Starting phenix.real_space_refine on Sun Mar 17 17:03:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo4_7118/03_2024/6bo4_7118.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo4_7118/03_2024/6bo4_7118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo4_7118/03_2024/6bo4_7118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo4_7118/03_2024/6bo4_7118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo4_7118/03_2024/6bo4_7118.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo4_7118/03_2024/6bo4_7118.pdb" } resolution = 4.0 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= 0.002 sd= 0.006 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 80 5.16 5 C 11992 2.51 5 N 3128 2.21 5 O 3232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18432 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4608 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'CIS': 7, 'PTRANS': 25, 'TRANS': 592} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 463 Unresolved non-hydrogen angles: 581 Unresolved non-hydrogen dihedrals: 384 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 278 Chain: "D" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4608 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'CIS': 7, 'PTRANS': 25, 'TRANS': 592} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 463 Unresolved non-hydrogen angles: 581 Unresolved non-hydrogen dihedrals: 384 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 278 Chain: "B" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4608 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'CIS': 7, 'PTRANS': 25, 'TRANS': 592} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 463 Unresolved non-hydrogen angles: 581 Unresolved non-hydrogen dihedrals: 384 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 278 Chain: "C" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4608 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'CIS': 7, 'PTRANS': 25, 'TRANS': 592} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 463 Unresolved non-hydrogen angles: 581 Unresolved non-hydrogen dihedrals: 384 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 278 Time building chain proxies: 10.21, per 1000 atoms: 0.55 Number of scatterers: 18432 At special positions: 0 Unit cell: (128.75, 128.75, 116.25, 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 80 16.00 O 3232 8.00 N 3128 7.00 C 11992 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: 7.01 Conformation dependent library (CDL) restraints added in 3.6 seconds 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4712 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 8 sheets defined 58.7% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 119 through 127 removed outlier: 4.358A pdb=" N ASN A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.656A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 185 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 260 through 275 removed outlier: 4.074A pdb=" N TYR A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 323 through 327 removed outlier: 4.286A pdb=" N LEU A 326 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.642A pdb=" N MET A 372 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 373 " --> pdb=" O HIS A 370 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 374 " --> pdb=" O ARG A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 374' Processing helix chain 'A' and resid 375 through 389 removed outlier: 3.791A pdb=" N TRP A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 413 removed outlier: 4.180A pdb=" N ASN A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 460 removed outlier: 4.149A pdb=" N TYR A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 493 removed outlier: 3.572A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 removed outlier: 4.100A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 517 removed outlier: 3.869A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 558 removed outlier: 5.618A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 604 Processing helix chain 'A' and resid 619 through 635 removed outlier: 3.707A pdb=" N VAL A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 675 removed outlier: 4.183A pdb=" N LEU A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 642 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 653 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP A 654 " --> pdb=" O ASN A 650 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASN A 655 " --> pdb=" O HIS A 651 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 119 through 127 removed outlier: 4.359A pdb=" N ASN D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 148 through 154 Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.654A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 185 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 260 through 275 removed outlier: 4.075A pdb=" N TYR D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 303 Processing helix chain 'D' and resid 307 through 317 Processing helix chain 'D' and resid 323 through 327 removed outlier: 4.286A pdb=" N LEU D 326 " --> pdb=" O TYR D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 361 