Starting phenix.real_space_refine on Thu Feb 15 08:16:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/02_2024/6ksw_0775.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/02_2024/6ksw_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_0775/02_2024/6ksw_0775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/02_2024/6ksw_0775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/02_2024/6ksw_0775.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ksw_0775/02_2024/6ksw_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.91, per 1000 atoms: 0.51 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: 4.70 Conformation dependent library (CDL) restraints added in 2.3 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: 1.10 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: 3.63 Time building geometry restraints manager: 5.08 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: 0.700 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: 3.500 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 32.970 Find NCS groups from input model: 0.670 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.950 ------------------------------------------------------------------------------- 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 : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.5699 (ptp90) REVERT: C 106 ILE cc_start: 0.8217 (mp) cc_final: 0.8014 (pt) REVERT: C 183 VAL cc_start: 0.9108 (t) cc_final: 0.8856 (p) REVERT: C 228 ARG cc_start: 0.8132 (tmm-80) cc_final: 0.7016 (mmm160) REVERT: C 280 TYR cc_start: 0.8608 (p90) cc_final: 0.8334 (p90) REVERT: C 337 ASN cc_start: 0.9011 (m-40) cc_final: 0.8651 (m-40) REVERT: C 370 SER cc_start: 0.8947 (m) cc_final: 0.8742 (p) REVERT: C 515 LYS cc_start: 0.8643 (tmmt) cc_final: 0.8201 (ttpp) REVERT: C 549 ILE cc_start: 0.8925 (mp) cc_final: 0.8646 (mt) REVERT: C 555 ILE cc_start: 0.8700 (mt) cc_final: 0.8392 (mm) REVERT: C 569 SER cc_start: 0.8624 (m) cc_final: 0.7890 (t) REVERT: C 600 THR cc_start: 0.8905 (m) cc_final: 0.8680 (p) REVERT: A 103 ARG cc_start: 0.7407 (ttm-80) cc_final: 0.5630 (ptp90) REVERT: A 183 VAL cc_start: 0.9083 (t) cc_final: 0.8842 (p) REVERT: A 211 TYR cc_start: 0.8259 (m-80) cc_final: 0.7801 (m-80) REVERT: A 228 ARG cc_start: 0.8075 (tmm-80) cc_final: 0.6939 (mtp180) REVERT: A 300 MET cc_start: 0.7736 (mmm) cc_final: 0.7496 (mmt) REVERT: A 337 ASN cc_start: 0.8999 (m-40) cc_final: 0.8752 (m-40) REVERT: A 390 LEU cc_start: 0.9328 (tt) cc_final: 0.9037 (tt) REVERT: A 477 ASP cc_start: 0.7761 (m-30) cc_final: 0.7504 (m-30) REVERT: A 549 ILE cc_start: 0.8849 (mp) cc_final: 0.7986 (mt) REVERT: A 555 ILE cc_start: 0.8819 (mt) cc_final: 0.8448 (mm) REVERT: B 103 ARG cc_start: 0.7085 (ttm-80) cc_final: 0.5310 (ptp90) REVERT: B 228 ARG cc_start: 0.8206 (tmm-80) cc_final: 0.6903 (mtp180) REVERT: B 500 VAL cc_start: 0.8569 (t) cc_final: 0.8320 (t) REVERT: B 600 THR cc_start: 0.8831 (m) cc_final: 0.8509 (p) outliers start: 3 outliers final: 0 residues processed: 540 average time/residue: 0.2449 time to fit residues: 183.7829 Evaluate side-chains 370 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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: 1.9990 chunk 64 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 310 GLN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11976 Z= 0.230 Angle : 0.699 7.837 16314 Z= 0.360 Chirality : 0.041 0.171 1905 Planarity : 0.006 0.052 1995 Dihedral : 5.471 21.878 1626 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.99 % Allowed : 15.27 % Favored : 80.75 % 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: -3.06 (0.18), residues: 1527 helix: -1.74 (0.12), residues: 1143 sheet: None (None), residues: 0 loop : -2.31 