Starting phenix.real_space_refine on Sat Dec 9 06:01:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y68_33637/12_2023/7y68_33637.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y68_33637/12_2023/7y68_33637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y68_33637/12_2023/7y68_33637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y68_33637/12_2023/7y68_33637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y68_33637/12_2023/7y68_33637.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y68_33637/12_2023/7y68_33637.pdb" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.073 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 62 5.16 5 C 6642 2.51 5 N 1668 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 579": "OD1" <-> "OD2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 713": "OD1" <-> "OD2" Residue "A PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 321": "NH1" <-> "NH2" Residue "B TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 579": "OD1" <-> "OD2" Residue "B TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 713": "OD1" <-> "OD2" Residue "B PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 782": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10264 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5019 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 627} Chain breaks: 2 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 136 Chain: "B" Number of atoms: 5019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5019 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 627} Chain breaks: 2 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 136 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.97, per 1000 atoms: 0.58 Number of scatterers: 10264 At special positions: 0 Unit cell: (102.837, 81.1875, 133.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 62 16.00 O 1890 8.00 N 1668 7.00 C 6642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 570 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 787 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 787 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 902 " - " ASN A 27 " " NAG A 903 " - " ASN A 141 " " NAG A 904 " - " ASN A 123 " " NAG A 905 " - " ASN A 60 " " NAG B 902 " - " ASN B 27 " " NAG B 903 " - " ASN B 141 " " NAG B 904 " - " ASN B 123 " " NAG B 905 " - " ASN B 60 " " NAG C 1 " - " ASN A 54 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN B 54 " " NAG F 1 " - " ASN B 165 " Time building additional restraints: 4.30 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 568 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 568 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 800 " 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 46.0% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 290 through 319 removed outlier: 3.775A pdb=" N VAL A 294 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 479 removed outlier: 3.558A pdb=" N LEU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Proline residue: A 463 - end of helix removed outlier: 4.724A pdb=" N VAL A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 506 through 531 removed outlier: 3.782A pdb=" N ILE A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 568 removed outlier: 3.535A pdb=" N ALA A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 562 " --> pdb=" O MET A 558 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 4.333A pdb=" N THR A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 576 through 581' Processing helix chain 'A' and resid 582 through 599 removed outlier: 3.966A pdb=" N ILE A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU A 594 " --> pdb=" O CYS A 590 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 626 removed outlier: 3.824A pdb=" N TYR A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 614 " --> pdb=" O TYR A 610 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 652 removed outlier: 3.722A pdb=" N ALA A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 710 removed outlier: 3.638A pdb=" N LEU A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A 693 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 704 " --> pdb=" O TRP A 700 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET A 709 " --> pdb=" O TYR A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 739 removed outlier: 3.602A pdb=" N ALA A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 769 removed outlier: 3.512A pdb=" N VAL A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 755 " --> pdb=" O CYS A 751 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 769 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 782 removed outlier: 3.635A pdb=" N GLU A 782 " --> pdb=" O ALA A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 817 removed outlier: 3.711A