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.642A pdb=" N MET D 372 " --> pdb=" O ARG D 369 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL D 373 " --> pdb=" O HIS D 370 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 374 " --> pdb=" O ARG D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 369 through 374' Processing helix chain 'D' and resid 375 through 389 removed outlier: 3.791A pdb=" N TRP D 386 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 413 removed outlier: 4.181A pdb=" N ASN D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 460 removed outlier: 4.148A pdb=" N TYR D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 493 removed outlier: 3.572A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 511 removed outlier: 4.099A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 517 removed outlier: 3.868A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 558 removed outlier: 5.619A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 604 Processing helix chain 'D' and resid 619 through 635 removed outlier: 3.707A pdb=" N VAL D 635 " --> pdb=" O LEU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 675 removed outlier: 4.183A pdb=" N LEU D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE D 642 " --> pdb=" O LEU D 638 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA D 653 " --> pdb=" O VAL D 649 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP D 654 " --> pdb=" O ASN D 650 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASN D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 658 " --> pdb=" O ASP D 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 119 through 127 removed outlier: 4.359A pdb=" N ASN B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 148 through 154 Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.655A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 185 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 260 through 275 removed outlier: 4.074A pdb=" N TYR B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 323 through 327 removed outlier: 4.287A pdb=" N LEU B 326 " --> pdb=" O TYR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.642A pdb=" N MET B 372 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL B 373 " --> pdb=" O HIS B 370 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 374 " --> pdb=" O ARG B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 374' Processing helix chain 'B' and resid 375 through 389 removed outlier: 3.790A pdb=" N TRP B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 413 removed outlier: 4.181A pdb=" N ASN B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 460 removed outlier: 4.149A pdb=" N TYR B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 493 removed outlier: 3.572A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 511 removed outlier: 4.098A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 517 removed outlier: 3.868A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 558 removed outlier: 5.620A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 604 Processing helix chain 'B' and resid 619 through 635 removed outlier: 3.707A pdb=" N VAL B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 675 removed outlier: 4.183A pdb=" N LEU B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE B 642 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 653 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP B 654 " --> pdb=" O ASN B 650 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASN B 655 " --> pdb=" O HIS B 651 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 119 through 127 removed outlier: 4.358A pdb=" N ASN C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 148 through 154 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.655A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 185 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 260 through 275 removed outlier: 4.074A pdb=" N TYR C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 303 Processing helix chain 'C' and resid 307 through 317 Processing helix chain 'C' and resid 323 through 327 removed outlier: 4.287A pdb=" N LEU C 326 " --> pdb=" O TYR C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.642A pdb=" N MET C 372 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL C 373 " --> pdb=" O HIS C 370 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 369 through 374' Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.790A pdb=" N TRP C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 413 removed outlier: 4.180A pdb=" N ASN C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 460 removed outlier: 4.149A pdb=" N TYR C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 493 removed outlier: 3.572A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 4.099A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 517 removed outlier: 3.868A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 558 removed outlier: 5.618A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 604 Processing helix chain 'C' and resid 619 through 635 removed outlier: 3.707A pdb=" N VAL C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 675 removed outlier: 4.183A