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 530 HIS 0.010 0.001 HIS A 532 PHE 0.019 0.002 PHE A 251 TYR 0.018 0.001 TYR C 211 ARG 0.006 0.001 ARG B 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 451 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 404 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 188 PHE cc_start: 0.7869 (m-10) cc_final: 0.7605 (m-80) REVERT: C 211 TYR cc_start: 0.8182 (m-80) cc_final: 0.7567 (m-80) REVERT: C 370 SER cc_start: 0.8782 (m) cc_final: 0.8408 (p) REVERT: C 549 ILE cc_start: 0.8917 (mp) cc_final: 0.8461 (mt) REVERT: C 555 ILE cc_start: 0.8637 (mt) cc_final: 0.8434 (mm) REVERT: C 569 SER cc_start: 0.8618 (m) cc_final: 0.8144 (t) REVERT: A 211 TYR cc_start: 0.8251 (m-80) cc_final: 0.7579 (m-80) REVERT: A 216 PHE cc_start: 0.8364 (t80) cc_final: 0.8118 (t80) REVERT: A 300 MET cc_start: 0.7896 (mmm) cc_final: 0.7642 (mmt) REVERT: A 302 MET cc_start: 0.8151 (mtp) cc_final: 0.7945 (mtm) REVERT: A 312 ILE cc_start: 0.8618 (mt) cc_final: 0.8369 (mt) REVERT: A 533 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8425 (tt) REVERT: A 535 LYS cc_start: 0.7937 (mptm) cc_final: 0.7650 (mtmt) REVERT: A 549 ILE cc_start: 0.8753 (mp) cc_final: 0.8049 (mt) REVERT: A 555 ILE cc_start: 0.8802 (mt) cc_final: 0.8527 (mm) REVERT: B 330 GLU cc_start: 0.7568 (tp30) cc_final: 0.7362 (tp30) REVERT: B 392 THR cc_start: 0.9050 (m) cc_final: 0.8735 (p) REVERT: B 494 PHE cc_start: 0.8641 (m-80) cc_final: 0.8412 (m-80) REVERT: B 501 GLU cc_start: 0.7186 (tp30) cc_final: 0.6724 (tm-30) REVERT: B 519 ASN cc_start: 0.8145 (p0) cc_final: 0.7938 (p0) outliers start: 47 outliers final: 16 residues processed: 431 average time/residue: 0.1755 time to fit residues: 116.8451 Evaluate side-chains 358 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 341 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 477 ASP 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: 0.8980 chunk 115 optimal weight: 0.4980 chunk 94 optimal weight: 0.0000 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 466 ASN C 532 HIS ** C 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS B 127 HIS B 532 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11976 Z= 0.198 Angle : 0.644 7.582 16314 Z= 0.325 Chirality : 0.041 0.137 1905 Planarity : 0.005 0.046 1995 Dihedral : 4.948 20.821 1626 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.99 % Allowed : 19.00 % Favored : 77.01 % 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: -1.60 (0.20), residues: 1527 helix: -0.59 (0.14), residues: 1149 sheet: None (None), residues: 0 loop : -2.16 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 530 HIS 0.006 0.001 HIS B 526 PHE 0.026 0.002 PHE C 483 TYR 0.015 0.001 TYR B 559 ARG 0.005 0.001 ARG B 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 431 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 384 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 TYR cc_start: 0.8202 (m-80) cc_final: 0.7336 (m-80) REVERT: C 214 LEU cc_start: 0.8738 (mt) cc_final: 0.8200 (mt) REVERT: C 216 PHE cc_start: 0.8325 (t80) cc_final: 0.8119 (t80) REVERT: C 220 LYS cc_start: 0.4229 (mttm) cc_final: 0.3847 (mmtm) REVERT: C 401 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8599 (p) REVERT: C 549 ILE cc_start: 0.8700 (mp) cc_final: 0.8331 (mt) REVERT: C 555 ILE cc_start: 0.8573 (mt) cc_final: 0.8290 (mm) REVERT: C 569 SER cc_start: 0.8513 (m) cc_final: 0.8186 (t) REVERT: A 211 TYR cc_start: 0.8236 (m-80) cc_final: 0.7333 (m-80) REVERT: A 214 LEU cc_start: 0.8860 (mt) cc_final: 0.8436 (mt) REVERT: A 435 GLU cc_start: 0.6940 (tt0) cc_final: 0.6651 (tt0) REVERT: A 502 TRP cc_start: 0.8378 (t-100) cc_final: 0.7799 (t60) REVERT: A 533 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8254 (tt) REVERT: A 555 ILE cc_start: 0.8819 (mt) cc_final: 0.8568 (mm) REVERT: B 330 GLU cc_start: 0.7533 (tp30) cc_final: 0.7285 (tp30) REVERT: B 519 ASN cc_start: 0.8222 (p0) cc_final: 0.8011 (p0) REVERT: B 549 ILE cc_start: 0.8810 (mt) cc_final: 0.8137 (mt) outliers start: 47 outliers final: 21 residues processed: 409 average time/residue: 0.1757 time to fit residues: 110.7263 Evaluate side-chains 367 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 344 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 139 optimal weight: 0.0870 chunk 147 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 342 GLN C 503 GLN B 104 HIS B 127 HIS B 503 GLN B 532 HIS ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11976 Z= 0.188 Angle : 0.625 6.841 16314 Z= 0.313 Chirality : 0.041 0.154 1905 Planarity : 0.004 0.045 1995 Dihedral : 4.646 18.155 1626 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.65 % Allowed : 21.12 % Favored : 75.23 % 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: -0.80 (0.21), residues: 1527 helix: 0.04 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -2.04 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 471 HIS 0.009 0.001 HIS C 104 PHE 0.024 0.002 PHE A 251 TYR 0.012 0.001 TYR B 559 ARG 0.004 0.000 ARG B 246 *********************** 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 434 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 391 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 220 LYS cc_start: 0.4027 (mttm) cc_final: 0.3688 (mmtm) REVERT: C 228 ARG cc_start: 0.8053 (tmm-80) cc_final: 0.6661 (mmm160) REVERT: C 304 TYR cc_start: 0.7599 (t80) cc_final: 0.7106 (t80) REVERT: C 532 HIS cc_start: 0.7046 (m90) cc_final: 0.6785 (m-70) REVERT: C 549 ILE cc_start: 0.8395 (mp) cc_final: 0.7851 (mt) REVERT: C 605 MET cc_start: 0.7633 (mtt) cc_final: 0.7204 (mtt) REVERT: A 211 TYR cc_start: 0.8155 (m-80) cc_final: 0.7544 (m-80) REVERT: A 502 TRP cc_start: 0.8345 (t-100) cc_final: 0.7779 (t60) REVERT: A 533 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8272 (tt) REVERT: A 555 ILE cc_start: 0.8672 (mt) cc_final: 0.8437 (mm) REVERT: B 252 ILE cc_start: 0.8762 (tt) cc_final: 0.8459 (pt) outliers start: 43 outliers final: 25 residues processed: 416 average time/residue: 0.1889 time to fit residues: 120.4311 Evaluate side-chains 364 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 338 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 477 ASP 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: 8.9990 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 37 optimal weight: 0.0670 chunk 49 optimal weight: 3.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- 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** C 342 GLN C 466 ASN A 104 HIS ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11976 Z= 0.328 Angle : 0.692 9.940 16314 Z= 0.352 Chirality : 0.045 0.221 1905 Planarity : 0.005 0.050 1995 Dihedral : 4.832 19.267 1626 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.26 % Allowed : 22.56 % Favored : 72.18 % 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: -0.65 (0.21), residues: 1527 helix: 0.10 (0.15), residues: 1149 sheet: None (None), residues: 0 loop : -1.82 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 318 HIS 0.012 0.001 HIS C 104 PHE 0.036 0.002 PHE C 188 TYR 0.017 0.001 TYR B 559 ARG 0.006 0.001 ARG C 103 *********************** 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 424 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 362 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7210 (OUTLIER) cc_final: 0.5839 (p-80) REVERT: C 211 TYR cc_start: 0.8238 (m-80) cc_final: 0.7962 (m-80) REVERT: C 390 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9120 (tt) REVERT: C 462 LEU cc_start: 0.8970 (tp) cc_final: 0.8766 (tp) REVERT: C 504 ASP cc_start: 0.7362 (m-30) cc_final: 0.7055 (t0) REVERT: C 549 ILE cc_start: 0.8289 (mp) cc_final: 0.7731 (mt) REVERT: C 555 ILE cc_start: 0.8541 (mm) cc_final: 0.8331 (mm) REVERT: A 188 PHE cc_start: 0.8036 (m-80) cc_final: 0.7828 (m-80) REVERT: A 211 TYR cc_start: 0.8334 (m-80) cc_final: 0.7938 (m-80) REVERT: A 330 GLU cc_start: 0.7495 (tp30) cc_final: 0.7248 (tp30) REVERT: A 435 GLU cc_start: 0.7169 (tt0) cc_final: 0.6902 (tt0) REVERT: A 475 MET cc_start: 0.7937 (mmp) cc_final: 0.7641 (mmm) REVERT: A 525 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8206 (pp20) REVERT: A 533 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8362 (tt) REVERT: A 535 LYS cc_start: 0.8098 (mptm) cc_final: 0.7894 (mptt) REVERT: A 555 ILE cc_start: 0.8603 (mt) cc_final: 0.8387 (mm) REVERT: B 205 PHE cc_start: 0.8930 (t80) cc_final: 0.8570 (t80) outliers start: 62 outliers final: 42 residues processed: 399 average time/residue: 0.1728 time to fit residues: 106.8905 Evaluate side-chains 368 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 322 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 578 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 0.0010 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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** B 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11976 Z= 0.198 Angle : 0.642 10.121 16314 Z= 0.320 Chirality : 0.042 0.244 1905 Planarity : 0.004 0.052 1995 Dihedral : 4.640 22.036 1626 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.50 % Allowed : 24.09 % Favored : 71.42 % 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: 0.41 (0.16), residues: 1155 sheet: None (None), residues: 0 loop : -1.80 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 318 HIS 0.008 0.001 HIS C 104 PHE 0.023 0.001 PHE C 205 TYR 0.010 0.001 TYR B 559 ARG 0.003 0.000 ARG B 246 *********************** 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 404 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 351 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.6896 (OUTLIER) cc_final: 0.5528 (p-80) REVERT: C 215 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8106 (mm) REVERT: C 220 LYS cc_start: 0.4174 (mttm) cc_final: 0.3938 (mmtm) REVERT: C 497 MET cc_start: 0.8055 (tpp) cc_final: 0.7821 (tpt) REVERT: C 549 ILE cc_start: 0.8366 (mp) cc_final: 0.8049 (mt) REVERT: A 117 MET cc_start: 0.7156 (tpp) cc_final: 0.6792 (tpp) REVERT: A 182 LEU cc_start: 0.8858 (mm) cc_final: 0.8492 (pp) REVERT: A 188 PHE cc_start: 0.8068 (m-80) cc_final: 0.7823 (m-80) REVERT: A 211 TYR cc_start: 0.8234 (m-80) cc_final: 0.7742 (m-80) REVERT: A 435 GLU cc_start: 0.7053 (tt0) cc_final: 0.6785 (tt0) REVERT: A 475 MET cc_start: 0.7550 (mmp) cc_final: 0.7286 (mmm) REVERT: A 525 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8270 (pp20) REVERT: A 533 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8269 (tt) REVERT: B 252 ILE cc_start: 0.8766 (tt) cc_final: 0.8509 (pt) outliers start: 53 outliers final: 38 residues processed: 383 average time/residue: 0.1747 time to fit residues: 103.3500 Evaluate side-chains 372 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 330 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 586 ARG Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 566 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 83 optimal weight: 0.0030 chunk 124 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 68 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 154 HIS ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 HIS B 546 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11976 Z= 0.187 Angle : 0.646 