Starting phenix.real_space_refine on Thu Mar 5 05:27:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oen_20031/03_2026/6oen_20031.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oen_20031/03_2026/6oen_20031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oen_20031/03_2026/6oen_20031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oen_20031/03_2026/6oen_20031.map" model { file = "/net/cci-nas-00/data/ceres_data/6oen_20031/03_2026/6oen_20031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oen_20031/03_2026/6oen_20031.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Zn 2 6.06 5 P 204 5.49 5 S 106 5.16 5 C 11787 2.51 5 N 3467 2.21 5 O 4082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19649 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4770 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4820 Classifications: {'peptide': 609} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 583} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2664 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2663 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1154 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 936 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 938 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1171 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "N" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 242 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 288 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 3, 'TRANS': 51} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 5, 'TYR:plan': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 97 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2544 SG CYS A 727 97.270 46.943 96.475 1.00117.57 S ATOM 2565 SG CYS A 730 99.151 45.527 97.280 1.00124.23 S ATOM 7340 SG CYS C 727 36.280 108.692 97.953 1.00 91.24 S ATOM 7361 SG CYS C 730 34.348 110.329 99.354 1.00 95.05 S Time building chain proxies: 3.97, per 1000 atoms: 0.20 Number of scatterers: 19649 At special positions: 0 Unit cell: (133.75, 160.5, 155.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 1 19.99 S 106 16.00 P 204 15.00 O 4082 8.00 N 3467 7.00 C 11787 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 - 3.00 Amino acid : True - 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: 1.16 Conformation dependent library (CDL) restraints added in 701.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 937 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 727 " Number of angles added : 4 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3734 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 20 sheets defined 39.7% alpha, 21.1% beta 100 base pairs and 177 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 400 through 408 Processing helix chain 'A' and resid 408 through 423 Processing helix chain 'A' and resid 426 through 442 Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.938A pdb=" N ALA A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 475 removed outlier: 3.648A pdb=" N CYS A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.707A pdb=" N LEU A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.606A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 812 removed outlier: 3.966A pdb=" N ASN A 800 " --> pdb=" O CYS A 796 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 803 " --> pdb=" O GLY A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 841 Processing helix chain 'A' and resid 850 through 858 removed outlier: 3.512A pdb=" N ALA A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 Processing helix chain 'A' and resid 874 through 894 removed outlier: 3.606A pdb=" N ALA A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Proline residue: A 891 - end of helix Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.747A pdb=" N LEU A 906 " --> pdb=" O CYS A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 923 Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 942 through 951 removed outlier: 3.934A pdb=" N ILE A 946 " --> pdb=" O HIS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 975 removed outlier: 3.629A pdb=" N ASN A 975 " --> pdb=" O PHE A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 995 removed outlier: 4.203A pdb=" N GLU A 985 " --> pdb=" O CYS A 981 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1004 Processing helix chain 'C' and resid 400 through 423 removed outlier: 5.457A pdb=" N GLU C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 441 Processing helix chain 'C' and resid 444 through 457 Processing helix chain 'C' and resid 463 through 475 removed outlier: 3.852A pdb=" N CYS C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 509 Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 664 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 776 Processing helix chain 'C' and resid 792 through 814 removed outlier: 3.877A pdb=" N LYS C 806 " --> pdb=" O ALA C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 841 Processing helix chain 'C' and resid 850 through 858 removed outlier: 3.697A pdb=" N MET C 858 " --> pdb=" O ALA C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 868 Processing helix chain 'C' and resid 873 through 894 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 902 through 907 Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 943 through 950 Processing helix chain 'C' and resid 963 through 975 removed outlier: 3.558A pdb=" N ASN C 975 " --> pdb=" O PHE C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 995 removed outlier: 4.228A pdb=" N GLU C 985 " --> pdb=" O CYS