pdb=" N LEU C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE C 642 " --> pdb=" O LEU C 638 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C 653 " --> pdb=" O VAL C 649 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP C 654 " --> pdb=" O ASN C 650 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASN C 655 " --> pdb=" O HIS C 651 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 658 " --> pdb=" O ASP C 654 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 158 removed outlier: 4.844A pdb=" N CYS A 157 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 342 Processing sheet with id=AA3, first strand: chain 'D' and resid 157 through 158 removed outlier: 4.844A pdb=" N CYS D 157 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 339 through 342 Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 158 removed outlier: 4.844A pdb=" N CYS B 157 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 342 Processing sheet with id=AA7, first strand: chain 'C' and resid 157 through 158 removed outlier: 4.844A pdb=" N CYS C 157 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 339 through 342 980 hydrogen bonds defined for protein. 2892 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: 4.95 Time building geometry restraints manager: 7.65 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: 4503 1.33 - 1.45: 3997 1.45 - 1.57: 10248 1.57 - 1.69: 0 1.69 - 1.81: 124 Bond restraints: 18872 Sorted by residual: bond pdb=" CA TRP C 676 " pdb=" C TRP C 676 " ideal model delta sigma weight residual 1.523 1.557 -0.034 1.34e-02 5.57e+03 6.45e+00 bond pdb=" CA TRP B 676 " pdb=" C TRP B 676 " ideal model delta sigma weight residual 1.523 1.557 -0.034 1.34e-02 5.57e+03 6.31e+00 bond pdb=" CA TRP D 676 " pdb=" C TRP D 676 " ideal model delta sigma weight residual 1.523 1.557 -0.033 1.34e-02 5.57e+03 6.24e+00 bond pdb=" CA TRP A 676 " pdb=" C TRP A 676 " ideal model delta sigma weight residual 1.523 1.556 -0.033 1.34e-02 5.57e+03 5.96e+00 bond pdb=" CB VAL B 153 " pdb=" CG1 VAL B 153 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.61e+00 ... (remaining 18867 not shown) Histogram of bond angle deviations from ideal: 97.66 - 105.03: 360 105.03 - 112.39: 9470 112.39 - 119.76: 6895 119.76 - 127.12: 8787 127.12 - 134.49: 288 Bond angle restraints: 25800 Sorted by residual: angle pdb=" N TRP B 676 " pdb=" CA TRP B 676 " pdb=" C TRP B 676 " ideal model delta sigma weight residual 110.80 122.71 -11.91 2.13e+00 2.20e-01 3.13e+01 angle pdb=" N TRP A 676 " pdb=" CA TRP A 676 " pdb=" C TRP A 676 " ideal model delta sigma weight residual 110.80 122.69 -11.89 2.13e+00 2.20e-01 3.12e+01 angle pdb=" N TRP D 676 " pdb=" CA TRP D 676 " pdb=" C TRP D 676 " ideal model delta sigma weight residual 110.80 122.68 -11.88 2.13e+00 2.20e-01 3.11e+01 angle pdb=" N TRP C 676 " pdb=" CA TRP C 676 " pdb=" C TRP C 676 " ideal model delta sigma weight residual 110.80 122.66 -11.86 2.13e+00 2.20e-01 3.10e+01 angle pdb=" C TRP C 676 " pdb=" N TRP C 677 " pdb=" CA TRP C 677 " ideal model delta sigma weight residual 121.70 131.43 -9.73 1.80e+00 3.09e-01 2.92e+01 ... (remaining 25795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.31: 8956 9.31 - 18.61: 1416 18.61 - 27.92: 356 27.92 - 37.23: 215 37.23 - 46.53: 73 Dihedral angle restraints: 11016 sinusoidal: 3728 harmonic: 7288 Sorted by residual: dihedral pdb=" CA PHE B 519 " pdb=" C PHE B 519 " pdb=" N GLN B 520 " pdb=" CA GLN B 520 " ideal model delta harmonic sigma weight residual -180.00 -136.06 -43.94 0 5.00e+00 4.00e-02 7.72e+01 dihedral pdb=" CA PHE A 519 " pdb=" C PHE A 519 " pdb=" N GLN A 520 " pdb=" CA GLN A 520 " ideal model delta harmonic sigma weight residual -180.00 -136.11 -43.89 0 5.00e+00 4.00e-02 7.70e+01 dihedral pdb=" CA PHE C 519 " pdb=" C PHE C 519 " pdb=" N GLN C 520 " pdb=" CA GLN C 520 " ideal model delta harmonic sigma weight residual -180.00 -136.13 -43.87 0 5.00e+00 4.00e-02 7.70e+01 ... (remaining 11013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1766 0.045 - 0.090: 843 0.090 - 0.135: 314 0.135 - 0.180: 99 0.180 - 0.225: 22 Chirality restraints: 3044 Sorted by residual: chirality pdb=" CG LEU B 121 " pdb=" CB LEU B 121 " pdb=" CD1 LEU B 121 " pdb=" CD2 LEU B 121 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CG LEU D 121 " pdb=" CB LEU D 121 " pdb=" CD1 LEU D 121 " pdb=" CD2 LEU D 121 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CG LEU C 121 " pdb=" CB LEU C 121 " pdb=" CD1 LEU C 121 " pdb=" CD2 LEU C 121 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3041 not shown) Planarity restraints: 3264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 366 " -0.053 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO B 367 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 367 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 367 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 366 " 0.053 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO C 367 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 367 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 367 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 366 " -0.053 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO A 367 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " -0.046 