Starting phenix.real_space_refine on Sat Dec 9 16:34:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/12_2023/6ksw_0775.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/12_2023/6ksw_0775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/12_2023/6ksw_0775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/12_2023/6ksw_0775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/12_2023/6ksw_0775.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/12_2023/6ksw_0775.pdb" } resolution = 3.6 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7740 2.51 5 N 1863 2.21 5 O 1995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 534": "NH1" <-> "NH2" Residue "A TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 594": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11661 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3887 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 494} Chain breaks: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 97 Chain: "A" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3887 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 494} Chain breaks: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3887 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 494} Chain breaks: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 6.98, per 1000 atoms: 0.60 Number of scatterers: 11661 At special positions: 0 Unit cell: (123.76, 125.84, 72.8, 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 63 16.00 O 1995 8.00 N 1863 7.00 C 7740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.5 seconds 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2850 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'C' and resid 102 through 124 removed outlier: 4.229A pdb=" N ILE C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 121 " --> pdb=" O MET C 117 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 123 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 152 removed outlier: 3.590A pdb=" N VAL C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET C 149 " --> pdb=" O TRP C 145 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 150 " --> pdb=" O ASP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.618A pdb=" N ASP C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 190 removed outlier: 3.766A pdb=" N LEU C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE C 172 " --> pdb=" O ASN C 168 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP C 173 " --> pdb=" O SER C 169 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP C 176 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER C 180 " --> pdb=" O TRP C 176 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL C 183 " --> pdb=" O TRP C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 200 through 217 removed outlier: 3.501A pdb=" N MET C 210 " --> pdb=" O GLY C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 245 removed outlier: 4.427A pdb=" N VAL C 230 " --> pdb=" O TYR C 226 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 234 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 268 removed outlier: 3.614A pdb=" N VAL C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 264 " --> pdb=" O GLN C 260 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C 268 " --> pdb=" O PHE C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 277 through 282 removed outlier: 4.495A pdb=" N LYS C 281 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 288 Processing helix chain 'C' and resid 288 through 306 removed outlier: 3.597A pdb=" N SER C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 325 removed outlier: 3.565A pdb=" N ILE C 313 " --> pdb=" O MET C 309 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 323 " --> pdb=" O ILE C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.745A pdb=" N ILE C 356 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 removed outlier: 3.565A pdb=" N THR C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 384 removed outlier: 3.851A pdb=" N GLY C 384 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 409 removed outlier: 3.932A pdb=" N ALA C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) Proline residue: C 399 - end of helix removed outlier: 4.168A pdb=" N LEU C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 443 removed outlier: 3.536A pdb=" N ALA C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 474 removed outlier: 3.728A pdb=" N LEU C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 470 " --> pdb=" O ASN C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'C' and resid 482 through 491 Processing helix chain 'C' and resid 491 through 498 Processing helix chain 'C' and resid 501 through 518 removed outlier: 4.146A pdb=" N PHE C 506 " --> pdb=" O TRP C 502 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N MET C 507 " --> pdb=" O GLN C 503 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG C 510 " --> pdb=" O PHE C 506 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU C 511 " --> pdb=" O MET C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 536 removed outlier: 3.849A pdb=" N ALA C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TRP C 530 " --> pdb=" O HIS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 560 Processing helix chain 'C' and resid 568 through 579 removed outlier: 4.034A pdb=" N ILE C 572 " --> pdb=" O GLY C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 583 No H-bonds generated for 'chain 'C' and resid 581 through 583' Processing helix chain 'C' and resid 584 through 613 removed outlier: 4.654A pdb=" N VAL C 593 " --> pdb=" O ALA C 589 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG C 594 " --> pdb=" O SER C 590 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 