C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1004 Processing helix chain 'C' and resid 1005 through 1008 Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.900A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.900A pdb=" N LEU D 14 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'N' and resid 100 through 117 Proline residue: N 111 - end of helix Processing helix chain 'N' and resid 123 through 136 Processing helix chain 'H' and resid 102 through 117 Proline residue: H 111 - end of helix Processing helix chain 'H' and resid 121 through 136 Processing helix chain 'H' and resid 141 through 155 removed outlier: 3.665A pdb=" N GLU H 145 " --> pdb=" O LYS H 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 5.695A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 519 removed outlier: 5.695A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 518 through 519 removed outlier: 10.352A pdb=" N PHE C 591 " --> pdb=" O PHE C 700 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N PHE C 702 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N VAL C 593 " --> pdb=" O PHE C 702 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N GLY C 704 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 10.913A pdb=" N VAL C 595 " --> pdb=" O GLY C 704 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLY C 706 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU C 597 " --> pdb=" O GLY C 706 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET C 602 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL C 620 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP C 604 " --> pdb=" O LYS C 618 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LYS C 618 " --> pdb=" O ASP C 604 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 518 through 519 removed outlier: 10.352A pdb=" N PHE C 591 " --> pdb=" O PHE C 700 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N PHE C 702 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N VAL C 593 " --> pdb=" O PHE C 702 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N GLY C 704 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 10.913A pdb=" N VAL C 595 " --> pdb=" O GLY C 704 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLY C 706 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU C 597 " --> pdb=" O GLY C 706 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET C 602 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL C 620 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP C 604 " --> pdb=" O LYS C 618 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LYS C 618 " --> pdb=" O ASP C 604 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 5 Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 24 removed outlier: 4.765A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 58 " --> pdb=" O HIS B 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.701A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 75 through 80 Processing sheet with id=AA9, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.328A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 193 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 182 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 183 " --> pdb=" O LEU B 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.607A pdb=" N ARG B 212 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 215 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 263 through 267 removed outlier: 7.100A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 271 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 2 through 5 Processing sheet with id=AB5, first strand: chain 'D' and resid 20 through 24 removed outlier: 4.765A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS D 58 " --> pdb=" O HIS D 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.701A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 75 through 80 Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.329A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 193 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 182 " --> pdb=" O TYR D 195 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE D 183 " --> pdb=" O LEU D 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AC1, first strand: chain 'D' and resid 208 through 212 removed outlier: 3.607A pdb=" N ARG D 212 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR D 215 " --> pdb=" O ARG D 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 263 through 267 removed outlier: 7.100A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE D 271 " --> pdb=" O VAL D 290 " (cutoff:3.500A) 739 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 249 hydrogen bonds 498 hydrogen bond angles 0 basepair planarities 100 basepair parallelities 177 stacking parallelities Total time for adding SS restraints: 4.90 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5325 1.34 - 1.46: 6095 1.46 - 1.58: 8514 1.58 - 1.71: 404 1.71 - 1.83: 160 Bond restraints: 20498 Sorted by residual: bond pdb=" N HIS A 942 " pdb=" CA HIS A 942 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.12e-02 7.97e+03 1.02e+01 bond pdb=" N CYS C 730 " pdb=" CA CYS C 730 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.72e+00 bond pdb=" N HIS C 942 " pdb=" CA HIS C 942 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.38e+00 bond pdb=" N LEU A 718 " pdb=" CA LEU A 718 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.79e+00 bond pdb=" N GLU A 983 " pdb=" CA GLU A 983 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.19e-02 7.06e+03 6.46e+00 ... (remaining 20493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 