Starting phenix.real_space_refine on Sat Jan 20 00:21:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t90_25749/01_2024/7t90_25749_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t90_25749/01_2024/7t90_25749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t90_25749/01_2024/7t90_25749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t90_25749/01_2024/7t90_25749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t90_25749/01_2024/7t90_25749_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t90_25749/01_2024/7t90_25749_neut_updated.pdb" } 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 Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 103": "OD1" <-> "OD2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 26": "OD1" <-> "OD2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 303": "OD1" <-> "OD2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 5.96, per 1000 atoms: 0.71 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 2.2 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... running ksdssp... Secondary structure from input PDB file: 29 helices and 14 sheets defined 34.3% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 23 through 50 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 57 through 86 removed outlier: 4.160A pdb=" N PHE A 61 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 72 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 74 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE A 75 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A 76 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET A 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A 85 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 86 " --> pdb=" O TYR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 126 removed outlier: 3.781A pdb=" N LEU A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 137 through 164 Proline residue: A 157 - end of helix removed outlier: 3.629A pdb=" N LEU A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 186 through 213 removed outlier: 3.693A pdb=" N THR A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Proline residue: A 198 - end of helix Processing helix chain 'A' and resid 382 through 412 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 422 through 430 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 432 through 441 Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 445 through 455 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 10 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 46 through 50 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 243 through 255 Processing helix chain 'B' and resid 272 through 280 removed outlier: 3.779A pdb=" N LYS B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 297 through 311 removed outlier: 4.207A pdb=" N LYS B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 351 removed outlier: 3.574A pdb=" N GLN B 333 " --> pdb=" O ASN B 330 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS B 351 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'D' and resid 8 through 22 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' 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 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 319 through 324 removed outlier: 6.775A pdb=" N ILE B 265 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N HIS B 322 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 267 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N THR B 324 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU B 269 " --> pdb=" O THR B 324 " (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) removed outlier: 4.023A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 37 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N CYS B 225 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N HIS B 196 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU B 36 " --> pdb=" O HIS B 196 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG B 198 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU B 38 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE B 200 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 190 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP B 201 " --> pdb=" O VAL B 186 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.990A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) 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: 3.505A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, 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: 3.704A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, 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= E, first strand: chain 'C' and resid 198 through 203 removed outlier: 4.112A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, 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: 3.726A pdb=" N CYS C 250 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 294 through 298 removed outlier: 3.509A pdb=" N SER C 277 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= H, 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= I, 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= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.948A