Starting phenix.real_space_refine on Mon Dec 30 05:44:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t94_25751/12_2024/7t94_25751.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t94_25751/12_2024/7t94_25751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t94_25751/12_2024/7t94_25751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t94_25751/12_2024/7t94_25751.map" model { file = "/net/cci-nas-00/data/ceres_data/7t94_25751/12_2024/7t94_25751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t94_25751/12_2024/7t94_25751.cif" } resolution = 3.16 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= 0.001 sd= 0.024 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: 5 Type Number sf(0) Gaussians S 58 5.16 5 Cl 1 4.86 5 C 5344 2.51 5 N 1412 2.21 5 O 1573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8388 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1946 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1711 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'2CU': 1, 'ACH': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 5.67, per 1000 atoms: 0.68 Number of scatterers: 8388 At special positions: 0 Unit cell: (90.95, 120.7, 124.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 58 16.00 O 1573 8.00 N 1412 7.00 C 5344 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=2.02 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=2.04 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 37.0% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 25 through 52 removed outlier: 3.849A pdb=" N GLY A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 49 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 87 removed outlier: 3.966A pdb=" N MET A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 127 removed outlier: 3.779A pdb=" N TRP A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 136 through 167 removed outlier: 3.621A pdb=" N SER A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Proline residue: A 157 - end of helix removed outlier: 4.478A pdb=" N GLN A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 195 removed outlier: 3.528A pdb=" N ALA A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 213 removed outlier: 3.694A pdb=" N ILE A 200 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 412 removed outlier: 3.508A pdb=" N VAL A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) Proline residue: A 402 - end of helix removed outlier: 3.669A pdb=" N LEU A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 421 through 440 removed outlier: 4.000A pdb=" N CYS A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 431 " --> pdb=" O TRP A 427 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.787A pdb=" N LYS A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 444 through 450' Processing helix chain 'B' and resid 10 through 31 removed outlier: 3.628A pdb=" N GLU B 14 " --> pdb=" O LYS B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.854A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 removed outlier: 4.143A pdb=" N TRP B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 217 Processing helix chain 'B' and resid 242 through 256 Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.864A pdb=" N ILE B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 332 through 351 removed outlier: 3.788A pdb=" N ALA B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.516A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.753A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'E' and resid 28 through 32 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: 4.204A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.798A pdb=" N ASP E 223 " --> pdb=" O GLU E 220 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 220 through 224' Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 191 removed outlier: 3.607A pdb=" N VAL B 186 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 190 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU B 39 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ALA B 227 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 7.086A 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 51 removed outlier: 