27123 1.95 - 3.91: 1317 3.91 - 5.86: 141 5.86 - 7.81: 27 7.81 - 9.77: 17 Bond angle restraints: 28625 Sorted by residual: angle pdb=" C SER A 895 " pdb=" N SER A 896 " pdb=" CA SER A 896 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C MET A 568 " pdb=" N ASP A 569 " pdb=" CA ASP A 569 " ideal model delta sigma weight residual 122.54 114.97 7.57 1.65e+00 3.67e-01 2.10e+01 angle pdb=" C CYS A 907 " pdb=" N GLN A 908 " pdb=" CA GLN A 908 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C GLN A 962 " pdb=" N SER A 963 " pdb=" CA SER A 963 " ideal model delta sigma weight residual 120.54 126.51 -5.97 1.35e+00 5.49e-01 1.96e+01 angle pdb=" N SER A 723 " pdb=" CA SER A 723 " pdb=" C SER A 723 " ideal model delta sigma weight residual 110.33 115.55 -5.22 1.29e+00 6.01e-01 1.64e+01 ... (remaining 28620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 10546 35.73 - 71.46: 1193 71.46 - 107.20: 14 107.20 - 142.93: 5 142.93 - 178.66: 6 Dihedral angle restraints: 11764 sinusoidal: 5975 harmonic: 5789 Sorted by residual: dihedral pdb=" CA ARG D 212 " pdb=" C ARG D 212 " pdb=" N ASN D 213 " pdb=" CA ASN D 213 " ideal model delta harmonic sigma weight residual 180.00 151.49 28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ARG B 212 " pdb=" C ARG B 212 " pdb=" N ASN B 213 " pdb=" CA ASN B 213 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA PHE A 557 " pdb=" C PHE A 557 " pdb=" N ARG A 558 " pdb=" CA ARG A 558 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 11761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2252 0.050 - 0.100: 699 0.100 - 0.151: 176 0.151 - 0.201: 47 0.201 - 0.251: 7 Chirality restraints: 3181 Sorted by residual: chirality pdb=" CB ILE B 331 " pdb=" CA ILE B 331 " pdb=" CG1 ILE B 331 " pdb=" CG2 ILE B 331 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE D 331 " pdb=" CA ILE D 331 " pdb=" CG1 ILE D 331 " pdb=" CG2 ILE D 331 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL A 724 " pdb=" CA VAL A 724 " pdb=" CG1 VAL A 724 " pdb=" CG2 VAL A 724 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 3178 not shown) Planarity restraints: 2970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 511 " -0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO C 512 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 512 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 512 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 511 " 0.044 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO A 512 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 941 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.00e+00 pdb=" C ALA A 941 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA A 941 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS A 942 " -0.015 2.00e-02 2.50e+03 ... (remaining 2967 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2400 2.75 - 3.28: 17795 3.28 - 3.82: 36874 3.82 - 4.36: 39239 4.36 - 4.90: 62007 Nonbonded interactions: 158315 Sorted by model distance: nonbonded pdb=" C2' DA F 33 " pdb=" O5' DG F 34 " model vdw 2.208 3.440 nonbonded pdb=" OD1 ASP A 536 " pdb=" NZ LYS A 555 " model vdw 2.282 3.120 nonbonded pdb=" O CYS A 902 " pdb=" OG SER A 905 " model vdw 2.309 3.040 nonbonded pdb=" O SER C 539 " pdb=" OG SER C 539 " model vdw 2.315 3.040 nonbonded pdb=" OD2 ASP A 569 " pdb=" OG SER A 996 " model vdw 2.318 3.040 ... (remaining 158310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 400 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB )) or resid 408 through 427 or (resid 428 through 429 \ and (name N or name CA or name C or name O or name CB )) or resid 430 through 45 \ 7 or (resid 458 and (name N or name CA or name C or name O or name CB )) or resi \ d 459 through 584 or (resid 585 and (name N or name CA or name C or name O or na \ me CB )) or resid 586 through 606 or (resid 607 through 609 and (name N or name \ CA or name C or name O or name CB )) or resid 610 through 847 or (resid 848 and \ (name N or name CA or name C or name O or name CB )) or resid 849 through 903 or \ (resid 904 and (name N or name CA or name C or name O or name CB )) or resid 90 \ 5 through 954 or resid 961 through 1101)) selection = (chain 'C' and (resid 400 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB )) or resid 410 through 631 or (resid 632 and (name N \ or name CA or name C or name O or name CB )) or resid 633 through 638 or (resid \ 639 and (name N or name CA or name C or name O or name CB )) or resid 640 throug \ h 751 or (resid 752 and (name N or name CA or name C or name O or name CB )) or \ resid 753 through 757 or (resid 758 and (name N or name CA or name C or name O o \ r name CB )) or resid 759 through 810 or (resid 811 and (name N or name CA or na \ me C or name O or name CB )) or resid 812 through 819 or (resid 820 through 821 \ and (name N or name CA or name C or name O or name CB )) or resid 822 or (resid \ 823 and (name N or name CA or name C or name O or name CB )) or resid 824 throug \ h 834 or (resid 835 and (name N or name CA or name C or name O or name CB )) or \ resid 836 through 837 or (resid 838 through 839 and (name N or name CA or name C \ or name O or name CB )) or resid 840 through 860 or (resid 861 and (name N or n \ ame CA or name C or name O or name CB )) or resid 862 through 926 or (resid 927 \ through 928 and (name N or name CA or name C or name O or name CB )) or resid 92 \ 9 through 947 or (resid 948 and (name N or name CA or name C or name O or name C \ B )) or resid 949 through 954 or resid 961 through 1101)) } ncs_group { reference = (chain 'B' and (resid 1 through 117 or (resid 118 and (name N or name CA or name \ C or name O or name CB )) or resid 119 through 351)) selection = (chain 'D' and (resid 1 through 338 or (resid 339 and (name N or name CA or name \ C or name O or name CB )) or resid 340 through 351)) } 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: 1.940 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.150 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.010 0.791 20506 Z= 0.361 Angle : 1.038 39.266 28629 Z= 0.552 Chirality : 0.054 0.251 3181 Planarity : 0.007 0.071 2970 Dihedral : 23.636 178.659 8030 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.61 % Allowed : 10.03 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.15), residues: 1976 helix: -2.30 (0.14), residues: 716 sheet: -2.27 (0.24), residues: 350 loop : -2.84 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 713 TYR 0.027 0.002 TYR A 998 PHE 0.019 0.002 PHE C 418 TRP 0.021 0.002 TRP N 133 HIS 0.009 0.002 HIS C1006 Details of bonding type rmsd covalent geometry : bond 0.00622 (20498) covalent geometry : angle 0.95140 (28625) hydrogen bonds : bond 0.15032 ( 965) hydrogen bonds : angle 6.47006 ( 2574) metal coordination : bond 0.37295 ( 8) metal coordination : angle 35.21477 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 228 time to evaluate : 0.622 Fit side-chains REVERT: A 402 ARG cc_start: 0.2700 (ttt90) cc_final: 0.2232 (mmm160) REVERT: A 507 GLU cc_start: 0.8763 (tp30) cc_final: 0.8310 (tp30) REVERT: A 578 MET cc_start: 0.9118 (ttp) cc_final: 0.8674 (tpp) REVERT: A 678 GLU cc_start: 0.9036 (pp20) cc_final: 0.8808 (pp20) REVERT: A 687 LEU cc_start: 0.9043 (tp) cc_final: 0.8797 (tp) REVERT: A 889 MET cc_start: 0.8556 (mtm) cc_final: 0.8139 (mtm) REVERT: A 993 LEU cc_start: 0.9116 (mm) cc_final: 0.8827 (mp) REVERT: A 1003 MET cc_start: 0.8609 (mmm) cc_final: 0.8401 (mmm) REVERT: C 412 LYS cc_start: 0.9452 (tttt) cc_final: 0.9212 (tmtt) REVERT: C 617 GLU cc_start: 0.8265 (tt0) cc_final: 0.7998 (tt0) REVERT: B 20 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8134 (t) REVERT: B 49 ASP cc_start: 0.6997 (m-30) cc_final: 0.6609 (m-30) REVERT: D 110 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7893 (mmm) outliers start: 59 outliers final: 8 residues processed: 272 average time/residue: 0.1420 time to fit residues: 58.7605 Evaluate side-chains 137 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 0.0020 chunk 77 optimal weight: 0.7980 overall best weight: 3.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 501 HIS A 525 ASN A 581 GLN A 744 HIS A 753 ASN A 755 GLN ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 GLN A 990 HIS C 636 GLN C 755 GLN ** C 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 HIS C 852 ASN C 991 HIS B 33 GLN B 222 HIS B 282 GLN D 282 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.065611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046922 restraints weight = 122892.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048051 restraints weight = 68447.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048751 restraints weight = 46151.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049214 restraints weight = 35850.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.049437 restraints weight = 30459.630| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 20506 Z= 0.194 Angle : 0.654 12.579 28629 Z= 0.359 Chirality : 0.042 0.198 3181 Planarity : 0.005 0.050 2970 Dihedral : 25.920 179.892 4421 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.43 % Allowed : 6.42 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.17), residues: 1976 helix: -0.40 (0.18), residues: 727 sheet: -1.87 (0.27), residues: 291 loop : -2.44 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 504 TYR 0.020 0.001 TYR A 998 PHE 0.024 0.002 PHE C 641 TRP 0.012 0.001 TRP B 317 HIS 0.008 0.001 HIS C 937 Details of bonding type rmsd covalent geometry : bond 0.00418 (20498) covalent geometry : angle 0.64712 (28625) hydrogen bonds : bond 0.04596 ( 965) hydrogen bonds : angle 4.70861 ( 2574) metal coordination : bond 0.04744 ( 8) metal coordination : angle 7.73605 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.2147 (ttt90) cc_final: 0.1883 (mmm160) REVERT: A 467 CYS cc_start: 0.9297 (m) cc_final: 0.9073 (m) REVERT: A 481 TYR cc_start: 0.8935 (t80) cc_final: 0.8686 (t80) REVERT: A 507 GLU cc_start: 0.8763 (tp30) cc_final: 0.8427 (tp30) REVERT: A 578 MET cc_start: 0.9305 (ttp) cc_final: 0.8643 (tpp) REVERT: A 687 LEU cc_start: 0.9384 (tp) cc_final: 0.9003 (tp) REVERT: A 753 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.9056 (p0) REVERT: A 795 HIS cc_start: 0.8888 (m90) cc_final: 0.8682 (m90) REVERT: A 889 MET cc_start: 0.9159 (mtm) cc_final: 0.8664 (mtm) REVERT: A 986 ASP cc_start: 0.8671 (t70) cc_final: 0.8390 (t0) REVERT: C 412 LYS cc_start: 0.9385 (tttt) cc_final: 0.9136 (tmtt) REVERT: C 504 ARG cc_start: 0.8644 (mtm-85) cc_final: 0.8408 (mtm-85) REVERT: C 617 GLU cc_start: 0.8598 (tt0) cc_final: 0.8164 (tt0) REVERT: C 986 ASP cc_start: 0.9079 (t70) cc_final: 0.8861 (t0) REVERT: B 49 ASP cc_start: 0.7182 (m-30) cc_final: 0.6808 (m-30) REVERT: B 57 LEU cc_start: 0.9030 (tp) cc_final: 0.8756 (tp) REVERT: B 152 MET cc_start: 0.9000 (tpp) cc_final: 0.8589 (tpp) REVERT: B 214 ASP cc_start: 0.7501 (t0) cc_final: 0.7190 (t0) REVERT: D 110 MET cc_start: 0.8712 (tpp) cc_final: 0.8398 (tpp) REVERT: D 126 GLU cc_start: 0.8361 (pp20) cc_final: 0.8124 (pp20) REVERT: D 152 MET cc_start: 0.9075 (tpp) cc_final: 0.8863 (tpp) outliers start: 7 outliers final: 2 residues processed: 185 average time/residue: 0.1347 time to fit residues: 39.6391 Evaluate side-chains 122 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 211 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 85 optimal weight: 0.1980 chunk 142 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 102 optimal weight: 0.0170 chunk 21 optimal weight: 10.0000 chunk 197 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 overall best weight: 2.0424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 795 HIS B 33 GLN B 201 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS D 282 GLN D 313 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.065770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.047460 restraints weight = 118378.