pdb=" N VAL E 12 " --> pdb=" O THR E 118 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.585A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 146 through 148 removed outlier: 5.903A pdb=" N LYS E 244 " --> 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= M, first strand: chain 'E' and resid 155 through 160 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= N, first strand: chain 'E' and resid 229 through 231 removed outlier: 3.747A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 856 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: 2.40 Time building geometry restraints manager: 3.64 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: 97.88 - 105.22: 143 105.22 - 112.56: 4471 112.56 - 119.90: 3051 119.90 - 127.24: 3987 127.24 - 134.57: 92 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: 270 2.70 - 3.25: 8271 3.25 - 3.80: 12632 3.80 - 4.35: 16161 4.35 - 4.90: 27523 Nonbonded interactions: 64857 Sorted by model distance: nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.146 2.440 nonbonded pdb=" O LEU A 43 " pdb=" OG SER A 47 " model vdw 2.162 2.440 nonbonded pdb=" ND2 ASN C 119 " pdb=" O GLY C 144 " model vdw 2.190 2.520 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.226 2.440 nonbonded pdb=" O SER C 67 " pdb=" OG SER C 67 " model vdw 2.228 2.440 ... (remaining 64852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 7.310 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 28.190 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 8629 Z= 0.369 Angle : 0.945 13.621 11744 Z= 0.628 Chirality : 0.063 0.415 1364 Planarity : 0.005 0.050 1483 Dihedral : 12.713 89.660 2944 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.23 % Allowed : 0.92 % Favored : 98.85 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.26), residues: 1107 helix: 1.79 (0.29), residues: 337 sheet: -1.36 (0.33), residues: 262 loop : -1.64 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.006 0.001 HIS C 225 PHE 0.015 0.001 PHE C 235 TYR 0.021 0.002 TYR A 426 ARG 0.004 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 0.852 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: 0.2023 time to fit residues: 50.2176 Evaluate side-chains 130 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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: 10.0000 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 E 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 8629 Z= 0.424 Angle : 0.700 9.426 11744 Z= 0.376 Chirality : 0.048 0.213 1364 Planarity : 0.005 0.040 1483 Dihedral : 5.213 35.367 1205 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.08 % Allowed : 11.89 % Favored : 86.03 % 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: -0.97 (0.25), residues: 1107 helix: 1.50 (0.28), residues: 343 sheet: -1.41 (0.32), residues: 270 loop : -1.75 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.010 0.002 HIS C 225 PHE 0.018 0.002 PHE C 235 TYR 0.030 0.002 TYR E 94 ARG 0.004 0.001 ARG E 98 *********************** 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 149 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: B 226 VAL cc_start: 0.9448 (OUTLIER) cc_final: 0.9122 (m) REVERT: B 246 GLU cc_start: 0.7721 (tt0) cc_final: 0.7126 (mt-10) REVERT: D 21 MET cc_start: 0.7444 (mtt) cc_final: 0.7236 (mpp) REVERT: E 82 GLN cc_start: 0.6386 (mm110) cc_final: 0.6157 (mm110) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 0.2007 time to fit residues: 39.9724 Evaluate side-chains 125 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 C residue 120 ILE Chi-restraints excluded: chain C residue 243 THR 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 Chi-restraints excluded: chain E residue 223 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 8629 Z= 0.187 Angle : 0.548 8.673 11744 Z= 0.293 Chirality : 0.043 0.164 1364 Planarity : 0.004 0.038 1483 Dihedral : 4.502 20.269 1205 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.19 % Allowed : 14.20 % Favored : 83.60 % 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: -0.65 (0.25), residues: 1107 helix: 1.61 (0.28), residues: 344 sheet: -1.06 (0.32), residues: 267 loop : -1.54 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS C 225 PHE 0.011 0.001 PHE A 451 TYR 0.012 0.001 TYR E 190 ARG 0.006 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 218 LYS cc_start: 0.6503 (mmtt) cc_final: 0.6291 (mmtm) REVERT: B 226 VAL cc_start: 0.9404 (OUTLIER) cc_final: 0.9106 (m) REVERT: B 246 GLU cc_start: 0.7709 (tt0) cc_final: 0.7153 (mt-10) REVERT: E 82 GLN cc_start: 0.6088 (mm110) cc_final: 0.5844 (mm110) outliers start: 19 outliers final: 13 residues processed: 137 average time/residue: 0.1841 time to fit residues: 35.7407 Evaluate side-chains 135 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 ASP 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 91 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 0.0970 chunk 66 optimal weight: 0.0970 chunk 99 optimal weight: 0.4980 chunk 105 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 0.0020 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.095 8629 Z= 0.151 Angle : 0.499 9.298 11744 Z= 0.265 Chirality : 0.041 0.147 1364 Planarity : 0.004 