609 " --> pdb=" O MET C 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 124 removed outlier: 4.230A pdb=" N ILE A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 152 removed outlier: 3.589A pdb=" N VAL A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET A 149 " --> pdb=" O TRP A 145 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.618A pdb=" N ASP A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 190 removed outlier: 3.765A pdb=" N LEU A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TRP A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A 180 " --> pdb=" O TRP A 176 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 200 through 217 removed outlier: 3.501A pdb=" N MET A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 removed outlier: 4.428A pdb=" N VAL A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 268 removed outlier: 3.615A pdb=" N VAL A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 268 " --> pdb=" O PHE A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.494A pdb=" N LYS A 281 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 288 through 306 removed outlier: 3.598A pdb=" N SER A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 325 removed outlier: 3.564A pdb=" N ILE A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.745A pdb=" N ILE A 356 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.565A pdb=" N THR A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.851A pdb=" N GLY A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 409 removed outlier: 3.934A pdb=" N ALA A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Proline residue: A 399 - end of helix removed outlier: 4.168A pdb=" N LEU A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 443 removed outlier: 3.535A pdb=" N ALA A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 474 removed outlier: 3.728A pdb=" N LEU A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 477 No H-bonds generated for 'chain 'A' and resid 475 through 477' Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 491 through 498 Processing helix chain 'A' and resid 501 through 518 removed outlier: 4.146A pdb=" N PHE A 506 " --> pdb=" O TRP A 502 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N MET A 507 " --> pdb=" O GLN A 503 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A 510 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 511 " --> pdb=" O MET A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 536 removed outlier: 3.848A pdb=" N ALA A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP A 530 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG A 534 " --> pdb=" O TRP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 568 through 579 removed outlier: 4.034A pdb=" N ILE A 572 " --> pdb=" O GLY A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 584 through 613 removed outlier: 4.654A pdb=" N VAL A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 609 " --> pdb=" O MET A 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 124 removed outlier: 4.230A pdb=" N ILE B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 152 removed outlier: 3.589A pdb=" N VAL B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET B 149 " --> pdb=" O TRP B 145 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.618A pdb=" N ASP B 157 " --> pdb=" O GLU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 190 removed outlier: 3.767A pdb=" N LEU B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TRP B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 180 " --> pdb=" O TRP B 176 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 183 " --> pdb=" O TRP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 200 through 217 removed outlier: 3.501A pdb=" N MET B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 245 removed outlier: 4.427A pdb=" N VAL B 230 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 268 removed outlier: 3.614A pdb=" N VAL B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 268 " --> pdb=" O PHE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 277 through 282 removed outlier: 4.495A pdb=" N LYS B 281 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 288 through 306 removed outlier: 3.597A pdb=" N SER B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET B 302 " --> pdb=" O THR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 325 removed outlier: 3.564A pdb=" N ILE B 313 " --> pdb=" O MET B 309 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 323 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.744A pdb=" N ILE B 356 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 371 removed outlier: 3.565A pdb=" N THR B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.850A pdb=" N GLY B 384 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 409 removed outlier: 3.933A pdb=" N ALA B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) Proline residue: B 399 - end of helix removed outlier: 4.168A pdb=" N LEU B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 443 removed outlier: 3.534A pdb=" N ALA B 436 " --> pdb=" O ASN B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 474 removed outlier: 3.728A pdb=" N LEU B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 470 " --> pdb=" O ASN B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'B' and resid 482 through 491 Processing helix chain 'B' and resid 491 through 498 Processing helix chain 'B' and resid 501 through 518 removed outlier: 4.145A pdb=" N PHE B 506 " --> pdb=" O TRP B 502 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N MET B 507 " --> pdb=" O GLN B 503 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B 510 " --> pdb=" O PHE B 506 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU B 511 " --> pdb=" O MET B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 536 removed outlier: 3.849A pdb=" N ALA B 523 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP B 530 " --> pdb=" O HIS B 526 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG B 534 " --> pdb=" O TRP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 560 Processing helix chain 'B' and resid 568 through 579 removed outlier: 4.033A pdb=" N ILE B 572 " --> pdb=" O GLY B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 584 through 613 removed outlier: 4.654A pdb=" N VAL B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG B 594 " --> pdb=" O SER B 590 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 609 " --> pdb=" O MET B 605 " (cutoff:3.500A) 772 hydrogen bonds defined for protein. 