5.00e-02 4.00e+02 ... (remaining 3261 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2539 2.75 - 3.28: 19395 3.28 - 3.82: 31463 3.82 - 4.36: 35930 4.36 - 4.90: 56359 Nonbonded interactions: 145686 Sorted by model distance: nonbonded pdb=" O ILE D 593 " pdb=" OG SER D 597 " model vdw 2.208 2.440 nonbonded pdb=" O ILE B 593 " pdb=" OG SER B 597 " model vdw 2.208 2.440 nonbonded pdb=" O ILE C 593 " pdb=" OG SER C 597 " model vdw 2.208 2.440 nonbonded pdb=" O ILE A 593 " pdb=" OG SER A 597 " model vdw 2.209 2.440 nonbonded pdb=" O ALA A 653 " pdb=" OG SER A 656 " model vdw 2.272 2.440 ... (remaining 145681 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' selection = chain 'D' } 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: 0.230 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: 1.980 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 47.630 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.090 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 0.074 18872 Z= 0.516 Angle : 1.323 18.187 25800 Z= 0.672 Chirality : 0.061 0.225 3044 Planarity : 0.008 0.081 3264 Dihedral : 11.915 46.533 6304 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.50 % Favored : 90.34 % Rotamer: Outliers : 0.75 % Allowed : 8.12 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.17 % Twisted Proline : 4.00 % Twisted General : 0.67 % 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: -4.58 (0.14), residues: 2484 helix: -3.13 (0.10), residues: 1244 sheet: -4.40 (0.39), residues: 56 loop : -2.79 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 454 HIS 0.022 0.004 HIS C 165 PHE 0.027 0.004 PHE C 209 TYR 0.032 0.004 TYR B 323 ARG 0.009 0.001 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 322 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.8226 (m-80) cc_final: 0.8007 (m-80) REVERT: A 351 TRP cc_start: 0.8164 (p-90) cc_final: 0.7952 (p-90) REVERT: A 354 ASN cc_start: 0.8904 (m-40) cc_final: 0.8696 (t0) REVERT: A 503 LEU cc_start: 0.8192 (tp) cc_final: 0.7965 (tp) REVERT: A 644 LEU cc_start: 0.5338 (pp) cc_final: 0.4057 (pp) REVERT: D 258 ASP cc_start: 0.7891 (m-30) cc_final: 0.7301 (m-30) REVERT: D 351 TRP cc_start: 0.8319 (p-90) cc_final: 0.8068 (p-90) REVERT: D 354 ASN cc_start: 0.8977 (m-40) cc_final: 0.8773 (t0) REVERT: D 503 LEU cc_start: 0.8277 (tp) cc_final: 0.8068 (tp) REVERT: D 644 LEU cc_start: 0.5457 (pp) cc_final: 0.3919 (pp) REVERT: B 258 ASP cc_start: 0.7344 (m-30) cc_final: 0.6508 (m-30) REVERT: B 351 TRP cc_start: 0.8510 (p-90) cc_final: 0.8252 (p-90) REVERT: B 354 ASN cc_start: 0.8993 (m-40) cc_final: 0.8772 (t0) REVERT: C 122 MET cc_start: 0.8900 (mmt) cc_final: 0.8699 (mmm) REVERT: C 351 TRP cc_start: 0.8354 (p-90) cc_final: 0.8103 (p-90) REVERT: C 644 LEU cc_start: 0.5108 (pp) cc_final: 0.4582 (pp) outliers start: 13 outliers final: 0 residues processed: 333 average time/residue: 0.3050 time to fit residues: 151.6887 Evaluate side-chains 173 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 7.9990 chunk 187 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 64 optimal weight: 0.0670 chunk 126 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 overall best weight: 1.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN D 234 HIS ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 520 GLN B 234 HIS ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 650 ASN C 234 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18872 Z= 0.213 Angle : 0.829 15.138 25800 Z= 0.405 Chirality : 0.042 0.167 3044 Planarity : 0.006 0.053 3264 Dihedral : 6.763 38.649 2664 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.11 % Allowed : 11.75 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -3.03 (0.16), residues: 2484 helix: -1.22 (0.13), residues: 1420 sheet: -4.42 (0.43), residues: 56 loop : -2.97 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 454 HIS 0.005 0.001 HIS B 313 PHE 0.023 0.001 PHE B 311 TYR 0.025 0.002 TYR C 323 ARG 0.004 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 236 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.8289 (m-80) cc_final: 0.7955 (m-80) REVERT: A 351 TRP cc_start: 0.8149 (p-90) cc_final: 0.7949 (p-90) REVERT: D 122 MET cc_start: 0.8541 (mmt) cc_final: 0.8249 (mmm) REVERT: D 216 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7569 (pp) REVERT: D 351 TRP cc_start: 0.8314 (p-90) cc_final: 0.8061 (p-90) REVERT: D 360 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7092 (mm) REVERT: D 503 LEU cc_start: 0.8308 (tp) cc_final: 0.8047 (tp) REVERT: B 216 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7549 (pp) REVERT: B 404 MET cc_start: 0.9111 (tpp) cc_final: 0.8816 (tpt) REVERT: C 216 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7219 (pp) REVERT: C 351 TRP cc_start: 0.8272 (p-90) cc_final: 0.8045 (p-90) outliers start: 54 outliers final: 11 residues processed: 281 average time/residue: 0.2560 time to fit residues: 113.1414 Evaluate side-chains 188 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 173 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 390 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 187 optimal weight: 0.4980 chunk 153 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 