0.037 1483 Dihedral : 4.025 18.454 1205 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.54 % Allowed : 14.55 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1107 helix: 1.85 (0.28), residues: 344 sheet: -0.72 (0.33), residues: 250 loop : -1.33 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.006 0.001 HIS B 189 PHE 0.011 0.001 PHE A 451 TYR 0.010 0.001 TYR E 190 ARG 0.005 0.000 ARG B 209 *********************** 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 168 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: B 21 LYS cc_start: 0.8421 (mtpp) cc_final: 0.8114 (mtpp) REVERT: B 246 GLU cc_start: 0.7667 (tt0) cc_final: 0.7172 (mt-10) REVERT: E 82 GLN cc_start: 0.5994 (mm110) cc_final: 0.5746 (mm110) outliers start: 22 outliers final: 17 residues processed: 160 average time/residue: 0.1707 time to fit residues: 39.0266 Evaluate side-chains 145 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE 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 232 ASP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 8629 Z= 0.218 Angle : 0.533 9.293 11744 Z= 0.284 Chirality : 0.042 0.162 1364 Planarity : 0.004 0.037 1483 Dihedral : 4.100 18.323 1205 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.19 % Allowed : 16.51 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1107 helix: 1.90 (0.28), residues: 340 sheet: -0.70 (0.33), residues: 255 loop : -1.25 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.005 0.001 HIS B 196 PHE 0.008 0.001 PHE A 451 TYR 0.012 0.001 TYR E 190 ARG 0.003 0.000 ARG B 209 *********************** 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 148 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.6640 (mmt) cc_final: 0.6413 (mmp) REVERT: B 196 HIS cc_start: 0.7396 (t-90) cc_final: 0.7153 (t-170) REVERT: B 246 GLU cc_start: 0.7680 (tt0) cc_final: 0.7167 (mt-10) REVERT: E 82 GLN cc_start: 0.6087 (mm110) cc_final: 0.5820 (mm110) REVERT: E 156 SER cc_start: 0.8290 (t) cc_final: 0.7986 (m) outliers start: 19 outliers final: 17 residues processed: 141 average time/residue: 0.1753 time to fit residues: 35.7753 Evaluate side-chains 145 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE 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 232 ASP Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 223 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 101 optimal weight: 0.0030 overall best weight: 1.0792 ------------------------------------------------------------------------------- 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** C 220 GLN C 237 ASN C 239 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 8629 Z= 0.221 Angle : 0.534 9.555 11744 Z= 0.282 Chirality : 0.042 0.164 1364 Planarity : 0.004 0.036 1483 Dihedral : 4.135 18.315 1205 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.35 % Allowed : 16.17 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1107 helix: 1.85 (0.28), residues: 340 sheet: -0.68 (0.33), residues: 256 loop : -1.22 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.005 0.001 HIS C 225 PHE 0.009 0.001 PHE C 335 TYR 0.012 0.001 TYR E 190 ARG 0.003 0.000 ARG B 209 *********************** 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 157 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 406 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6094 (mpp) REVERT: B 246 GLU cc_start: 0.7712 (tt0) cc_final: 0.7152 (mt-10) REVERT: C 52 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7384 (mtt-85) REVERT: E 156 SER cc_start: 0.8355 (t) cc_final: 0.8037 (m) outliers start: 29 outliers final: 21 residues processed: 148 average time/residue: 0.1842 time to fit residues: 38.8238 Evaluate side-chains 142 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE 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 34 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain 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 109 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 223 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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** C 220 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 8629 Z= 0.260 Angle : 0.561 9.764 11744 Z= 0.299 Chirality : 0.043 0.165 1364 Planarity : 0.004 0.037 1483 Dihedral : 4.308 19.892 1205 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.46 % Allowed : 16.28 % Favored : 80.25 % 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: 1.80 (0.28), residues: 340 sheet: -0.76 (0.33), residues: 256 loop : -1.19 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS C 225 PHE 0.009 0.001 PHE E 110 TYR 0.014 0.001 TYR E 190 ARG 0.002 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6111 (mpp) REVERT: B 246 GLU cc_start: 0.7742 (tt0) cc_final: 0.7147 (mt-10) REVERT: C 52 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7434 (mtt-85) outliers start: 30 outliers final: 22 residues processed: 134 average time/residue: 0.1762 time to fit residues: 33.9892 Evaluate side-chains 134 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE 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 34 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain 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 