pdb=" N SER A 804 " --> pdb=" O HIS A 800 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 813 " --> pdb=" O GLY A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 290 through 319 removed outlier: 3.775A pdb=" N VAL B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 479 removed outlier: 3.558A pdb=" N LEU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Proline residue: B 463 - end of helix removed outlier: 4.725A pdb=" N VAL B 474 " --> pdb=" O THR B 470 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 506 through 531 removed outlier: 3.782A pdb=" N ILE B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 568 removed outlier: 3.536A pdb=" N ALA B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 562 " --> pdb=" O MET B 558 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 581 removed outlier: 4.333A pdb=" N THR B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 576 through 581' Processing helix chain 'B' and resid 582 through 599 removed outlier: 3.966A pdb=" N ILE B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU B 594 " --> pdb=" O CYS B 590 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 626 removed outlier: 3.824A pdb=" N TYR B 607 " --> pdb=" O ASN B 603 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS B 612 " --> pdb=" O SER B 608 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA B 614 " --> pdb=" O TYR B 610 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 652 removed outlier: 3.723A pdb=" N ALA B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN B 651 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 710 removed outlier: 3.638A pdb=" N LEU B 692 " --> pdb=" O ARG B 688 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL B 693 " --> pdb=" O MET B 689 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET B 694 " --> pdb=" O VAL B 690 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN B 699 " --> pdb=" O GLY B 695 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 704 " --> pdb=" O TRP B 700 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR B 705 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET B 709 " --> pdb=" O TYR B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 739 removed outlier: 3.602A pdb=" N ALA B 720 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 769 removed outlier: 3.512A pdb=" N VAL B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 755 " --> pdb=" O CYS B 751 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 769 " --> pdb=" O PHE B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 782 removed outlier: 3.635A pdb=" N GLU B 782 " --> pdb=" O ALA B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 817 removed outlier: 3.711A pdb=" N SER B 804 " --> pdb=" O HIS B 800 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 813 " --> pdb=" O GLY B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 820 No H-bonds generated for 'chain 'B' and resid 818 through 820' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 32 removed outlier: 6.635A pdb=" N ASN A 27 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE A 50 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER A 29 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR A 52 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS A 31 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASN A 54 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU A 47 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR A 136 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.925A pdb=" N GLY A 64 " --> pdb=" O MET A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.871A pdb=" N LYS A 106 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 166 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.645A pdb=" N SER A 198 " --> pdb=" O MET A 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 32 removed outlier: 6.634A pdb=" N ASN B 27 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE B 50 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER B 29 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR B 52 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS B 31 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N ASN B 54 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU B 47 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR B 136 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.925A pdb=" N GLY B 64 " --> pdb=" O MET B 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.870A pdb=" N LYS B 106 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 166 Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.646A pdb=" N SER B 198 " --> pdb=" O MET B 225 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1632 1.30 - 1.43: 2862 1.43 - 1.56: 5902 1.56 - 1.69: 0 1.69 - 1.82: 94 Bond restraints: 10490 