225 optimal weight: 0.3980 chunk 243 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 chunk 223 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18872 Z= 0.193 Angle : 0.783 13.467 25800 Z= 0.382 Chirality : 0.042 0.245 3044 Planarity : 0.005 0.059 3264 Dihedral : 6.240 36.313 2664 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.86 % Allowed : 14.00 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.16), residues: 2484 helix: -0.46 (0.13), residues: 1452 sheet: -4.44 (0.45), residues: 56 loop : -2.97 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 677 HIS 0.004 0.001 HIS D 313 PHE 0.024 0.001 PHE A 311 TYR 0.031 0.002 TYR A 675 ARG 0.007 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 212 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.8305 (m-80) cc_final: 0.7879 (m-80) REVERT: A 351 TRP cc_start: 0.8169 (p-90) cc_final: 0.7961 (p-90) REVERT: A 354 ASN cc_start: 0.8456 (t0) cc_final: 0.8197 (t0) REVERT: A 503 LEU cc_start: 0.7942 (tp) cc_final: 0.7683 (tt) REVERT: A 662 LEU cc_start: 0.9102 (tt) cc_final: 0.8866 (tp) REVERT: D 122 MET cc_start: 0.8353 (mmt) cc_final: 0.8105 (mmm) REVERT: D 351 TRP cc_start: 0.8342 (p-90) cc_final: 0.8081 (p-90) REVERT: D 354 ASN cc_start: 0.8498 (t0) cc_final: 0.8227 (t0) REVERT: D 360 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.6972 (mm) REVERT: D 519 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.5747 (p90) REVERT: D 641 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.6013 (tt) REVERT: B 258 ASP cc_start: 0.7057 (m-30) cc_final: 0.6833 (m-30) REVERT: B 404 MET cc_start: 0.9219 (tpp) cc_final: 0.8951 (tpt) REVERT: B 433 MET cc_start: 0.9006 (ptm) cc_final: 0.8625 (ptm) REVERT: B 548 LEU cc_start: 0.8089 (tp) cc_final: 0.7851 (tp) REVERT: C 106 LEU cc_start: 0.5650 (tp) cc_final: 0.5347 (mt) REVERT: C 216 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7408 (pp) REVERT: C 351 TRP cc_start: 0.8314 (p-90) cc_final: 0.8076 (p-90) REVERT: C 519 PHE cc_start: 0.6106 (OUTLIER) cc_final: 0.5296 (p90) outliers start: 67 outliers final: 25 residues processed: 263 average time/residue: 0.2465 time to fit residues: 105.0075 Evaluate side-chains 193 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 623 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 151 optimal weight: 0.0870 chunk 226 optimal weight: 20.0000 chunk 239 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN D 148 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 GLN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18872 Z= 0.233 Angle : 0.789 13.825 25800 Z= 0.385 Chirality : 0.043 0.239 3044 Planarity : 0.005 0.063 3264 Dihedral : 5.998 34.856 2664 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 5.18 % Allowed : 14.80 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.92 (0.17), residues: 2484 helix: -0.10 (0.14), residues: 1436 sheet: -4.38 (0.48), residues: 56 loop : -2.90 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 677 HIS 0.004 0.001 HIS B 234 PHE 0.031 0.002 PHE C 311 TYR 0.021 0.002 TYR C 323 ARG 0.005 0.000 ARG D 539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 181 time to evaluate : 2.323 Fit side-chains revert: symmetry clash REVERT: A 199 PHE cc_start: 0.8419 (m-80) cc_final: 0.8005 (m-80) REVERT: A 351 TRP cc_start: 0.8297 (p-90) cc_final: 0.8060 (p-90) REVERT: A 519 PHE cc_start: 0.5940 (OUTLIER) cc_final: 0.5171 (p90) REVERT: D 351 TRP cc_start: 0.8427 (p-90) cc_final: 0.8172 (p-90) REVERT: D 360 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6648 (mm) REVERT: D 404 MET cc_start: 0.8606 (tpt) cc_final: 0.8383 (tpp) REVERT: D 433 MET cc_start: 0.9068 (ptm) cc_final: 0.8849 (ptp) REVERT: D 519 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.5786 (p90) REVERT: B 221 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7738 (tmtt) REVERT: B 258 ASP cc_start: 0.7232 (m-30) cc_final: 0.6981 (m-30) REVERT: B 433 MET cc_start: 0.9078 (ptm) cc_final: 0.8651 (ptm) REVERT: B 519 PHE cc_start: 0.6585 (OUTLIER) cc_final: 0.5897 (p90) REVERT: B 548 LEU cc_start: 0.8011 (tp) cc_final: 0.7796 (tp) REVERT: C 106 LEU cc_start: 0.5253 (tp) cc_final: 0.5041 (mt) REVERT: C 216 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7463 (pp) REVERT: C 221 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7987 (tmtt) REVERT: C 351 TRP cc_start: 0.8355 (p-90) cc_final: 0.8106 (p-90) REVERT: C 519 PHE cc_start: 0.5887 (OUTLIER) cc_final: 0.5121 (p90) outliers start: 90 outliers final: 35 residues processed: 251 average time/residue: 0.2463 time to fit residues: 101.2394 Evaluate side-chains 202 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 160 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 618 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 632 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 2.9990 chunk 136 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 chunk 98 optimal weight: 0.2980 chunk 204 optimal weight: 0.0070 chunk 165 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 30.0000 chunk 215 optimal weight: 7.9990 chunk 60 optimal weight: 0.0020 overall best weight: 0.3206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN A 520 GLN D 148 