9.389 16314 Z= 0.321 Chirality : 0.042 0.245 1905 Planarity : 0.004 0.058 1995 Dihedral : 4.563 23.986 1626 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.33 % Allowed : 25.02 % Favored : 70.65 % 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: 0.02 (0.22), residues: 1527 helix: 0.60 (0.16), residues: 1158 sheet: None (None), residues: 0 loop : -1.70 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 502 HIS 0.008 0.001 HIS C 104 PHE 0.041 0.001 PHE C 188 TYR 0.010 0.001 TYR B 559 ARG 0.003 0.000 ARG B 246 *********************** 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 412 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 361 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.6770 (OUTLIER) cc_final: 0.5490 (p-80) REVERT: C 124 LEU cc_start: 0.7662 (pt) cc_final: 0.7362 (pp) REVERT: C 200 GLN cc_start: 0.8495 (mp10) cc_final: 0.8248 (mt0) REVERT: C 390 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9015 (tt) REVERT: C 549 ILE cc_start: 0.8207 (mp) cc_final: 0.7663 (mt) REVERT: A 182 LEU cc_start: 0.8855 (mm) cc_final: 0.8484 (pp) REVERT: A 188 PHE cc_start: 0.7977 (m-80) cc_final: 0.7769 (m-80) REVERT: A 210 MET cc_start: 0.8293 (tmm) cc_final: 0.7649 (ttt) REVERT: A 211 TYR cc_start: 0.8187 (m-80) cc_final: 0.7750 (m-80) REVERT: A 485 LEU cc_start: 0.8780 (tt) cc_final: 0.8074 (mt) REVERT: A 502 TRP cc_start: 0.8351 (t60) cc_final: 0.7425 (t60) REVERT: A 525 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8258 (pp20) REVERT: A 533 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8394 (tt) REVERT: B 117 MET cc_start: 0.7239 (tpp) cc_final: 0.6807 (tpp) REVERT: B 205 PHE cc_start: 0.8815 (t80) cc_final: 0.8562 (t80) REVERT: B 210 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7979 (ptm) REVERT: B 252 ILE cc_start: 0.8742 (tt) cc_final: 0.8481 (pt) outliers start: 51 outliers final: 35 residues processed: 389 average time/residue: 0.1826 time to fit residues: 109.2591 Evaluate side-chains 372 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 332 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 586 ARG Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 566 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 141 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** C 342 GLN A 154 HIS ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5568 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= 0.206 Angle : 0.664 9.656 16314 Z= 0.329 Chirality : 0.044 0.286 1905 Planarity : 0.004 0.058 1995 Dihedral : 4.552 26.520 1626 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.50 % Allowed : 25.87 % Favored : 69.64 % 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: 0.10 (0.22), residues: 1527 helix: 0.67 (0.16), residues: 1155 sheet: None (None), residues: 0 loop : -1.65 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 502 HIS 0.008 0.001 HIS C 104 PHE 0.033 0.001 PHE B 251 TYR 0.010 0.001 TYR B 548 ARG 0.003 0.000 ARG B 552 *********************** 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 400 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 347 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.6675 (OUTLIER) cc_final: 0.5501 (p-80) REVERT: C 390 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9035 (tt) REVERT: C 479 PRO cc_start: 0.7379 (Cg_exo) cc_final: 0.6712 (Cg_endo) REVERT: C 480 GLN cc_start: 0.7814 (pm20) cc_final: 0.7190 (pm20) REVERT: C 504 ASP cc_start: 0.7708 (t0) cc_final: 0.7414 (t0) REVERT: A 117 MET cc_start: 0.7196 (tpp) cc_final: 0.6702 (tpp) REVERT: A 188 PHE cc_start: 0.8022 (m-80) cc_final: 0.7795 (m-80) REVERT: A 190 LEU cc_start: 0.8689 (mt) cc_final: 0.8382 (mt) REVERT: A 205 PHE cc_start: 0.8750 (t80) cc_final: 0.8432 (t80) REVERT: A 211 