Sorted by residual: bond pdb=" N ARG A 100 " pdb=" CA ARG A 100 " ideal model delta sigma weight residual 1.455 1.384 0.070 1.25e-02 6.40e+03 3.18e+01 bond pdb=" C ARG B 100 " pdb=" N GLY B 101 " ideal model delta sigma weight residual 1.325 1.265 0.060 1.27e-02 6.20e+03 2.24e+01 bond pdb=" C ARG B 100 " pdb=" O ARG B 100 " ideal model delta sigma weight residual 1.234 1.176 0.057 1.25e-02 6.40e+03 2.10e+01 bond pdb=" CA ARG B 100 " pdb=" C ARG B 100 " ideal model delta sigma weight residual 1.524 1.466 0.059 1.31e-02 5.83e+03 2.02e+01 bond pdb=" C ARG A 100 " pdb=" N GLY A 101 " ideal model delta sigma weight residual 1.331 1.265 0.066 1.46e-02 4.69e+03 2.01e+01 ... (remaining 10485 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.51: 224 106.51 - 113.38: 5870 113.38 - 120.26: 3797 120.26 - 127.13: 4316 127.13 - 134.00: 81 Bond angle restraints: 14288 Sorted by residual: angle pdb=" C LEU A 99 " pdb=" N ARG A 100 " pdb=" CA ARG A 100 " ideal model delta sigma weight residual 123.05 111.00 12.05 1.79e+00 3.12e-01 4.53e+01 angle pdb=" N ARG A 100 " pdb=" CA ARG A 100 " pdb=" C ARG A 100 " ideal model delta sigma weight residual 110.14 118.11 -7.97 1.47e+00 4.63e-01 2.94e+01 angle pdb=" C LEU B 99 " pdb=" N ARG B 100 " pdb=" CA ARG B 100 " ideal model delta sigma weight residual 122.74 114.23 8.51 1.82e+00 3.02e-01 2.19e+01 angle pdb=" N ARG B 100 " pdb=" CA ARG B 100 " pdb=" C ARG B 100 " ideal model delta sigma weight residual 110.42 117.50 -7.08 1.55e+00 4.16e-01 2.09e+01 angle pdb=" N PHE B 195 " pdb=" CA PHE B 195 " pdb=" C PHE B 195 " ideal model delta sigma weight residual 109.81 117.83 -8.02 2.21e+00 2.05e-01 1.32e+01 ... (remaining 14283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 5760 21.71 - 43.43: 407 43.43 - 65.14: 97 65.14 - 86.86: 38 86.86 - 108.57: 92 Dihedral angle restraints: 6394 sinusoidal: 2570 harmonic: 3824 Sorted by residual: dihedral pdb=" CA PHE A 195 " pdb=" C PHE A 195 " pdb=" N PRO A 196 " pdb=" CA PRO A 196 " ideal model delta harmonic sigma weight residual 180.00 126.21 53.79 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA PHE B 195 " pdb=" C PHE B 195 " pdb=" N PRO B 196 " pdb=" CA PRO B 196 " ideal model delta harmonic sigma weight residual 180.00 126.29 53.71 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CB CYS B 197 " pdb=" SG CYS B 197 " pdb=" SG CYS B 256 " pdb=" CB CYS B 256 " ideal model delta sinusoidal sigma weight residual 93.00 162.11 -69.11 1 1.00e+01 1.00e-02 6.18e+01 ... (remaining 6391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1686 0.128 - 0.255: 20 0.255 - 0.382: 6 0.382 - 0.510: 1 0.510 - 0.637: 1 Chirality restraints: 1714 Sorted by residual: chirality pdb=" CA ARG A 100 " pdb=" N ARG A 100 " pdb=" C ARG A 100 " pdb=" CB ARG A 100 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA ARG B 100 " pdb=" N ARG B 100 " pdb=" C ARG B 100 " pdb=" CB ARG B 100 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 27 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 1711 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 195 " -0.062 5.00e-02 4.00e+02 9.34e-02 1.40e+01 pdb=" N PRO B 196 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 195 " -0.062 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO A 196 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 462 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO B 463 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " -0.030 5.00e-02 4.00e+02 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1421 2.75 - 3.29: 10036 3.29 - 3.83: 16595 3.83 - 4.36: 20204 4.36 - 4.90: 34093 Nonbonded interactions: 82349 Sorted by model distance: nonbonded pdb=" OD1 ASN A 506 " pdb=" OG SER A 564 " model vdw 2.213 2.440 nonbonded pdb=" OD1 ASN B 506 " pdb=" OG SER B 564 " model vdw 2.214 2.440 nonbonded pdb=" O LEU A 702 " pdb=" OH TYR A 717 " model vdw 2.220 2.440 nonbonded pdb=" O LEU B 702 " pdb=" OH TYR B 717 " model vdw 2.220 2.440 nonbonded pdb=" NE2 GLN A 472 " pdb=" O VAL A 569 " model vdw 2.227 2.520 ... (remaining 82344 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' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 4.040 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.270 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 : 0.005 0.070 10490 Z= 0.334 Angle : 0.700 12.054 14288 Z= 0.381 Chirality : 0.052 0.637 1714 Planarity : 0.005 0.093 1790 Dihedral : 22.415 108.571 3894 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.09 % Allowed : 0.95 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -1.61 (0.23), residues: 1288 helix: -0.90 (0.23), residues: 482 sheet: 0.12 (0.30), residues: 284 loop : -1.81 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 634 HIS 0.005 0.001 HIS A 492 PHE 0.013 0.002 PHE A 764 TYR 0.020 0.002 TYR A 729 ARG 0.007 0.001 ARG