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18872 Z= 0.177 Angle : 0.773 13.993 25800 Z= 0.365 Chirality : 0.041 0.152 3044 Planarity : 0.004 0.063 3264 Dihedral : 5.537 29.893 2664 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.46 % Allowed : 16.30 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.17 % 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: -1.63 (0.17), residues: 2484 helix: 0.16 (0.14), residues: 1440 sheet: -4.12 (0.56), residues: 56 loop : -2.83 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 677 HIS 0.003 0.001 HIS A 169 PHE 0.021 0.001 PHE A 519 TYR 0.016 0.001 TYR B 323 ARG 0.005 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 223 time to evaluate : 2.218 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: A 199 PHE cc_start: 0.7982 (m-80) cc_final: 0.7502 (m-80) REVERT: A 351 TRP cc_start: 0.8161 (p-90) cc_final: 0.7945 (p-90) REVERT: A 519 PHE cc_start: 0.5514 (OUTLIER) cc_final: 0.4778 (p90) REVERT: D 351 TRP cc_start: 0.8326 (p-90) cc_final: 0.8074 (p-90) REVERT: D 360 ILE cc_start: 0.6012 (OUTLIER) cc_final: 0.5686 (mm) REVERT: D 519 PHE cc_start: 0.5693 (OUTLIER) cc_final: 0.5164 (p90) REVERT: B 207 PHE cc_start: 0.7951 (m-10) cc_final: 0.7637 (m-10) REVERT: B 221 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7592 (tmtt) REVERT: B 433 MET cc_start: 0.9091 (ptm) cc_final: 0.8754 (ptm) REVERT: B 519 PHE cc_start: 0.6266 (OUTLIER) cc_final: 0.5368 (p90) REVERT: B 548 LEU cc_start: 0.7881 (tp) cc_final: 0.7562 (tp) REVERT: C 86 ARG cc_start: 0.8354 (tpp80) cc_final: 0.8112 (tpp80) REVERT: C 106 LEU cc_start: 0.5552 (tp) cc_final: 0.5113 (mp) REVERT: C 221 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7657 (tmtt) REVERT: C 351 TRP cc_start: 0.8268 (p-90) cc_final: 0.8017 (p-90) REVERT: C 519 PHE cc_start: 0.5721 (OUTLIER) cc_final: 0.4847 (p90) REVERT: C 641 LEU cc_start: 0.4997 (tt) cc_final: 0.4513 (tt) outliers start: 60 outliers final: 25 residues processed: 267 average time/residue: 0.2646 time to fit residues: 112.1043 Evaluate side-chains 206 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 618 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 618 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 649 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 0.9980 chunk 215 optimal weight: 50.0000 chunk 47 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18872 Z= 0.224 Angle : 0.795 15.064 25800 Z= 0.381 Chirality : 0.042 0.174 3044 Planarity : 0.004 0.061 3264 Dihedral : 5.539 30.510 2664 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.80 % Allowed : 17.97 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.45 (0.17), residues: 2484 helix: 0.31 (0.14), residues: 1440 sheet: -3.98 (0.57), residues: 56 loop : -2.78 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 676 HIS 0.005 0.001 HIS B 313 PHE 0.034 0.001 PHE D 311 TYR 0.017 0.002 TYR B 323 ARG 0.003 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 182 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.8296 (m-80) cc_final: 0.7812 (m-80) REVERT: A 351 TRP cc_start: 0.8309 (p-90) cc_final: 0.8062 (p-90) REVERT: A 519 PHE cc_start: 0.5520 (OUTLIER) cc_final: 0.4790 (p90) REVERT: A 548 LEU cc_start: 0.7502 (tp) cc_final: 0.7098 (tp) REVERT: D 351 TRP cc_start: 0.8415 (p-90) cc_final: 0.8156 (p-90) REVERT: D 360 ILE cc_start: 0.6478 (OUTLIER) cc_final: 0.6056 (mm) REVERT: D 519 PHE cc_start: 0.5987 (OUTLIER) cc_final: 0.5117 (p90) REVERT: D 522 THR cc_start: 0.7777 (p) cc_final: 0.6649 (p) REVERT: B 122 MET cc_start: 0.8914 (mmm) cc_final: 0.8259 (mmm) REVERT: B 221 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7670 (tmtt) REVERT: B 433 MET cc_start: 0.9152 (ptm) cc_final: 0.8804 (ptm) REVERT: B 441 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8740 (tp) REVERT: B 519 PHE cc_start: 0.6526 (OUTLIER) cc_final: 0.5531 (p90) REVERT: B 528 MET cc_start: 0.8691 (ttt) cc_final: 0.8413 (tpp) REVERT: C 86 ARG cc_start: 0.8314 (tpp80) cc_final: 0.7921 (tpp80) REVERT: C 221 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7724 (tmtt) REVERT: C 351 TRP cc_start: 0.8329 (p-90) cc_final: 0.8090 (p-90) REVERT: C 519 PHE cc_start: 0.5623 (OUTLIER) cc_final: 0.4755 (p90) REVERT: C 528 MET cc_start: 0.8391 (tpp) cc_final: 0.8093 (tpp) outliers start: 66 outliers final: 42 residues processed: 229 average time/residue: 0.2463 time to fit residues: 91.7103 Evaluate side-chains 215 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 618 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 618 PHE Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 649 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 239 optimal weight: 0.0980 chunk 149 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18872 Z= 0.209 Angle : 0.788 13.280 25800 Z= 0.376 Chirality : 0.042 0.187 3044 Planarity : 0.004 0.061 3264 Dihedral : 5.495 29.258 2664 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 4.26 % Allowed : 18.32 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.17 % 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: -1.37 (0.17), residues: 2484 helix: 0.40 (0.14), residues: 1436 sheet: -3.84 (0.59), residues: 56 loop : -2.78 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 