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.048626 restraints weight = 64992.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.049378 restraints weight = 43160.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049862 restraints weight = 32729.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.050159 restraints weight = 27347.535| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20506 Z= 0.153 Angle : 0.613 12.964 28629 Z= 0.335 Chirality : 0.041 0.161 3181 Planarity : 0.004 0.058 2970 Dihedral : 25.725 179.964 4421 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.18), residues: 1976 helix: 0.15 (0.19), residues: 743 sheet: -1.48 (0.28), residues: 280 loop : -2.21 (0.18), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 504 TYR 0.016 0.001 TYR B 217 PHE 0.024 0.001 PHE C 641 TRP 0.012 0.001 TRP N 133 HIS 0.007 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00336 (20498) covalent geometry : angle 0.60994 (28625) hydrogen bonds : bond 0.04077 ( 965) hydrogen bonds : angle 4.39145 ( 2574) metal coordination : bond 0.02016 ( 8) metal coordination : angle 4.80870 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8819 (mmp) cc_final: 0.8543 (mmm) REVERT: A 481 TYR cc_start: 0.8949 (t80) cc_final: 0.8686 (t80) REVERT: A 578 MET cc_start: 0.9278 (ttp) cc_final: 0.8823 (tpp) REVERT: A 627 MET cc_start: 0.8788 (pmm) cc_final: 0.8377 (pmm) REVERT: A 687 LEU cc_start: 0.9321 (tp) cc_final: 0.8933 (tp) REVERT: A 795 HIS cc_start: 0.8776 (m90) cc_final: 0.8562 (m90) REVERT: A 800 ASN cc_start: 0.9467 (m110) cc_final: 0.9211 (m-40) REVERT: A 881 GLU cc_start: 0.8971 (pt0) cc_final: 0.8588 (pp20) REVERT: A 889 MET cc_start: 0.9084 (mtm) cc_final: 0.8545 (mtm) REVERT: A 986 ASP cc_start: 0.8612 (t70) cc_final: 0.8338 (t0) REVERT: A 1003 MET cc_start: 0.8900 (tpp) cc_final: 0.8664 (tpp) REVERT: C 412 LYS cc_start: 0.9382 (tttt) cc_final: 0.9132 (tmtt) REVERT: C 504 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.8190 (mtm-85) REVERT: C 507 GLU cc_start: 0.8611 (pt0) cc_final: 0.8155 (pp20) REVERT: C 617 GLU cc_start: 0.8386 (tt0) cc_final: 0.8175 (tt0) REVERT: C 658 MET cc_start: 0.9028 (pmm) cc_final: 0.8394 (pmm) REVERT: C 986 ASP cc_start: 0.9103 (t70) cc_final: 0.8858 (t0) REVERT: B 57 LEU cc_start: 0.8940 (tp) cc_final: 0.8623 (tp) REVERT: B 152 MET cc_start: 0.9043 (tpp) cc_final: 0.8822 (mmm) REVERT: D 110 MET cc_start: 0.8728 (tpp) cc_final: 0.8311 (mmm) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.1136 time to fit residues: 31.6879 Evaluate side-chains 120 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 7.9990 chunk 184 optimal weight: 0.4980 chunk 207 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 10 optimal weight: 0.0980 chunk 188 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN C 495 GLN B 33 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.065873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046801 restraints weight = 121840.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047958 restraints weight = 66656.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048700 restraints weight = 44268.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.049197 restraints weight = 33975.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049447 restraints weight = 28611.149| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20506 Z= 0.170 Angle : 0.613 12.040 28629 Z= 0.336 Chirality : 0.040 0.169 3181 Planarity : 0.004 0.053 2970 Dihedral : 25.630 179.681 4421 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.18), residues: 1976 helix: 0.44 (0.19), residues: 746 sheet: -1.18 (0.30), residues: 281 loop : -2.05 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 235 TYR 0.018 0.001 TYR C 998 PHE 0.019 0.001 PHE C 641 TRP 0.012 0.001 TRP A 519 HIS 0.006 0.001 HIS A 795 Details of bonding type rmsd covalent geometry : bond 0.00370 (20498) covalent geometry : angle 0.60986 (28625) hydrogen bonds : bond 0.04151 ( 965) hydrogen bonds : angle 4.24831 ( 2574) metal coordination : bond 0.02541 ( 8) metal coordination : angle 5.66620 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8796 (mmp) cc_final: 0.8479 (mmp) REVERT: A 481 TYR cc_start: 0.8971 (t80) cc_final: 0.8697 (t80) REVERT: A 578 MET cc_start: 0.9281 (ttp) cc_final: 0.8661 (tpp) REVERT: A 687 LEU cc_start: 0.9317 (tp) cc_final: 0.9012 (tp) REVERT: A 795 HIS cc_start: 0.8763 (m90) cc_final: 0.8521 (m-70) REVERT: A 800 ASN cc_start: 0.9426 (m110) cc_final: 0.9160 (m-40) REVERT: A 881 GLU cc_start: 0.8952 (pt0) cc_final: 0.8733 (pp20) REVERT: A 889 MET cc_start: 0.9083 (mtm) cc_final: 0.8613 (mtm) REVERT: A 986 ASP cc_start: 0.8700 (t70) cc_final: 0.8454 (t0) REVERT: C 412 LYS cc_start: 0.9373 (tttt) cc_final: 0.9099 (tmtt) REVERT: C 504 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.8216 (mtm-85) REVERT: C 507 GLU cc_start: 0.8601 (pt0) cc_final: 0.8169 (pp20) REVERT: C 508 LYS cc_start: 0.9230 (ttmt) cc_final: 0.8991 (ttmm) REVERT: C 602 MET cc_start: 0.9257 (mpp) cc_final: 0.9033 (mpp) REVERT: C 986 ASP cc_start: 0.9082 (t70) cc_final: 0.8857 (t0) REVERT: B 110 MET cc_start: 0.8302 (tpt) cc_final: 0.7856 (tpt) REVERT: B 152 MET cc_start: 0.9061 (tpp) cc_final: 0.8850 (mmm) REVERT: B 172 TRP cc_start: 0.9256 (t-100) cc_final: 0.8785 (t-100) REVERT: D 110 MET cc_start: 0.8711 (tpp) cc_final: 0.8498 (mmm) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.1163 time to fit residues: 32.4557 Evaluate side-chains 124 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 3.9990 chunk 99 optimal weight: 0.0980 chunk 111 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 197 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.065521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.046614 restraints weight = 123236.