B 523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 2 residues processed: 134 average time/residue: 0.9225 time to fit residues: 136.7327 Evaluate side-chains 101 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 1.1097 time to fit residues: 3.9326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 496 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN A 712 ASN B 476 ASN B 496 ASN ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN B 712 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10490 Z= 0.216 Angle : 0.693 8.165 14288 Z= 0.339 Chirality : 0.050 0.292 1714 Planarity : 0.005 0.084 1790 Dihedral : 18.239 74.127 1728 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.09 % Allowed : 8.82 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -1.45 (0.22), residues: 1288 helix: -0.50 (0.21), residues: 558 sheet: 0.06 (0.29), residues: 290 loop : -2.14 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 317 HIS 0.004 0.001 HIS B 599 PHE 0.022 0.001 PHE A 582 TYR 0.021 0.002 TYR A 717 ARG 0.003 0.001 ARG B 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 4 residues processed: 126 average time/residue: 0.7381 time to fit residues: 104.7551 Evaluate side-chains 106 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.3759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN B 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10490 Z= 0.362 Angle : 0.705 9.945 14288 Z= 0.341 Chirality : 0.050 0.321 1714 Planarity : 0.005 0.081 1790 Dihedral : 12.212 58.508 1728 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.09 % Allowed : 13.28 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -1.10 (0.23), residues: 1288 helix: -0.02 (0.22), residues: 548 sheet: 0.16 (0.29), residues: 290 loop : -2.16 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 317 HIS 0.005 0.001 HIS B 492 PHE 0.015 0.002 PHE B 730 TYR 0.015 0.002 TYR A 173 ARG 0.008 0.001 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 4 residues processed: 123 average time/residue: 0.7417 time to fit residues: 103.2306 Evaluate side-chains 104 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.4943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 30.0000 chunk 88 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN A 712 ASN B 476 ASN B 572 ASN B 712 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10490 Z= 0.182 Angle : 0.580 9.828 14288 Z= 0.288 Chirality : 0.046 0.287 1714 Planarity : 0.004 0.070 1790 Dihedral : 7.969 58.133 1728 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.71 % Allowed : 15.46 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.23), residues: 1288 helix: 0.35 (0.22), residues: 560 sheet: 0.29 (0.28), residues: 290 loop : -1.94 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 773 HIS 0.003 0.001 HIS B 492 PHE 0.013 0.001 PHE A 576 TYR 0.011 0.001 TYR B 471 ARG 0.003 0.000 ARG B 523 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 5 residues processed: 128 average time/residue: 0.7402 time to fit residues: 107.1008 Evaluate side-chains 108 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.5754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 6.9990 chunk 71 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 86 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 112 optimal weight: 40.0000 chunk 31 optimal weight: 4.9990 overall best weight: 3.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 572 ASN A 712 ASN B 712 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 10490 Z= 0.442 Angle : 0.663 10.338 14288 Z= 0.337 Chirality : 0.048 0.270 1714 Planarity : 0.005 0.081 1790 Dihedral : 7.827 59.866 1728 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.23 % Allowed : 16.98 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1288 helix: 0.36 (0.22), residues: 560 sheet: 0.32 (0.29), residues: 290 loop : -2.03 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 773 HIS 0.006 0.001 HIS B 492 PHE 0.016 0.002 PHE B 730 TYR 0.017 0.002 TYR B 173 ARG 0.010 0.001 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 104 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 11 residues processed: 128 average time/residue: 0.8097 time to fit residues: 116.2391 Evaluate side-chains 114 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 1.0684 time to fit residues: 2.6395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10490 Z= 0.277 Angle : 0.597 10.093 14288 Z= 0.301 Chirality : 0.046 0.246 1714 Planarity : 0.004 0.069 1790 Dihedral : 7.420 58.380 1728 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.04 % Allowed : 17.36 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1288 helix: 0.67 (0.22), residues: 550 sheet: 0.35 (0.28), residues: 290 loop : -1.89 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 317 HIS 0.004 0.001 HIS B 492 PHE 