454 HIS 0.004 0.001 HIS D 234 PHE 0.019 0.001 PHE A 519 TYR 0.023 0.002 TYR A 525 ARG 0.002 0.000 ARG C 458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 179 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.8297 (m-80) cc_final: 0.7819 (m-80) REVERT: A 351 TRP cc_start: 0.8307 (p-90) cc_final: 0.8057 (p-90) REVERT: A 519 PHE cc_start: 0.5528 (OUTLIER) cc_final: 0.4786 (p90) REVERT: A 548 LEU cc_start: 0.7525 (tp) cc_final: 0.7313 (tp) REVERT: D 122 MET cc_start: 0.8912 (mmm) cc_final: 0.8238 (mmm) REVERT: D 351 TRP cc_start: 0.8424 (p-90) cc_final: 0.8153 (p-90) REVERT: D 360 ILE cc_start: 0.6566 (OUTLIER) cc_final: 0.6166 (mm) REVERT: D 519 PHE cc_start: 0.6167 (OUTLIER) cc_final: 0.5205 (p90) REVERT: D 522 THR cc_start: 0.7828 (p) cc_final: 0.6636 (p) REVERT: B 221 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7738 (tmtt) REVERT: B 433 MET cc_start: 0.9160 (ptm) cc_final: 0.8829 (ptm) REVERT: B 441 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8731 (tp) REVERT: B 519 PHE cc_start: 0.6534 (OUTLIER) cc_final: 0.5561 (p90) REVERT: B 528 MET cc_start: 0.8677 (ttt) cc_final: 0.8376 (tpp) REVERT: B 548 LEU cc_start: 0.7798 (tp) cc_final: 0.7455 (tp) REVERT: C 86 ARG cc_start: 0.8303 (tpp80) cc_final: 0.7908 (tpp80) REVERT: C 221 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7789 (tmtt) REVERT: C 351 TRP cc_start: 0.8372 (p-90) cc_final: 0.8116 (p-90) REVERT: C 519 PHE cc_start: 0.5545 (OUTLIER) cc_final: 0.4727 (p90) outliers start: 74 outliers final: 46 residues processed: 232 average time/residue: 0.2466 time to fit residues: 94.1258 Evaluate side-chains 218 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 165 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 618 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 618 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 649 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 0.0170 chunk 72 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 162 optimal weight: 0.0070 chunk 118 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 187 optimal weight: 30.0000 chunk 217 optimal weight: 7.9990 overall best weight: 3.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18872 Z= 0.223 Angle : 0.806 13.942 25800 Z= 0.385 Chirality : 0.043 0.159 3044 Planarity : 0.004 0.061 3264 Dihedral : 5.516 29.696 2664 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.97 % Allowed : 18.55 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.17 % 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: -1.37 (0.17), residues: 2484 helix: 0.39 (0.14), residues: 1444 sheet: -3.78 (0.58), residues: 56 loop : -2.78 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 677 HIS 0.005 0.001 HIS D 234 PHE 0.018 0.001 PHE A 519 TYR 0.020 0.002 TYR A 525 ARG 0.010 0.000 ARG D 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 176 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.8360 (m-80) cc_final: 0.7896 (m-80) REVERT: A 270 MET cc_start: 0.7907 (tpp) cc_final: 0.7594 (tpp) REVERT: A 351 TRP cc_start: 0.8291 (p-90) cc_final: 0.8035 (p-90) REVERT: A 519 PHE cc_start: 0.5502 (OUTLIER) cc_final: 0.4731 (p90) REVERT: A 548 LEU cc_start: 0.7692 (tp) cc_final: 0.7471 (tp) REVERT: D 270 MET cc_start: 0.7883 (tpp) cc_final: 0.7592 (tpp) REVERT: D 351 TRP cc_start: 0.8448 (p-90) cc_final: 0.8174 (p-90) REVERT: D 360 ILE cc_start: 0.6605 (OUTLIER) cc_final: 0.6181 (mm) REVERT: D 519 PHE cc_start: 0.6367 (OUTLIER) cc_final: 0.5398 (p90) REVERT: D 522 THR cc_start: 0.7986 (p) cc_final: 0.6502 (p) REVERT: B 221 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7802 (tmtt) REVERT: B 433 MET cc_start: 0.9188 (ptm) cc_final: 0.8862 (ptm) REVERT: B 441 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8730 (tp) REVERT: B 519 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.5274 (p90) REVERT: B 528 MET cc_start: 0.8647 (ttt) cc_final: 0.8357 (tpp) REVERT: B 548 LEU cc_start: 0.7804 (tp) cc_final: 0.7449 (tp) REVERT: C 86 ARG cc_start: 0.8283 (tpp80) cc_final: 0.7907 (tpp80) REVERT: C 221 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7826 (tmtt) REVERT: C 351 TRP cc_start: 0.8429 (p-90) cc_final: 0.8170 (p-90) REVERT: C 519 PHE cc_start: 0.5582 (OUTLIER) cc_final: 0.4723 (p90) outliers start: 69 outliers final: 44 residues processed: 228 average time/residue: 0.2451 time to fit residues: 91.9797 Evaluate side-chains 220 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 169 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 618 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 618 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 649 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 201 optimal weight: 0.6980 chunk 210 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18872 Z= 0.255 Angle : 0.838 13.166 25800 Z= 0.401 Chirality : 0.044 0.183 3044 Planarity : 0.005 0.060 3264 Dihedral : 5.636 29.255 2664 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.40 % Allowed : 19.87 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.17 % 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: -1.39 (0.17), residues: 2484 helix: 0.35 (0.14), residues: 1444 sheet: -3.76 (0.57), residues: 56 loop : -2.77 