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047727 restraints weight = 69072.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.048451 restraints weight = 46716.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.048902 restraints weight = 36133.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049201 restraints weight = 30672.129| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20506 Z= 0.188 Angle : 0.627 12.454 28629 Z= 0.343 Chirality : 0.041 0.170 3181 Planarity : 0.004 0.047 2970 Dihedral : 25.613 178.351 4421 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.19), residues: 1976 helix: 0.61 (0.19), residues: 747 sheet: -0.99 (0.29), residues: 305 loop : -1.94 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 826 TYR 0.019 0.001 TYR N 109 PHE 0.015 0.001 PHE C 916 TRP 0.022 0.001 TRP B 317 HIS 0.007 0.001 HIS A 795 Details of bonding type rmsd covalent geometry : bond 0.00406 (20498) covalent geometry : angle 0.62220 (28625) hydrogen bonds : bond 0.04294 ( 965) hydrogen bonds : angle 4.25326 ( 2574) metal coordination : bond 0.02464 ( 8) metal coordination : angle 6.60953 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8820 (mmp) cc_final: 0.8485 (mmp) REVERT: A 481 TYR cc_start: 0.9008 (t80) cc_final: 0.8730 (t80) REVERT: A 578 MET cc_start: 0.9306 (ttp) cc_final: 0.8674 (tpp) REVERT: A 627 MET cc_start: 0.8781 (pmm) cc_final: 0.8470 (pmm) REVERT: A 687 LEU cc_start: 0.9313 (tp) cc_final: 0.8989 (tp) REVERT: A 795 HIS cc_start: 0.8822 (m90) cc_final: 0.8546 (m-70) REVERT: A 881 GLU cc_start: 0.8949 (pt0) cc_final: 0.8666 (pp20) REVERT: A 889 MET cc_start: 0.9066 (mtm) cc_final: 0.8713 (mtm) REVERT: A 986 ASP cc_start: 0.8774 (t70) cc_final: 0.8543 (t0) REVERT: C 412 LYS cc_start: 0.9354 (tttt) cc_final: 0.9045 (tmtt) REVERT: C 504 ARG cc_start: 0.8779 (mtm-85) cc_final: 0.8191 (mtm-85) REVERT: C 507 GLU cc_start: 0.8588 (pt0) cc_final: 0.8109 (pp20) REVERT: C 602 MET cc_start: 0.9307 (mpp) cc_final: 0.9021 (mpp) REVERT: C 658 MET cc_start: 0.9016 (pmm) cc_final: 0.7606 (pmm) REVERT: C 986 ASP cc_start: 0.9119 (t70) cc_final: 0.8865 (t0) REVERT: B 110 MET cc_start: 0.8460 (tpt) cc_final: 0.8247 (tpt) REVERT: B 302 MET cc_start: 0.7316 (mmm) cc_final: 0.6956 (tpp) REVERT: D 110 MET cc_start: 0.8735 (tpp) cc_final: 0.8516 (mmm) REVERT: D 339 MET cc_start: 0.7044 (mmt) cc_final: 0.6814 (mmt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1150 time to fit residues: 29.2029 Evaluate side-chains 110 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 122 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN D 313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.065784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.046520 restraints weight = 121279.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.047699 restraints weight = 66879.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.048469 restraints weight = 44681.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.048949 restraints weight = 34169.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.049259 restraints weight = 28824.584| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20506 Z= 0.168 Angle : 0.613 8.086 28629 Z= 0.335 Chirality : 0.040 0.170 3181 Planarity : 0.004 0.050 2970 Dihedral : 25.559 178.257 4421 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.19), residues: 1976 helix: 0.70 (0.19), residues: 748 sheet: -0.84 (0.29), residues: 305 loop : -1.90 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 696 TYR 0.016 0.001 TYR C 559 PHE 0.012 0.001 PHE A 641 TRP 0.013 0.001 TRP B 317 HIS 0.006 0.001 HIS A 795 Details of bonding type rmsd covalent geometry : bond 0.00366 (20498) covalent geometry : angle 0.60784 (28625) hydrogen bonds : bond 0.03986 ( 965) hydrogen bonds : angle 4.23014 ( 2574) metal coordination : bond 0.02989 ( 8) metal coordination : angle 6.45068 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8875 (mmp) cc_final: 0.8397 (mmp) REVERT: A 481 TYR cc_start: 0.8983 (t80) cc_final: 0.8752 (t80) REVERT: A 578 MET cc_start: 0.9339 (ttp) cc_final: 0.8922 (tpp) REVERT: A 627 MET cc_start: 0.8776 (pmm) cc_final: 0.8443 (pmm) REVERT: A 687 LEU cc_start: 0.9351 (tp) cc_final: 0.9032 (tp) REVERT: A 795 HIS cc_start: 0.8871 (m90) cc_final: 0.8595 (m-70) REVERT: A 889 MET cc_start: 0.9111 (mtm) cc_final: 0.8649 (mtm) REVERT: A 999 LEU cc_start: 0.9412 (mp) cc_final: 0.9095 (mp) REVERT: C 412 LYS cc_start: 0.9357 (tttt) cc_final: 0.9043 (tmtt) REVERT: C 504 ARG cc_start: 0.8776 (mtm-85) cc_final: 0.8197 (mtm-85) REVERT: C 507 GLU cc_start: 0.8540 (pt0) cc_final: 0.8106 (pp20) REVERT: C 658 MET cc_start: 0.9083 (pmm) cc_final: 0.7811 (pmm) REVERT: C 986 ASP cc_start: 0.9091 (t70) cc_final: 0.8851 (t0) REVERT: B 110 MET cc_start: 0.8471 (tpt) cc_final: 0.8209 (tpt) REVERT: B 298 GLU cc_start: 0.8652 (tp30) cc_final: 0.8340 (pp20) REVERT: D 110 MET cc_start: 0.8788 (tpp) cc_final: 0.8582 (mmm) REVERT: D 339 MET cc_start: 0.7037 (mmt) cc_final: 0.6812 (mmt) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1131 time to fit residues: 29.9815 Evaluate side-chains 112 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 87 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 chunk 111 optimal weight: 0.5980 chunk 213 optimal weight: 4.9990 chunk 24 optimal weight: 0.0000 chunk 192 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.066351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.047391 restraints weight = 115387.