0.014 0.001 PHE A 730 TYR 0.013 0.001 TYR A 729 ARG 0.002 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 108 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 127 average time/residue: 0.7132 time to fit residues: 103.1879 Evaluate side-chains 119 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 1.0943 time to fit residues: 2.6224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 71 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10490 Z= 0.166 Angle : 0.556 10.108 14288 Z= 0.278 Chirality : 0.044 0.222 1714 Planarity : 0.004 0.070 1790 Dihedral : 6.819 52.982 1728 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.09 % Allowed : 18.79 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1288 helix: 0.87 (0.23), residues: 554 sheet: 0.38 (0.28), residues: 290 loop : -1.69 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 317 HIS 0.003 0.001 HIS B 492 PHE 0.012 0.001 PHE A 730 TYR 0.014 0.001 TYR A 471 ARG 0.002 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 127 average time/residue: 0.7576 time to fit residues: 108.7989 Evaluate side-chains 114 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 1.0346 time to fit residues: 2.6493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 30.0000 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 0.0270 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10490 Z= 0.197 Angle : 0.567 9.369 14288 Z= 0.284 Chirality : 0.044 0.275 1714 Planarity : 0.004 0.067 1790 Dihedral : 6.570 49.569 1728 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.42 % Allowed : 20.21 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1288 helix: 0.98 (0.23), residues: 554 sheet: 0.44 (0.28), residues: 290 loop : -1.61 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 317 HIS 0.003 0.001 HIS B 492 PHE 0.013 0.001 PHE A 730 TYR 0.018 0.001 TYR A 729 ARG 0.004 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 123 average time/residue: 0.7538 time to fit residues: 104.7894 Evaluate side-chains 119 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 1.1747 time to fit residues: 2.7973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 110 optimal weight: 30.0000 chunk 76 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 10490 Z= 0.434 Angle : 0.674 9.621 14288 Z= 0.339 Chirality : 0.048 0.342 1714 Planarity : 0.005 0.078 1790 Dihedral : 6.802 49.373 1728 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.09 % Allowed : 20.87 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1288 helix: 0.93 (0.23), residues: 560 sheet: 0.41 (0.28), residues: 290 loop : -1.70 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 317 HIS 0.006 0.001 HIS A 492 PHE 0.020 0.002 PHE A 730 TYR 0.020 0.002 TYR B 173 ARG 0.003 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 117 average time/residue: 0.7966 time to fit residues: 105.0709 Evaluate side-chains 109 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.1496 time to fit residues: 2.7915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 chunk 129 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10490 Z= 0.200 Angle : 0.605 11.932 14288 Z= 0.299 Chirality : 0.045 0.263 1714 Planarity : 0.004 0.064 1790 Dihedral : 6.455 45.973 1728 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.85 % Allowed : 22.01 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.24), residues: 1288 helix: 1.01 (0.23), residues: 560 sheet: 0.44 (0.28), residues: 290 loop : -1.64 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 317 HIS 0.004 0.001 HIS A 492 PHE 0.015 0.001 PHE A 730 TYR 0.023 0.001 TYR A 729 ARG 0.002 0.000 ARG A 523 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 118 average time/residue: 0.8301 time to fit residues: 110.3691 Evaluate side-chains 112 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.5352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 0.0170 chunk 43 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.140813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.092264 restraints weight = 16037.733| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.97 r_work: 0.3129 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10490 Z= 0.192 Angle : 0.592 11.915 14288 Z= 0.292 Chirality : 0.044 0.245 1714 Planarity : 0.004 0.071 1790 Dihedral : 6.119 47.936 1728 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.95 % Allowed : 22.49 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1288 helix: 1.10 (0.23), residues: 560 sheet: 0.49 (0.27), residues: 290 loop : -1.52 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 317 HIS 0.003 0.001 HIS B 492 PHE 0.015 0.001 PHE B 730 TYR 0.021 0.001 TYR A 729 ARG 0.003 0.000 ARG A 598 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2775.53 seconds wall clock time: 50 minutes 41.67 seconds (3041.67 seconds total)