Angle : 0.553 10.310 11750 Z= 0.291 Chirality : 0.042 0.179 1364 Planarity : 0.003 0.034 1483 Dihedral : 4.038 17.982 1205 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.96 % Allowed : 18.24 % Favored : 79.79 % 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: 0.40 (0.26), residues: 1107 helix: 2.51 (0.28), residues: 356 sheet: -0.48 (0.33), residues: 256 loop : -1.00 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.005 0.001 HIS B 196 PHE 0.009 0.001 PHE A 451 TYR 0.018 0.001 TYR B 303 ARG 0.006 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 382) hydrogen bonds : angle 4.20202 ( 1075) SS BOND : bond 0.00370 ( 3) SS BOND : angle 0.71300 ( 6) covalent geometry : bond 0.00269 ( 8629) covalent geometry : angle 0.55326 (11744) ********************** 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 147 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 406 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6255 (mpp) REVERT: A 431 ILE cc_start: 0.8493 (tp) cc_final: 0.8073 (mt) REVERT: C 52 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.8033 (mtt-85) REVERT: C 220 GLN cc_start: 0.8040 (mt0) cc_final: 0.7757 (mt0) REVERT: E 82 GLN cc_start: 0.6267 (mm110) cc_final: 0.5895 (mp10) REVERT: E 156 SER cc_start: 0.8528 (t) cc_final: 0.8190 (m) outliers start: 17 outliers final: 14 residues processed: 141 average time/residue: 0.1806 time to fit residues: 37.0955 Evaluate side-chains 144 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.0670 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 270 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3854 r_free = 0.3854 target = 0.136975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107149 restraints weight = 34435.580| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 4.46 r_work: 0.3306 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 8632 Z= 0.121 Angle : 0.567 10.064 11750 Z= 0.297 Chirality : 0.043 0.187 1364 Planarity : 0.003 0.034 1483 Dihedral : 4.026 17.838 1205 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.08 % Allowed : 18.59 % Favored : 79.33 % 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: 0.42 (0.26), residues: 1107 helix: 2.55 (0.28), residues: 355 sheet: -0.55 (0.33), residues: 259 loop : -0.95 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.006 0.001 HIS B 196 PHE 0.013 0.001 PHE C 335 TYR 0.018 0.001 TYR B 303 ARG 0.006 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 382) hydrogen bonds : angle 4.17138 ( 1075) SS BOND : bond 0.00424 ( 3) SS BOND : angle 0.75476 ( 6) covalent geometry : bond 0.00289 ( 8629) covalent geometry : angle 0.56734 (11744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5081.95 seconds wall clock time: 89 minutes 16.69 seconds (5356.69 seconds total)