2289 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: 3.23 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2628 1.33 - 1.45: 2763 1.45 - 1.57: 6471 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 11976 Sorted by residual: bond pdb=" CG LEU A 265 " pdb=" CD1 LEU A 265 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.66e+00 bond pdb=" CG LEU C 265 " pdb=" CD1 LEU C 265 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.58e+00 bond pdb=" CG LEU B 265 " pdb=" CD1 LEU B 265 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.47e+00 bond pdb=" CG LEU A 455 " pdb=" CD2 LEU A 455 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.44e+00 bond pdb=" CG LEU C 455 " pdb=" CD2 LEU C 455 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.36e+00 ... (remaining 11971 not shown) Histogram of bond angle deviations from ideal: 96.90 - 104.39: 184 104.39 - 111.88: 5730 111.88 - 119.37: 4052 119.37 - 126.85: 6160 126.85 - 134.34: 188 Bond angle restraints: 16314 Sorted by residual: angle pdb=" C PRO C 479 " pdb=" N GLN C 480 " pdb=" CA GLN C 480 " ideal model delta sigma weight residual 125.66 134.07 -8.41 1.85e+00 2.92e-01 2.07e+01 angle pdb=" C PRO B 479 " pdb=" N GLN B 480 " pdb=" CA GLN B 480 " ideal model delta sigma weight residual 125.66 134.04 -8.38 1.85e+00 2.92e-01 2.05e+01 angle pdb=" C PRO A 479 " pdb=" N GLN A 480 " pdb=" CA GLN A 480 " ideal model delta sigma weight residual 125.66 134.04 -8.38 1.85e+00 2.92e-01 2.05e+01 angle pdb=" N SER B 161 " pdb=" CA SER B 161 " pdb=" C SER B 161 " ideal model delta sigma weight residual 109.81 118.20 -8.39 2.21e+00 2.05e-01 1.44e+01 angle pdb=" N SER A 161 " pdb=" CA SER A 161 " pdb=" C SER A 161 " ideal model delta sigma weight residual 109.81 118.15 -8.34 2.21e+00 2.05e-01 1.42e+01 ... (remaining 16309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 6352 14.96 - 29.91: 371 29.91 - 44.87: 120 44.87 - 59.82: 6 59.82 - 74.78: 6 Dihedral angle restraints: 6855 sinusoidal: 2421 harmonic: 4434 Sorted by residual: dihedral pdb=" CA HIS C 283 " pdb=" C HIS C 283 " pdb=" N PHE C 284 " pdb=" CA PHE C 284 " ideal model delta harmonic sigma weight residual 180.00 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA HIS B 283 " pdb=" C HIS B 283 " pdb=" N PHE B 284 " pdb=" CA PHE B 284 " ideal model delta harmonic sigma weight residual -180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA HIS A 283 " pdb=" C HIS A 283 " pdb=" N PHE A 284 " pdb=" CA PHE A 284 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 6852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1090 0.042 - 0.085: 604 0.085 - 0.127: 147 0.127 - 0.170: 49 0.170 - 0.212: 15 Chirality restraints: 1905 Sorted by residual: chirality pdb=" CA ARG C 350 " pdb=" N ARG C 350 " pdb=" C ARG C 350 " pdb=" CB ARG C 350 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ARG A 350 " pdb=" N ARG A 350 " pdb=" C ARG A 350 " pdb=" CB ARG A 350 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ARG B 350 " pdb=" N ARG B 350 " pdb=" C ARG B 350 " pdb=" CB ARG B 350 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1902 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 290 " 0.050 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO B 291 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 291 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 291 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 290 " -0.050 5.00e-02 4.00e+02 7.43e-02 8.83e+00 pdb=" N PRO A 291 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 290 " -0.050 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO C 291 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 291 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 291 " -0.042 5.00e-02 4.00e+02 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 3224 2.78 - 3.31: 11263 3.31 - 3.84: 20191 3.84 - 4.37: 24356 4.37 - 4.90: 40130 Nonbonded interactions: 99164 Sorted by model distance: nonbonded pdb=" O LEU C 243 " pdb=" OG1 THR C 247 " model vdw 2.245 2.440 nonbonded pdb=" O LEU B 243 " pdb=" OG1 THR B 247 " model vdw 2.245 2.440 nonbonded pdb=" O LEU A 243 " pdb=" OG1 THR A 247 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR A 380 " pdb=" OE2 GLU A 520 " model vdw 2.329 2.440 nonbonded pdb=" OH TYR B 380 " pdb=" OE2 GLU B 520 " model vdw 2.329 2.440 ... (remaining 99159 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.670 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 34.480 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.008 0.071 11976 Z= 0.541 Angle : 1.083 8.854 16314 Z= 0.589 Chirality : 0.056 0.212 1905 Planarity : 0.008 0.075 1995 Dihedral : 11.373 74.778 4005 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.25 % Allowed : 4.83 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.90 (0.13), residues: 1527 helix: -3.95 (0.08), residues: 1113 sheet: None (None), residues: 0 loop : -2.98 