6.643A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.879A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.937A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.529A 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: 6.774A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.505A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.527A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.970A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.526A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.005A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.667A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.548A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.692A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1107 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: 2.45 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1359 1.30 - 1.43: 2376 1.43 - 1.56: 4744 1.56 - 1.70: 2 1.70 - 1.83: 83 Bond restraints: 8564 Sorted by residual: bond pdb=" C01 2CU A 502 " pdb=" N02 2CU A 502 " ideal model delta sigma weight residual 1.445 1.258 0.187 2.00e-02 2.50e+03 8.72e+01 bond pdb=" C08 2CU A 502 " pdb=" N05 2CU A 502 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C24 2CU A 502 " pdb=" N26 2CU A 502 " ideal model delta sigma weight residual 1.353 1.466 -0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C18 2CU A 502 " pdb=" N19 2CU A 502 " ideal model delta sigma weight residual 1.356 1.465 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C12 2CU A 502 " pdb=" O11 2CU A 502 " ideal model delta sigma weight residual 1.323 1.414 -0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 8559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 11372 2.49 - 4.99: 235 4.99 - 7.48: 39 7.48 - 9.97: 10 9.97 - 12.46: 5 Bond angle restraints: 11661 Sorted by residual: angle pdb=" C GLU B 8 " pdb=" N ASP B 9 " pdb=" CA ASP B 9 " ideal model delta sigma weight residual 121.70 134.16 -12.46 1.80e+00 3.09e-01 4.79e+01 angle pdb=" N PRO A 418 " pdb=" CA PRO A 418 " pdb=" C PRO A 418 " ideal model delta sigma weight residual 111.14 100.44 10.70 1.56e+00 4.11e-01 4.70e+01 angle pdb=" N LEU A 43 " pdb=" CA LEU A 43 " pdb=" C LEU A 43 " ideal model delta sigma weight residual 113.19 105.25 7.94 1.19e+00 7.06e-01 4.45e+01 angle pdb=" N ASN A 41 " pdb=" CA ASN A 41 " pdb=" C ASN A 41 " ideal model delta sigma weight residual 111.82 104.32 7.50 1.16e+00 7.43e-01 4.19e+01 angle pdb=" CA PHE A 180 " pdb=" CB PHE A 180 " pdb=" CG PHE A 180 " ideal model delta sigma weight residual 113.80 119.82 -6.02 1.00e+00 1.00e+00 3.62e+01 ... (remaining 11656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.32: 4498 14.32 - 28.64: 385 28.64 - 42.96: 107 42.96 - 57.28: 16 57.28 - 71.60: 5 Dihedral angle restraints: 5011 sinusoidal: 1790 harmonic: 3221 Sorted by residual: dihedral pdb=" C THR A 420 " pdb=" N THR A 420 " pdb=" CA THR A 420 " pdb=" CB THR A 420 " ideal model delta harmonic sigma weight residual -122.00 -110.13 -11.87 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" N THR A 420 " pdb=" C THR A 420 " pdb=" CA THR A 420 " pdb=" CB THR A 420 " ideal model delta harmonic sigma weight residual 123.40 112.43 10.97 0 2.50e+00 1.60e-01 1.93e+01 dihedral pdb=" C THR A 187 " pdb=" N THR A 187 " pdb=" CA THR A 187 " pdb=" CB THR A 187 " ideal model delta harmonic sigma weight residual -122.00 -111.15 -10.85 0 2.50e+00 1.60e-01 1.88e+01 ... (remaining 5008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1076 0.060 - 0.120: 225 0.120 - 0.181: 37 0.181 - 0.241: 7 0.241 - 0.301: 11 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CA ASN B 330 " pdb=" N ASN B 330 " pdb=" C ASN B 330 " pdb=" CB ASN B 330 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA THR A 423 " pdb=" N THR A 423 " pdb=" C THR A 423 " pdb=" CB THR A 423 " both_signs ideal model delta sigma weight residual False 2.53 2.83 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA ASP E 74 " pdb=" N ASP E 74 " pdb=" C ASP E 74 " pdb=" CB ASP E 74 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1353 not shown) Planarity restraints: 1469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 74 " 0.024 2.00e-02 2.50e+03 4.78e-02 2.29e+01 