Starting phenix.real_space_refine (version: dev) on Mon Dec 12 18:39:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/12_2022/6ksw_0775.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/12_2022/6ksw_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_2022/6ksw_0775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/12_2022/6ksw_0775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/12_2022/6ksw_0775.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/12_2022/6ksw_0775.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 7.43, per 1000 atoms: 0.64 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: 5.34 Conformation dependent library (CDL) restraints added in 2.0 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: 0.58 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: 3.42 Time building geometry restraints manager: 5.71 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 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. 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: 0.000 Extract box with map and model: 4.390 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.100 Process input model: 34.430 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 % 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 *********************** 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 : 1.318 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: 0.2360 time to fit residues: 178.2372 Evaluate side-chains 363 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.446 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9117 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.8039 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 % 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 *********************** 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 : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 18 residues processed: 417 average time/residue: 0.1723 time to fit residues: 111.0465 Evaluate side-chains 357 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 339 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1019 time to fit residues: 5.2425 ------------------------------------------------------------------------------- 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: 3.9990 chunk 115 optimal weight: 0.9990 chunk 94 optimal weight: 0.0970 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 0.4980 chunk 150 optimal weight: 8.9990 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: 1.0582 ------------------------------------------------------------------------------- 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: 0.8069 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 11976 Z= 0.229 Angle : 0.663 7.444 16314 Z= 0.337 Chirality : 0.042 0.143 1905 Planarity : 0.005 0.047 1995 Dihedral : 5.015 22.241 1626 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 3.22 % 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: -1.62 (0.20), residues: 1527 helix: -0.58 (0.14), residues: 1149 sheet: None (None), residues: 0 loop : -2.24 (0.30), residues: 378 *********************** 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 396 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 358 time to evaluate : 1.292 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 10 residues processed: 382 average time/residue: 0.1788 time to fit residues: 106.3310 Evaluate side-chains 341 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 331 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1079 time to fit residues: 3.9232 ------------------------------------------------------------------------------- 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: 1.9990 chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11976 Z= 0.202 Angle : 0.636 7.178 16314 Z= 0.321 Chirality : 0.041 0.139 1905 Planarity : 0.004 0.046 1995 Dihedral : 4.778 22.542 1626 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 3.31 % 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: -0.88 (0.21), residues: 1527 helix: 0.01 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -2.15 (0.31), residues: 387 *********************** 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 409 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 370 time to evaluate : 1.632 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 19 residues processed: 389 average time/residue: 0.1748 time to fit residues: 105.2719 Evaluate side-chains 351 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 332 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1047 time to fit residues: 5.5632 ------------------------------------------------------------------------------- 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: 10.0000 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 126 optimal weight: 0.2980 chunk 102 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 0.0970 chunk 132 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 C 466 ASN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 11976 Z= 0.258 Angle : 0.663 7.517 16314 Z= 0.334 Chirality : 0.043 0.179 1905 Planarity : 0.004 0.049 1995 Dihedral : 4.774 22.689 1626 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 2.54 % 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: -0.56 (0.21), residues: 1527 helix: 0.19 (0.15), residues: 1149 sheet: None (None), residues: 0 loop : -1.89 (0.32), residues: 378 *********************** 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 380 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 350 time to evaluate : 1.424 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 366 average time/residue: 0.1882 time to fit residues: 106.7083 Evaluate side-chains 339 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 326 time to evaluate : 1.368 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1139 time to fit residues: 4.5160 ------------------------------------------------------------------------------- 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: 30.0000 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 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 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN B 127 HIS B 200 GLN B 546 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 11976 Z= 0.232 Angle : 0.658 7.648 16314 Z= 0.331 Chirality : 0.042 0.148 1905 Planarity : 0.004 0.050 1995 Dihedral : 4.724 22.482 1626 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 