TYR cc_start: 0.8105 (m-80) cc_final: 0.7808 (m-80) REVERT: A 485 LEU cc_start: 0.8821 (tt) cc_final: 0.8099 (mt) REVERT: A 502 TRP cc_start: 0.8067 (t60) cc_final: 0.7201 (t60) REVERT: A 525 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8165 (pp20) REVERT: A 533 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8403 (tt) REVERT: B 205 PHE cc_start: 0.8749 (t80) cc_final: 0.8529 (t80) REVERT: B 210 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7239 (ttt) REVERT: B 252 ILE cc_start: 0.8717 (tt) cc_final: 0.8408 (pt) REVERT: B 479 PRO cc_start: 0.7126 (Cg_exo) cc_final: 0.6317 (Cg_endo) REVERT: B 480 GLN cc_start: 0.7623 (pm20) cc_final: 0.7173 (pm20) REVERT: B 504 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7396 (t0) outliers start: 53 outliers final: 38 residues processed: 378 average time/residue: 0.1735 time to fit residues: 102.4259 Evaluate side-chains 370 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 326 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 586 ARG Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 566 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 6.9990 chunk 137 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 124 optimal weight: 0.0870 chunk 129 optimal weight: 5.9990 chunk 136 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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** C 342 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5735 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= 0.204 Angle : 0.677 10.515 16314 Z= 0.330 Chirality : 0.044 0.343 1905 Planarity : 0.004 0.059 1995 Dihedral : 4.531 27.869 1626 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.33 % Allowed : 26.29 % Favored : 69.38 % 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: 0.17 (0.22), residues: 1527 helix: 0.76 (0.16), residues: 1143 sheet: None (None), residues: 0 loop : -1.74 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 530 HIS 0.008 0.001 HIS C 104 PHE 0.034 0.001 PHE B 251 TYR 0.010 0.001 TYR C 211 ARG 0.004 0.000 ARG C 552 *********************** 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 390 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 339 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 252 ILE cc_start: 0.8702 (tt) cc_final: 0.8468 (pt) REVERT: C 355 TYR cc_start: 0.7343 (m-80) cc_final: 0.7091 (m-80) REVERT: C 390 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9038 (tt) REVERT: C 479 PRO cc_start: 0.7200 (Cg_exo) cc_final: 0.6567 (Cg_endo) REVERT: C 480 GLN cc_start: 0.7654 (pm20) cc_final: 0.7027 (pm20) REVERT: A 182 LEU cc_start: 0.8873 (mm) cc_final: 0.8541 (pp) REVERT: A 188 PHE cc_start: 0.8033 (m-80) cc_final: 0.7795 (m-80) REVERT: A 190 LEU cc_start: 0.8660 (mt) cc_final: 0.8360 (mt) REVERT: A 205 PHE cc_start: 0.8719 (t80) cc_final: 0.8347 (t80) REVERT: A 475 MET cc_start: 0.7248 (mmp) cc_final: 0.6966 (mmm) REVERT: A 502 TRP cc_start: 0.8025 (t60) cc_final: 0.7190 (t60) REVERT: A 525 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8027 (pp20) REVERT: A 533 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8315 (tt) REVERT: B 188 PHE cc_start: 0.7981 (m-80) cc_final: 0.7758 (m-80) REVERT: B 201 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: B 205 PHE cc_start: 0.8679 (t80) cc_final: 0.8445 (t80) REVERT: B 252 ILE cc_start: 0.8705 (tt) cc_final: 0.8304 (pt) REVERT: B 479 PRO cc_start: 0.7031 (Cg_exo) cc_final: 0.6162 (Cg_endo) REVERT: B 480 GLN cc_start: 0.7579 (pm20) cc_final: 0.7112 (pm20) outliers start: 51 outliers final: 37 residues processed: 370 average time/residue: 0.1727 time to fit residues: 100.3722 Evaluate side-chains 369 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 328 