pdb=" C VAL A 74 " -0.083 2.00e-02 2.50e+03 pdb=" O VAL A 74 " 0.031 2.00e-02 2.50e+03 pdb=" N PHE A 75 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 51 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C LYS B 51 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS B 51 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN B 52 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 40 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.37e+00 pdb=" C GLY A 40 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY A 40 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 41 " 0.017 2.00e-02 2.50e+03 ... (remaining 1466 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 115 2.65 - 3.21: 7721 3.21 - 3.77: 12096 3.77 - 4.34: 16584 4.34 - 4.90: 27987 Nonbonded interactions: 64503 Sorted by model distance: nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.081 3.040 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.139 3.040 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.177 3.040 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.237 3.040 nonbonded pdb=" O TRP A 148 " pdb=" OG SER A 151 " model vdw 2.257 3.040 ... (remaining 64498 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.880 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 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 : 0.007 0.187 8564 Z= 0.470 Angle : 0.928 12.464 11661 Z= 0.580 Chirality : 0.057 0.301 1356 Planarity : 0.005 0.048 1469 Dihedral : 12.228 71.603 2926 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.12 % Allowed : 0.46 % Favored : 99.42 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.26), residues: 1093 helix: 0.74 (0.29), residues: 342 sheet: -0.24 (0.31), residues: 284 loop : -1.45 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.007 0.002 HIS B 189 PHE 0.036 0.002 PHE A 180 TYR 0.018 0.002 TYR A 426 ARG 0.020 0.001 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 80 TYR cc_start: 0.6999 (t80) cc_final: 0.6635 (t80) REVERT: A 122 TYR cc_start: 0.7092 (t80) cc_final: 0.6846 (t80) REVERT: B 24 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7840 (ttmt) REVERT: C 61 MET cc_start: 0.7402 (tmm) cc_final: 0.7171 (tmm) REVERT: C 290 ASP cc_start: 0.7995 (m-30) cc_final: 0.7666 (m-30) REVERT: D 24 ASN cc_start: 0.7975 (t0) cc_final: 0.7581 (t0) REVERT: E 67 ARG cc_start: 0.8060 (mtm110) cc_final: 0.7662 (mtm180) REVERT: E 87 ARG cc_start: 0.7058 (ttm110) cc_final: 0.6767 (ttm110) REVERT: E 178 LEU cc_start: 0.8036 (tp) cc_final: 0.7779 (tt) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.2496 time to fit residues: 68.4987 Evaluate side-chains 186 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 84 optimal weight: 0.0020 chunk 32 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 ASN B 295 ASN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8564 Z= 0.180 Angle : 0.593 13.128 11661 Z= 0.322 Chirality : 0.045 0.225 1356 Planarity : 0.004 0.057 1469 Dihedral : 4.936 42.826 1204 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.16 % Allowed : 9.40 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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: 1093 helix: 1.52 (0.29), residues: 353 sheet: -0.04 (0.31), residues: 293 loop : -1.29 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 82 HIS 0.004 0.001 HIS B 196 PHE 0.018 0.001 PHE A 396 TYR 0.016 0.001 TYR E 190 ARG 0.006 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 187 time to evaluate : 0.944 Fit side-chains REVERT: B 24 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7866 (ttmt) REVERT: B 190 PHE cc_start: 0.7542 (p90) cc_final: 0.7317 (p90) REVERT: C 44 GLN cc_start: 0.8034 (pm20) cc_final: 0.7812 (mp10) REVERT: C 61 MET cc_start: 0.7444 (tmm) cc_final: 0.7079 (tmm) REVERT: C 246 ASP cc_start: 0.6894 (t0) cc_final: 0.6589 (t70) REVERT: C 258 ASP cc_start: 0.7083 (t70) cc_final: 0.6843 (t70) REVERT: C 289 TYR cc_start: 0.8372 (m-80) cc_final: 0.7998 (m-80) REVERT: C 290 ASP cc_start: 0.7945 (m-30) cc_final: 0.7616 (m-30) REVERT: E 67 ARG cc_start: 0.8180 (mtm110) cc_final: 0.7746 (mtm180) REVERT: E 87 ARG cc_start: 0.6957 (ttm110) cc_final: 0.6441 (ttm110) outliers start: 10 outliers