109 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 223 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.0870 chunk 91 optimal weight: 0.3980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.155 8629 Z= 0.195 Angle : 0.514 9.946 11744 Z= 0.272 Chirality : 0.041 0.157 1364 Planarity : 0.003 0.036 1483 Dihedral : 4.005 18.337 1205 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.35 % Allowed : 17.44 % Favored : 79.21 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1107 helix: 1.87 (0.29), residues: 344 sheet: -0.55 (0.33), residues: 256 loop : -1.12 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.000 HIS C 225 PHE 0.009 0.001 PHE C 335 TYR 0.012 0.001 TYR E 190 ARG 0.003 0.000 ARG E 98 *********************** 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 151 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 406 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6059 (mpp) REVERT: A 422 TRP cc_start: 0.5317 (t-100) cc_final: 0.4928 (t-100) REVERT: B 246 GLU cc_start: 0.7744 (tt0) cc_final: 0.7185 (mt-10) REVERT: C 52 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7336 (mtt-85) outliers start: 29 outliers final: 25 residues processed: 139 average time/residue: 0.1778 time to fit residues: 35.4954 Evaluate side-chains 144 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE 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 34 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 46 LYS 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 109 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 223 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 58 optimal weight: 0.0070 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.177 8629 Z= 0.207 Angle : 0.528 9.878 11744 Z= 0.279 Chirality : 0.042 0.185 1364 Planarity : 0.003 0.034 1483 Dihedral : 3.908 17.900 1205 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.89 % Allowed : 17.90 % Favored : 79.21 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1107 helix: 1.91 (0.29), residues: 343 sheet: -0.42 (0.33), residues: 258 loop : -1.00 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.002 0.001 HIS C 225 PHE 0.008 0.001 PHE A 451 TYR 0.011 0.001 TYR E 190 ARG 0.004 0.000 ARG A 135 *********************** 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 145 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 TRP cc_start: 0.5313 (t-100) cc_final: 0.4905 (t-100) REVERT: B 246 GLU cc_start: 0.7723 (tt0) cc_final: 0.7194 (mt-10) REVERT: E 155 VAL cc_start: 0.8637 (p) cc_final: 0.8388 (m) outliers start: 25 outliers final: 21 residues processed: 136 average time/residue: 0.1708 time to fit residues: 33.8958 Evaluate side-chains 140 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 354 TYR 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 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 223 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 8629 Z= 0.326 Angle : 0.616 10.190 11744 Z= 0.327 Chirality : 0.045 0.197 1364 Planarity : 0.004 0.032 1483 Dihedral : 4.499 21.894 1205 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.89 % Allowed : 18.24 % Favored : 78.87 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1107 helix: 1.63 (0.28), residues: 344 sheet: -0.56 (0.33), residues: 251 loop : -1.21 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.009 0.001 HIS B 196 PHE 0.013 0.001 PHE C 335 TYR 0.016 0.002 TYR E 190 ARG 0.004 0.000 ARG A 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8790 (mt0) cc_final: 0.8411 (mm-40) REVERT: A 406 MET cc_start: 0.7130 (mtm) cc_final: 0.5927 (mpp) REVERT: B 250 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8708 (tt) REVERT: C 52 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7472 (mtt-85) REVERT: D 46 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7327 (pttm) REVERT: E 155 VAL cc_start: 0.8712 (p) cc_final: 0.8485 (m) outliers start: 25 outliers final: 22 residues processed: 128 average time/residue: 0.1845 time to fit residues: 33.9253 Evaluate side-chains 138 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 46 LYS 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 146 SER Chi-restraints excluded: chain E residue 223 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.0370 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.135060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104801 restraints weight = 28360.159| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 4.29 r_work: 0.3279 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 8629 Z= 0.207 Angle : 0.557 9.897 11744 Z= 0.293 Chirality : 0.042 0.186 1364 Planarity : 0.004 0.036 1483 Dihedral : 4.165 18.674 1205 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.89 % Allowed : 18.59 % Favored : 78.52 % 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: 0.00 (0.26), residues: 1107 helix: 1.82 (0.29), residues: 343 sheet: -0.34 (0.34), residues: 250 loop : -1.07 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS B 189 PHE 0.008 0.001 PHE A 451 TYR 0.012 0.001 TYR E 190 ARG 0.003 0.000 ARG E 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2114.40 seconds wall clock time: 39 minutes 3.25 seconds (2343.25 seconds total)