3.73 % 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: -0.26 (0.22), residues: 1527 helix: 0.42 (0.15), residues: 1149 sheet: None (None), residues: 0 loop : -1.80 (0.33), residues: 378 *********************** 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 416 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 372 time to evaluate : 1.541 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 22 residues processed: 394 average time/residue: 0.2072 time to fit residues: 124.1399 Evaluate side-chains 350 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 328 time to evaluate : 1.410 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1291 time to fit residues: 6.6634 ------------------------------------------------------------------------------- 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: 0.9990 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 chunk 147 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 11976 Z= 0.204 Angle : 0.662 7.741 16314 Z= 0.332 Chirality : 0.042 0.184 1905 Planarity : 0.004 0.061 1995 Dihedral : 4.686 22.473 1626 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 1.53 % 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: 0.57 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -1.80 (0.33), residues: 369 *********************** 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 380 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 362 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 369 average time/residue: 0.1975 time to fit residues: 111.4972 Evaluate side-chains 320 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 314 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1196 time to fit residues: 3.2530 ------------------------------------------------------------------------------- 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: 9.9990 chunk 88 optimal weight: 0.9980 chunk 44 optimal weight: 0.0070 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 11976 Z= 0.211 Angle : 0.672 10.552 16314 Z= 0.335 Chirality : 0.042 0.169 1905 Planarity : 0.004 0.062 1995 Dihedral : 4.625 22.122 1626 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 1.44 % 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: 0.08 (0.22), residues: 1527 helix: 0.65 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -1.68 (0.33), residues: 369 *********************** 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 356 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 339 time to evaluate : 1.310 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 348 average time/residue: 0.1871 time to fit residues: 100.0350 Evaluate side-chains 333 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 324 time to evaluate : 1.320 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1021 time to fit residues: 3.4811 ------------------------------------------------------------------------------- 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: 2.9990 chunk 137 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** B 546 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 11976 Z= 0.242 Angle : 0.708 12.556 16314 Z= 0.354 Chirality : 0.044 0.253 1905 Planarity : 0.004 0.063 1995 Dihedral : 4.654 22.960 1626 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer Outliers : 1.27 % 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: 0.05 (0.22), residues: 1527 helix: 0.60 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -1.70 (0.34), residues: 351 *********************** 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 340 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 325 time to evaluate : 1.417 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 333 average time/residue: 0.1820 time to fit residues: 94.0865 Evaluate side-chains 320 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 312 time to evaluate : 1.432 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1058 time to fit residues: 3.3773 ------------------------------------------------------------------------------- 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: 8.9990 chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 0.0980 chunk 101 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 74 optimal weight: 0.0030 chunk 96 optimal weight: 0.9980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 11976 Z= 0.205 Angle : 0.709 12.821 16314 Z= 0.352 Chirality : 0.043 0.242 1905 Planarity : 0.004 0.062 1995 Dihedral : 4.629 25.848 1626 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.85 % 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: 0.08 (0.22), residues: 1527 helix: 0.73 (0.16), residues: 1149 sheet: None (None), residues: 0 loop : -1.95 (0.31), residues: 378 ********************** 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 334 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 324 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 329 average time/residue: 0.1765 time to fit residues: 91.0348 Evaluate side-chains 309 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 306 time to evaluate : 1.476 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1199 time to fit residues: 2.5316 ------------------------------------------------------------------------------- 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: 1.9990 chunk 37 optimal weight: 0.0770 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 50 optimal weight: 0.0070 chunk 124 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 106 optimal weight: 1.9990 overall best weight: 0.6156 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122057 restraints weight = 19130.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124939 restraints weight = 9881.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126780 restraints weight = 6429.983| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 11976 Z= 0.213 Angle : 0.712 12.560 16314 Z= 0.353 Chirality : 0.044 0.217 1905 Planarity : 0.004 0.062 1995 Dihedral : 4.601 27.280 1626 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 1.10 % 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: 0.19 (0.22), residues: 1527 helix: 0.80 (0.16), residues: 1152 sheet: None (None), residues: 0 loop : -1.87 (0.31), residues: 375 =============================================================================== Job complete usr+sys time: 2593.61 seconds wall clock time: 47 minutes 51.33 seconds (2871.33 seconds total)