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 ARG Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 498 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 12 optimal weight: 0.0370 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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** ** 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: 0.7902 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11976 Z= 0.212 Angle : 0.693 11.363 16314 Z= 0.340 Chirality : 0.044 0.342 1905 Planarity : 0.004 0.058 1995 Dihedral : 4.528 31.602 1626 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.16 % Allowed : 26.46 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.82 (0.16), residues: 1143 sheet: None (None), residues: 0 loop : -1.74 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 502 HIS 0.008 0.001 HIS C 104 PHE 0.036 0.001 PHE B 251 TYR 0.012 0.001 TYR B 548 ARG 0.003 0.000 ARG B 246 ********************** 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 392 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 343 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 ILE cc_start: 0.8693 (tt) cc_final: 0.8440 (pt) REVERT: C 342 GLN cc_start: 0.8207 (pt0) cc_final: 0.7993 (pt0) REVERT: C 355 TYR cc_start: 0.7435 (m-80) cc_final: 0.7182 (m-80) REVERT: C 390 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9023 (tt) REVERT: C 502 TRP cc_start: 0.8542 (t-100) cc_final: 0.8257 (t60) REVERT: A 182 LEU cc_start: 0.8889 (mm) cc_final: 0.8546 (pp) REVERT: A 188 PHE cc_start: 0.8046 (m-80) cc_final: 0.7788 (m-80) REVERT: A 190 LEU cc_start: 0.8681 (mt) cc_final: 0.8389 (mt) REVERT: A 205 PHE cc_start: 0.8752 (t80) cc_final: 0.8395 (t80) REVERT: A 237 GLN cc_start: 0.7825 (pt0) cc_final: 0.7555 (pt0) REVERT: A 475 MET cc_start: 0.7138 (mmp) cc_final: 0.6801 (mmm) REVERT: A 502 TRP cc_start: 0.7993 (t60) cc_final: 0.7108 (t60) REVERT: A 525 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7991 (pp20) REVERT: A 533 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8276 (tt) REVERT: B 188 PHE cc_start: 0.7935 (m-80) cc_final: 0.7723 (m-80) REVERT: B 201 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7888 (mp10) REVERT: B 252 ILE cc_start: 0.8732 (tt) cc_final: 0.8338 (pt) REVERT: B 525 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7885 (pp20) outliers start: 49 outliers final: 37 residues processed: 372 average time/residue: 0.1863 time to fit residues: 109.5350 Evaluate side-chains 365 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 324 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 498 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 124 optimal weight: 0.0010 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.136591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115433 restraints weight = 18918.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118401 restraints weight = 9703.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120158 restraints weight = 6256.314| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5892 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= 0.219 Angle : 0.694 12.333 16314 Z= 0.342 Chirality : 0.044 0.333 1905 Planarity : 0.004 0.059 1995 Dihedral : 4.530 30.641 1626 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.82 % Allowed : 26.63 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.31 (0.22), residues: 1527 helix: 0.90 (0.16), residues: 1137 sheet: None (None), residues: 0 loop : -1.77 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 502 HIS 0.008 0.001 HIS C 104 PHE 0.036 0.001 PHE B 251 TYR 0.014 0.001 TYR C 211 ARG 0.003 0.000 ARG B 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2698.03 seconds wall clock time: 49 minutes 59.34 seconds (2999.34 seconds total)