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 530 HIS 0.008 0.001 HIS A 389 PHE 0.039 0.004 PHE B 383 TYR 0.029 0.004 TYR B 478 ARG 0.006 0.001 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 540 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 540 average time/residue: 0.2521 time to fit residues: 188.6813 Evaluate side-chains 363 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 547 GLN A 547 GLN ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 547 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11976 Z= 0.228 Angle : 0.700 7.735 16314 Z= 0.359 Chirality : 0.041 0.174 1905 Planarity : 0.006 0.051 1995 Dihedral : 5.455 22.488 1626 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.07 % Allowed : 15.95 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.97 (0.18), residues: 1527 helix: -1.71 (0.13), residues: 1134 sheet: None (None), residues: 0 loop : -2.19 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 530 HIS 0.010 0.002 HIS A 532 PHE 0.020 0.002 PHE C 205 TYR 0.018 0.001 TYR C 211 ARG 0.007 0.001 ARG C 552 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 392 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 18 residues processed: 417 average time/residue: 0.1845 time to fit residues: 119.6774 Evaluate side-chains 357 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 339 time to evaluate : 3.074 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1041 time to fit residues: 5.4823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.0570 chunk 115 optimal weight: 0.7980 chunk 94 optimal weight: 0.0770 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 0.0070 chunk 150 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 HIS ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN C 466 ASN C 532 HIS ** C 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS B 127 HIS B 503 GLN B 532 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11976 Z= 0.186 Angle : 0.643 7.460 16314 Z= 0.324 Chirality : 0.041 0.151 1905 Planarity : 0.005 0.047 1995 Dihedral : 4.882 20.733 1626 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.80 % Allowed : 19.17 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.55 (0.20), residues: 1527 helix: -0.54 (0.14), residues: 1152 sheet: None (None), residues: 0 loop : -2.20 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 502 HIS 0.004 0.001 HIS B 526 PHE 0.025 0.002 PHE C 483 TYR 0.013 0.001 TYR B 559 ARG 0.005 0.001 ARG A 552 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 392 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 7 residues processed: 413 average time/residue: 0.1839 time to fit residues: 116.7151 Evaluate side-chains 345 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 338 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1018 time to fit residues: 3.0612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 HIS C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 503 GLN A 104 HIS ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 HIS B 127 HIS B 532 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11976 Z= 0.226 Angle : 0.643 7.194 16314 Z= 0.324 Chirality : 0.042 0.140 1905 Planarity : 0.004 0.050 1995 Dihedral : 4.710 19.235 1626 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.31 % Allowed : 21.54 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.21), residues: 1527 helix: 0.04 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -2.08 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 471 HIS 0.007 0.001 HIS C 104 PHE 0.032 0.002 PHE C 188 TYR 0.012 0.001 TYR B 548 ARG 0.004 0.000 ARG C 552 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 362 time to evaluate : 1.718 Fit side-chains outliers start: 39 outliers final: 20 residues processed: 386 average time/residue: 0.1879 time to fit residues: 112.8277 Evaluate side-chains 348 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 328 time to evaluate : 1.361 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1128 time to fit residues: 6.2558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 126 optimal weight: 0.0010 chunk 102 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 0.2980 chunk 132 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 HIS C 466 ASN B 127 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11976 Z= 0.212 Angle : 0.633 7.256 16314 Z= 0.318 Chirality : 0.041 0.132 1905 Planarity : 0.004 0.046 1995 Dihedral : 4.618 19.623 1626 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.71 % Allowed : 24.00 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.22), residues: 1527 helix: 0.33 (0.15), residues: 1149 sheet: None (None), residues: 0 loop : -1.96 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 318 HIS 0.003 0.001 HIS A 389 PHE 0.041 0.002 PHE C 188 TYR 0.010 0.001 TYR B 548 ARG 0.004 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 364 time to evaluate : 1.444 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 13 residues processed: 382 average time/residue: 0.1884 time to fit residues: 109.5698 Evaluate side-chains 338 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 325 time to evaluate : 1.468 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1080 time to fit residues: 4.5126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN B 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11976 Z= 0.192 Angle : 0.636 7.649 16314 Z= 0.317 Chirality : 0.041 0.166 1905 Planarity : 0.004 0.053 1995 Dihedral : 4.543 22.406 1626 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.46 % Allowed : 24.51 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.22), residues: 1527 helix: 0.52 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -1.88 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 502 HIS 0.007 0.001 HIS C 526 PHE 0.043 0.002 PHE C 188 TYR 0.008 0.001 TYR A 211 ARG 0.006 0.000 ARG C 350 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 357 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 370 average time/residue: 0.1837 time to fit residues: 104.0689 Evaluate side-chains 339 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 327 time to evaluate : 1.357 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1133 time to fit residues: 4.2575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.0050 chunk 91 optimal weight: 1.