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 454 HIS 0.007 0.001 HIS D 234 PHE 0.018 0.001 PHE A 519 TYR 0.023 0.002 TYR A 525 ARG 0.003 0.000 ARG D 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 171 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.8488 (m-80) cc_final: 0.8015 (m-80) REVERT: A 351 TRP cc_start: 0.8283 (p-90) cc_final: 0.8030 (p-90) REVERT: A 519 PHE cc_start: 0.5608 (OUTLIER) cc_final: 0.4770 (p90) REVERT: D 351 TRP cc_start: 0.8504 (p-90) cc_final: 0.8218 (p-90) REVERT: D 360 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6345 (mm) REVERT: B 221 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7951 (tmtt) REVERT: B 433 MET cc_start: 0.9147 (ptm) cc_final: 0.8844 (ptm) REVERT: B 519 PHE cc_start: 0.6496 (OUTLIER) cc_final: 0.5298 (p90) REVERT: B 528 MET cc_start: 0.8898 (ttt) cc_final: 0.8573 (tpp) REVERT: B 548 LEU cc_start: 0.7820 (tp) cc_final: 0.7432 (tp) REVERT: C 86 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7942 (tpp80) REVERT: C 221 LYS cc_start: 0.8343 (mtpt) cc_final: 0.8063 (tmtt) REVERT: C 351 TRP cc_start: 0.8447 (p-90) cc_final: 0.8184 (p-90) REVERT: C 519 PHE cc_start: 0.5935 (OUTLIER) cc_final: 0.4856 (p90) outliers start: 59 outliers final: 46 residues processed: 216 average time/residue: 0.2513 time to fit residues: 88.5333 Evaluate side-chains 215 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 164 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 618 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 618 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 649 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 247 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 151 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN D 247 ASN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18872 Z= 0.311 Angle : 0.893 13.591 25800 Z= 0.431 Chirality : 0.046 0.201 3044 Planarity : 0.005 0.059 3264 Dihedral : 5.909 31.293 2664 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 26.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 3.57 % Allowed : 20.10 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.61 (0.17), residues: 2484 helix: 0.17 (0.13), residues: 1444 sheet: -3.77 (0.56), residues: 56 loop : -2.85 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 454 HIS 0.009 0.002 HIS A 234 PHE 0.020 0.002 PHE D 311 TYR 0.026 0.002 TYR A 525 ARG 0.003 0.001 ARG D 517 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 166 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.8671 (m-80) cc_final: 0.8286 (m-80) REVERT: A 351 TRP cc_start: 0.8299 (p-90) cc_final: 0.8046 (p-90) REVERT: A 519 PHE cc_start: 0.5990 (OUTLIER) cc_final: 0.4883 (p90) REVERT: D 360 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6639 (mm) REVERT: D 519 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.5313 (p90) REVERT: B 122 MET cc_start: 0.9024 (mmm) cc_final: 0.8642 (mmm) REVERT: B 221 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8274 (tmtt) REVERT: B 250 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8219 (mt) REVERT: B 433 MET cc_start: 0.9165 (ptm) cc_final: 0.8856 (ptm) REVERT: B 441 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8709 (tp) REVERT: B 519 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.5538 (p90) REVERT: B 528 MET cc_start: 0.8917 (ttt) cc_final: 0.8534 (tpp) REVERT: C 86 ARG cc_start: 0.8327 (tpp80) cc_final: 0.7945 (tpp80) REVERT: C 351 TRP cc_start: 0.8516 (p-90) cc_final: 0.8229 (p-90) REVERT: C 519 PHE cc_start: 0.6496 (OUTLIER) cc_final: 0.5395 (p90) outliers start: 62 outliers final: 43 residues processed: 215 average time/residue: 0.2428 time to fit residues: 85.9763 Evaluate side-chains 212 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 161 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 618 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 618 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 649 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 82 optimal weight: 0.0770 chunk 202 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 173 optimal weight: 0.4980 overall best weight: 2.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.092517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.082862 restraints weight = 107282.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.084107 restraints weight = 73028.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.084970 restraints weight = 55439.263| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 18872 Z= 0.306 Angle : 1.016 59.197 25800 Z= 0.523 Chirality : 0.048 0.995 3044 Planarity : 0.005 0.059 3264 Dihedral : 5.909 31.120 2664 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 27.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 3.28 % Allowed : 20.33 % Favored : 76.38 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.17), residues: 2484 helix: 0.16 (0.13), residues: 1444 sheet: -3.77 (0.57), residues: 56 loop : -2.85 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 509 HIS 0.009 0.002 HIS A 234 PHE 0.017 0.002 PHE A 540 TYR 0.022 0.002 TYR A 525 ARG 0.003 0.000 ARG B 539 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3063.55 seconds wall clock time: 56 minutes 58.71 seconds (3418.71 seconds total)