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048574 restraints weight = 63205.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.049349 restraints weight = 41887.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049841 restraints weight = 31738.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050157 restraints weight = 26559.862| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20506 Z= 0.134 Angle : 0.594 6.982 28629 Z= 0.323 Chirality : 0.040 0.166 3181 Planarity : 0.004 0.050 2970 Dihedral : 25.461 178.210 4421 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.19), residues: 1976 helix: 0.84 (0.19), residues: 747 sheet: -0.66 (0.29), residues: 305 loop : -1.83 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 977 TYR 0.016 0.001 TYR A 586 PHE 0.037 0.001 PHE C 557 TRP 0.012 0.001 TRP B 317 HIS 0.005 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00295 (20498) covalent geometry : angle 0.59299 (28625) hydrogen bonds : bond 0.03499 ( 965) hydrogen bonds : angle 4.11154 ( 2574) metal coordination : bond 0.00873 ( 8) metal coordination : angle 3.23894 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8752 (mmp) cc_final: 0.8408 (mmm) REVERT: A 578 MET cc_start: 0.9374 (ttp) cc_final: 0.8649 (tpp) REVERT: A 583 LEU cc_start: 0.8827 (mt) cc_final: 0.7952 (mt) REVERT: A 627 MET cc_start: 0.8710 (pmm) cc_final: 0.8413 (pmm) REVERT: A 656 CYS cc_start: 0.7987 (p) cc_final: 0.7720 (p) REVERT: A 658 MET cc_start: 0.8757 (pmm) cc_final: 0.7950 (pmm) REVERT: A 687 LEU cc_start: 0.9377 (tp) cc_final: 0.9105 (tp) REVERT: A 795 HIS cc_start: 0.8937 (m90) cc_final: 0.8683 (m-70) REVERT: A 889 MET cc_start: 0.9048 (mtm) cc_final: 0.8619 (mtm) REVERT: C 412 LYS cc_start: 0.9333 (tttt) cc_final: 0.8985 (tmtt) REVERT: C 602 MET cc_start: 0.9214 (mpp) cc_final: 0.8608 (mpp) REVERT: C 658 MET cc_start: 0.9011 (pmm) cc_final: 0.7910 (pmm) REVERT: C 986 ASP cc_start: 0.9120 (t70) cc_final: 0.8833 (t0) REVERT: B 110 MET cc_start: 0.8476 (tpt) cc_final: 0.8082 (tpp) REVERT: B 152 MET cc_start: 0.8438 (tpp) cc_final: 0.8191 (tpp) REVERT: B 298 GLU cc_start: 0.8571 (tp30) cc_final: 0.8341 (pp20) REVERT: D 110 MET cc_start: 0.8815 (tpp) cc_final: 0.8600 (mmm) REVERT: D 152 MET cc_start: 0.9272 (tpp) cc_final: 0.8986 (tpt) REVERT: D 339 MET cc_start: 0.7193 (mmt) cc_final: 0.6950 (mmt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1104 time to fit residues: 31.6014 Evaluate side-chains 122 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 107 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 chunk 178 optimal weight: 0.0010 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 overall best weight: 1.0150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN D 222 HIS ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.067116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.048086 restraints weight = 114541.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.049305 restraints weight = 62435.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.050099 restraints weight = 41103.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050615 restraints weight = 31062.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.050922 restraints weight = 25809.734| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20506 Z= 0.127 Angle : 0.593 12.631 28629 Z= 0.319 Chirality : 0.040 0.160 3181 Planarity : 0.004 0.063 2970 Dihedral : 25.354 178.825 4421 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.19), residues: 1976 helix: 0.96 (0.19), residues: 749 sheet: -0.54 (0.29), residues: 310 loop : -1.77 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 875 TYR 0.014 0.001 TYR A 586 PHE 0.027 0.001 PHE C 557 TRP 0.009 0.001 TRP A 893 HIS 0.005 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00279 (20498) covalent geometry : angle 0.59160 (28625) hydrogen bonds : bond 0.03391 ( 965) hydrogen bonds : angle 3.97315 ( 2574) metal coordination : bond 0.01035 ( 8) metal coordination : angle 3.00155 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8696 (mmp) cc_final: 0.8451 (mmm) REVERT: A 480 GLN cc_start: 0.8833 (mp10) cc_final: 0.8616 (mp10) REVERT: A 578 MET cc_start: 0.9340 (ttp) cc_final: 0.8587 (tpp) REVERT: A 583 LEU cc_start: 0.8734 (mt) cc_final: 0.7793 (mt) REVERT: A 627 MET cc_start: 0.8976 (pmm) cc_final: 0.8604 (pmm) REVERT: A 658 MET cc_start: 0.8785 (pmm) cc_final: 0.8058 (pmm) REVERT: A 687 LEU cc_start: 0.9317 (tp) cc_final: 0.9029 (tp) REVERT: A 795 HIS cc_start: 0.8833 (m90) cc_final: 0.8615 (m-70) REVERT: A 889 MET cc_start: 0.8967 (mtm) cc_final: 0.8489 (mtt) REVERT: C 412 LYS cc_start: 0.9344 (tttt) cc_final: 0.8999 (tmtt) REVERT: C 602 MET cc_start: 0.9072 (mpp) cc_final: 0.8485 (mpp) REVERT: C 658 MET cc_start: 0.8977 (pmm) cc_final: 0.7971 (pmm) REVERT: C 986 ASP cc_start: 0.9001 (t70) cc_final: 0.8760 (t0) REVERT: B 67 CYS cc_start: 0.8542 (t) cc_final: 0.7745 (p) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1155 time to fit residues: 31.2978 Evaluate side-chains 122 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 178 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 74 optimal weight: 0.0870 chunk 90 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.066712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047671 restraints weight = 120419.