final: 4 residues processed: 191 average time/residue: 0.2283 time to fit residues: 58.1886 Evaluate side-chains 178 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 91 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8564 Z= 0.260 Angle : 0.598 13.429 11661 Z= 0.323 Chirality : 0.045 0.209 1356 Planarity : 0.004 0.060 1469 Dihedral : 4.944 44.569 1204 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.44 % Allowed : 12.30 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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: 1093 helix: 1.69 (0.29), residues: 356 sheet: 0.14 (0.31), residues: 293 loop : -1.29 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 82 HIS 0.005 0.001 HIS B 196 PHE 0.014 0.002 PHE A 180 TYR 0.017 0.002 TYR E 190 ARG 0.004 0.001 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.956 Fit side-chains REVERT: B 24 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7857 (ttmt) REVERT: B 35 LYS cc_start: 0.7854 (mtpp) cc_final: 0.7581 (mtpp) REVERT: C 61 MET cc_start: 0.7550 (tmm) cc_final: 0.7293 (tmm) REVERT: C 81 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.7175 (mt) REVERT: C 289 TYR cc_start: 0.8408 (m-80) cc_final: 0.8014 (m-80) REVERT: C 290 ASP cc_start: 0.8003 (m-30) cc_final: 0.7670 (m-30) REVERT: D 24 ASN cc_start: 0.8039 (t0) cc_final: 0.7772 (t0) REVERT: E 67 ARG cc_start: 0.8181 (mtm110) cc_final: 0.7757 (mtm180) REVERT: E 87 ARG cc_start: 0.6998 (ttm110) cc_final: 0.6439 (ttm110) outliers start: 21 outliers final: 13 residues processed: 203 average time/residue: 0.2237 time to fit residues: 61.1645 Evaluate side-chains 205 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 109 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 46 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN B 330 ASN C 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8564 Z= 0.203 Angle : 0.569 13.112 11661 Z= 0.306 Chirality : 0.044 0.212 1356 Planarity : 0.004 0.055 1469 Dihedral : 4.725 44.176 1204 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.25 % Allowed : 14.39 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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: 0.22 (0.26), residues: 1093 helix: 1.81 (0.29), residues: 355 sheet: 0.24 (0.31), residues: 288 loop : -1.29 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 196 PHE 0.023 0.001 PHE A 396 TYR 0.015 0.001 TYR E 190 ARG 0.003 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.994 Fit side-chains REVERT: A 179 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6730 (tp40) REVERT: B 24 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7847 (ttmt) REVERT: B 35 LYS cc_start: 0.7798 (mtpp) cc_final: 0.7573 (mtpp) REVERT: B 354 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6696 (m-80) REVERT: C 61 MET cc_start: 0.7558 (tmm) cc_final: 0.7269 (tmm) REVERT: C 81 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7129 (mt) REVERT: C 150 ARG cc_start: 0.8547 (mmp80) cc_final: 0.8304 (mpt180) REVERT: C 289 TYR cc_start: 0.8420 (m-80) cc_final: 0.8043 (m-80) REVERT: C 290 ASP cc_start: 0.7982 (m-30) cc_final: 0.7612 (m-30) REVERT: D 24 ASN cc_start: 0.8078 (t0) cc_final: 0.7818 (t0) REVERT: E 67 ARG cc_start: 0.8189 (mtm110) cc_final: 0.7766 (mtm180) REVERT: E 87 ARG cc_start: 0.6991 (ttm110) cc_final: 0.6425 (ttm110) outliers start: 28 outliers final: 20 residues processed: 209 average time/residue: 0.2475 time to fit residues: 67.4079 Evaluate side-chains 204 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 147 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN B 330 ASN C 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8564 Z= 0.252 Angle : 0.591 13.273 11661 Z= 0.320 Chirality : 0.045 0.212 1356 Planarity : 0.004 0.057 1469 Dihedral : 4.779 43.817 1204 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.36 % Allowed : 16.24 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1093 helix: 1.77 (0.29), residues: 355 sheet: 0.34 (0.32), residues: 286 loop : -1.30 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 212 HIS 0.005 0.001 HIS B 196 PHE 0.026 0.002 PHE A 396 TYR 0.016 0.001 TYR E 190 ARG 0.004 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7847 (ttmt) REVERT: B 35 LYS cc_start: 0.7833 (mtpp) cc_final: 0.7586 (mtpp) REVERT: B 354 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6951 (m-80) REVERT: C 61 MET cc_start: 0.7592 (tmm) cc_final: 0.7345 (tmm) REVERT: C 81 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.7153 (mt) REVERT: C 289 TYR cc_start: 0.8431 (m-80) cc_final: 0.8103 (m-80) REVERT: C 290 ASP cc_start: 0.7969 (m-30) cc_final: 0.7627 (m-30) REVERT: D 24 ASN cc_start: 0.8089 (t0) cc_final: 0.7842 (t0) REVERT: E 34 MET cc_start: 0.8048 (mmm) cc_final: 0.7845 (mmp) outliers start: 29 outliers final: 21 residues processed: 202 average time/residue: 0.2241 time to fit residues: 60.9794 Evaluate side-chains 201 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 147 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN B 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8564 Z= 0.276 Angle : 0.604 13.336 11661 Z= 0.327 Chirality : 0.045 0.209 1356 Planarity : 0.004 0.059 1469 Dihedral : 4.872 43.802 1204 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.71 % Allowed : 16.36 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1093 helix: 1.72 (0.29), residues: 355 sheet: 0.31 (0.32), residues: 289 loop : -1.30 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 212 HIS 0.005 0.001 HIS B 196 PHE 0.029 0.002 PHE A 396 TYR 0.017 0.002 TYR E 190 ARG 0.004 0.001 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.952 Fit side-chains REVERT: A 127 LYS cc_start: 0.7578 (mttt) cc_final: 0.7318 (mttt) REVERT: B 35 LYS cc_start: 0.7850 (mtpp) cc_final: 0.7638 (mtpp) REVERT: B 266 ILE cc_start: 0.8408 (tt) cc_final: 0.8180 (mt) REVERT: C 61 MET cc_start: 0.7633 (tmm) cc_final: 0.7382 (tmm) REVERT: C 81 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7163 (mt) REVERT: C 289 TYR cc_start: 0.8438 (m-80) cc_final: 0.8121 (m-80) REVERT: C 290 ASP cc_start: 0.7971 (m-30) cc_final: 0.7639 (m-30) REVERT: D 24 ASN cc_start: 0.8119 (t0) cc_final: 0.7874 (t0) REVERT: E 87 ARG cc_start: 0.6950 (ttm110) cc_final: 0.6649 (ttm110) outliers start: 32 outliers final: 25 residues processed: 204 average time/residue: 0.2242 time to fit residues: 61.4182 Evaluate side-chains 208 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 172 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 ASN C 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8564 Z= 0.265 Angle : 0.602 13.259 11661 Z= 0.324 Chirality : 0.045 0.216 1356 Planarity : 0.004 0.060 1469 Dihedral : 4.849 43.673 1204 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.60 % Allowed : 16.59 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1093 helix: 1.73 (0.29), residues: 355 sheet: 0.25 (0.32), residues: 291 loop : -1.33 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 212 HIS 0.006 0.001 HIS C 142 PHE 0.029 0.001 PHE A 396 TYR 0.017 0.002 TYR C 105 ARG 0.004 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: B 35 LYS cc_start: 0.7888 (mtpp) cc_final: 0.7627 (mtpp) REVERT: C 61 MET cc_start: 0.7644 (tmm) cc_final: 0.7396 (tmm) REVERT: C 81 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.7148 (mt) REVERT: C 289 TYR cc_start: 0.8436 (m-80) cc_final: 0.8136 (m-80) REVERT: D 24 ASN cc_start: 0.8139 (t0) cc_final: 0.7910 (t0) outliers start: 31 outliers final: 28 residues processed: 209 average time/residue: 0.2132 time to fit residues: 60.1563 Evaluate side-chains 219 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 172 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 ASN E 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8564 Z= 0.250 Angle : 0.604 13.177 11661 Z= 0.325 Chirality : 0.044 0.208 1356 Planarity : 0.004 0.062 1469 Dihedral : 4.812 43.406 1204 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.48 % Allowed : 18.33 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1093 helix: 1.77 (0.29), residues: 355 sheet: 0.24 (0.31), residues: 291 loop : -1.35 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 212 HIS 0.005 0.001 HIS B 196 PHE 0.029 0.001 PHE A 396 TYR 0.016 0.001 TYR C 105 ARG 0.006 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: B 35 LYS cc_start: 0.7898 (mtpp) cc_final: 0.7628 (mtpp) REVERT: C 61 MET cc_start: 0.7669 (tmm) cc_final: 0.7401 (tmm) REVERT: C 81 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7124 (mt) REVERT: C 289 TYR cc_start: 0.8434 (m-80) cc_final: 0.8090 (m-80) REVERT: C 290 ASP cc_start: 0.7955 (m-30) cc_final: 0.7613 (m-30) REVERT: D 24 ASN cc_start: 0.8139 (t0) cc_final: 0.7929 (t0) outliers start: 30 outliers final: 28 residues processed: 202 average time/residue: 0.2186 time to fit residues: 59.2708 Evaluate side-chains 213 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 172 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 0.1980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN B 330 ASN C 75 GLN E 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8564 Z= 0.250 Angle : 0.604 13.166 11661 Z= 0.326 Chirality : 0.045 0.213 1356 Planarity : 0.004 0.064 1469 Dihedral : 4.790 43.054 1204 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.71 % Allowed : 17.98 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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: 1093 helix: 1.81 (0.29), residues: 355 sheet: 0.19 (0.31), residues: 294 loop : -1.32 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 212 HIS 0.005 0.001 HIS B 196 PHE 0.030 0.001 PHE A 396 TYR 0.017 0.001 TYR C 105 ARG 0.005 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: B 35 LYS cc_start: 0.7908 (mtpp) cc_final: 0.7637 (mtpp) REVERT: C 61 MET cc_start: 0.7675 (tmm) cc_final: 0.7406 (tmm) REVERT: C 81 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7123 (mt) REVERT: C 289 TYR cc_start: 0.8433 (m-80) cc_final: 0.8084 (m-80) REVERT: C 290 ASP cc_start: 0.7950 (m-30) cc_final: 0.7608 (m-30) REVERT: E 87 ARG cc_start: 0.6830 (ttm110) cc_final: 0.6612 (ttm110) outliers start: 32 outliers final: 30 residues processed: 193 average time/residue: 0.2256 time to fit residues: 58.2714 Evaluate side-chains 203 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 0.0030 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.0050 overall best weight: 0.7406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 ASN C 142 HIS E 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8564 Z= 0.256 Angle : 0.614 13.188 11661 Z= 0.331 Chirality : 0.045 0.210 1356 Planarity : 0.004 0.065 1469 Dihedral : 4.807 42.590 1204 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.48 % Allowed : 18.45 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1093 helix: 1.87 (0.29), residues: 354 sheet: 0.18 (0.31), residues: 295 loop : -1.31 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 212 HIS 0.005 0.001 HIS B 196 PHE 0.030 0.001 PHE A 396 TYR 0.019 0.001 TYR C 105 ARG 0.004 0.000 ARG C 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: B 35 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7637 (mtpp) REVERT: C 61 MET cc_start: 0.7688 (tmm) cc_final: 0.7423 (tmm) REVERT: C 81 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7120 (mt) REVERT: C 289 TYR cc_start: 0.8428 (m-80) cc_final: 0.8079 (m-80) REVERT: C 290 ASP cc_start: 0.7950 (m-30) cc_final: 0.7607 (m-30) outliers start: 30 outliers final: 29 residues processed: 190 average time/residue: 0.2275 time to fit residues: 58.2774 Evaluate side-chains 198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.0270 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 ASN C 142 HIS E 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115134 restraints weight = 13201.376| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.01 r_work: 0.3433 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8564 Z= 0.213 Angle : 0.596 12.994 11661 Z= 0.323 Chirality : 0.044 0.208 1356 Planarity : 0.004 0.064 1469 Dihedral : 4.682 42.481 1204 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.48 % Allowed : 18.91 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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 (0.27), residues: 1093 helix: 1.96 (0.29), residues: 354 sheet: 0.22 (0.31), residues: 295 loop : -1.28 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 212 HIS 0.005 0.001 HIS B 196 PHE 0.028 0.001 PHE A 396 TYR 0.018 0.001 TYR C 105 ARG 0.004 0.000 ARG C 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2397.47 seconds wall clock time: 44 minutes 22.04 seconds (2662.04 seconds total)