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 GLN A 154 HIS ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11976 Z= 0.277 Angle : 0.689 9.734 16314 Z= 0.345 Chirality : 0.044 0.206 1905 Planarity : 0.005 0.062 1995 Dihedral : 4.627 19.490 1626 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.54 % Allowed : 25.45 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.22), residues: 1527 helix: 0.57 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -1.67 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 232 HIS 0.005 0.001 HIS C 526 PHE 0.040 0.002 PHE C 188 TYR 0.013 0.001 TYR B 548 ARG 0.004 0.000 ARG C 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 337 time to evaluate : 1.509 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 349 average time/residue: 0.1879 time to fit residues: 100.0115 Evaluate side-chains 322 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 308 time to evaluate : 1.379 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1454 time to fit residues: 5.1346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 134 optimal weight: 8.9990 chunk 141 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11976 Z= 0.246 Angle : 0.678 8.564 16314 Z= 0.340 Chirality : 0.043 0.157 1905 Planarity : 0.004 0.061 1995 Dihedral : 4.624 21.058 1626 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.44 % Allowed : 26.46 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1527 helix: 0.65 (0.15), residues: 1149 sheet: None (None), residues: 0 loop : -1.69 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 471 HIS 0.005 0.001 HIS C 526 PHE 0.041 0.002 PHE C 188 TYR 0.014 0.001 TYR A 211 ARG 0.005 0.000 ARG C 350 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 327 time to evaluate : 1.431 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 334 average time/residue: 0.1884 time to fit residues: 96.0755 Evaluate side-chains 314 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 304 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1071 time to fit residues: 3.7514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11976 Z= 0.221 Angle : 0.680 9.918 16314 Z= 0.338 Chirality : 0.043 0.164 1905 Planarity : 0.004 0.062 1995 Dihedral : 4.602 22.117 1626 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.93 % Allowed : 27.06 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.22), residues: 1527 helix: 0.72 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -1.69 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 471 HIS 0.004 0.001 HIS C 526 PHE 0.041 0.002 PHE C 188 TYR 0.016 0.001 TYR A 211 ARG 0.005 0.000 ARG C 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 330 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 339 average time/residue: 0.1825 time to fit residues: 96.3492 Evaluate side-chains 318 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 313 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1063 time to fit residues: 2.7712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 0.0050 chunk 101 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11976 Z= 0.199 Angle : 0.686 11.514 16314 Z= 0.339 Chirality : 0.042 0.169 1905 Planarity : 0.004 0.062 1995 Dihedral : 4.516 24.792 1626 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.42 % Allowed : 28.07 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1527 helix: 0.78 (0.16), residues: 1143 sheet: None (None), residues: 0 loop : -1.61 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 318 HIS 0.004 0.001 HIS C 526 PHE 0.040 0.002 PHE C 188 TYR 0.023 0.001 TYR A 211 ARG 0.005 0.000 ARG C 350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 332 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 335 average time/residue: 0.1832 time to fit residues: 95.1027 Evaluate side-chains 307 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 305 time to evaluate : 1.372 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1211 time to fit residues: 2.2121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 124 optimal weight: 0.0040 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122444 restraints weight = 19011.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125354 restraints weight = 9979.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.127145 restraints weight = 6511.720| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.6067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11976 Z= 0.215 Angle : 0.711 14.234 16314 Z= 0.353 Chirality : 0.044 0.279 1905 Planarity : 0.004 0.061 1995 Dihedral : 4.514 27.170 1626 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.13 % Favored : 95.81 % Rotamer: Outliers : 1.02 % Allowed : 28.58 % Favored : 70.40 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.22), residues: 1527 helix: 0.82 (0.16), residues: 1149 sheet: None (None), residues: 0 loop : -1.63 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 318 HIS 0.008 0.001 HIS A 526 PHE 0.045 0.002 PHE B 205 TYR 0.022 0.001 TYR A 211 ARG 0.005 0.000 ARG C 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2713.54 seconds wall clock time: 50 minutes 3.14 seconds (3003.14 seconds total)