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048761 restraints weight = 67893.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.049498 restraints weight = 46063.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049961 restraints weight = 35551.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.050149 restraints weight = 30218.726| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20506 Z= 0.144 Angle : 0.601 11.607 28629 Z= 0.325 Chirality : 0.040 0.163 3181 Planarity : 0.004 0.057 2970 Dihedral : 25.337 179.602 4421 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.19), residues: 1976 helix: 1.01 (0.19), residues: 749 sheet: -0.52 (0.29), residues: 310 loop : -1.74 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 446 TYR 0.014 0.001 TYR A 586 PHE 0.025 0.001 PHE C 557 TRP 0.009 0.001 TRP D 317 HIS 0.005 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00316 (20498) covalent geometry : angle 0.59944 (28625) hydrogen bonds : bond 0.03651 ( 965) hydrogen bonds : angle 4.00166 ( 2574) metal coordination : bond 0.01736 ( 8) metal coordination : angle 4.03784 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 CYS cc_start: 0.9257 (m) cc_final: 0.8797 (t) REVERT: A 578 MET cc_start: 0.9375 (ttp) cc_final: 0.8606 (tpp) REVERT: A 583 LEU cc_start: 0.8734 (mt) cc_final: 0.7767 (mt) REVERT: A 627 MET cc_start: 0.8914 (pmm) cc_final: 0.8587 (pmm) REVERT: A 658 MET cc_start: 0.8775 (pmm) cc_final: 0.8044 (pmm) REVERT: A 687 LEU cc_start: 0.9380 (tp) cc_final: 0.9061 (tp) REVERT: A 795 HIS cc_start: 0.8902 (m90) cc_final: 0.8645 (m-70) REVERT: A 889 MET cc_start: 0.8978 (mtm) cc_final: 0.8604 (mtm) REVERT: C 412 LYS cc_start: 0.9334 (tttt) cc_final: 0.8988 (tmtt) REVERT: C 602 MET cc_start: 0.9099 (mpp) cc_final: 0.8462 (mpp) REVERT: C 658 MET cc_start: 0.8964 (pmm) cc_final: 0.7822 (pmm) REVERT: C 858 MET cc_start: 0.8558 (tpp) cc_final: 0.8252 (tpt) REVERT: C 986 ASP cc_start: 0.9076 (t70) cc_final: 0.8827 (t0) REVERT: B 110 MET cc_start: 0.8551 (tpt) cc_final: 0.8266 (tpt) REVERT: B 152 MET cc_start: 0.8635 (tpp) cc_final: 0.8178 (tpp) REVERT: D 339 MET cc_start: 0.7257 (mmt) cc_final: 0.7021 (mmt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1074 time to fit residues: 28.5216 Evaluate side-chains 119 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 59 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.066691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.047603 restraints weight = 121798.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048739 restraints weight = 68554.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.049471 restraints weight = 46263.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049936 restraints weight = 35847.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.050236 restraints weight = 30447.285| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20506 Z= 0.153 Angle : 0.615 11.690 28629 Z= 0.332 Chirality : 0.040 0.213 3181 Planarity : 0.004 0.053 2970 Dihedral : 25.336 179.842 4421 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.19), residues: 1976 helix: 1.00 (0.19), residues: 748 sheet: -0.54 (0.29), residues: 303 loop : -1.73 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 446 TYR 0.014 0.001 TYR A 586 PHE 0.024 0.001 PHE C 557 TRP 0.008 0.001 TRP B 317 HIS 0.007 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00333 (20498) covalent geometry : angle 0.61285 (28625) hydrogen bonds : bond 0.03766 ( 965) hydrogen bonds : angle 4.03798 ( 2574) metal coordination : bond 0.01863 ( 8) metal coordination : angle 4.27852 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 CYS cc_start: 0.9203 (m) cc_final: 0.8739 (t) REVERT: A 578 MET cc_start: 0.9358 (ttp) cc_final: 0.8606 (tpp) REVERT: A 583 LEU cc_start: 0.8729 (mt) cc_final: 0.7772 (mt) REVERT: A 627 MET cc_start: 0.8929 (pmm) cc_final: 0.8593 (pmm) REVERT: A 687 LEU cc_start: 0.9362 (tp) cc_final: 0.9033 (tp) REVERT: A 795 HIS cc_start: 0.8874 (m90) cc_final: 0.8595 (m-70) REVERT: A 889 MET cc_start: 0.8958 (mtm) cc_final: 0.8596 (mtm) REVERT: C 412 LYS cc_start: 0.9330 (tttt) cc_final: 0.8994 (tmtt) REVERT: C 602 MET cc_start: 0.9098 (mpp) cc_final: 0.8460 (mpp) REVERT: C 658 MET cc_start: 0.9000 (pmm) cc_final: 0.7932 (pmm) REVERT: C 858 MET cc_start: 0.8549 (tpp) cc_final: 0.8322 (tpt) REVERT: C 986 ASP cc_start: 0.9062 (t70) cc_final: 0.8817 (t0) REVERT: B 110 MET cc_start: 0.8508 (tpt) cc_final: 0.8149 (tpt) REVERT: B 152 MET cc_start: 0.8606 (tpp) cc_final: 0.8129 (tpp) REVERT: D 339 MET cc_start: 0.7245 (mmt) cc_final: 0.7018 (mmt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1122 time to fit residues: 30.3076 Evaluate side-chains 120 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 115 optimal weight: 5.9990 chunk 55 optimal weight: 0.0970 chunk 144 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 53 optimal weight: 0.0040 chunk 107 optimal weight: 0.8980 chunk 142 optimal weight: 0.0370 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.4068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 222 HIS B 282 GLN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.068560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.049598 restraints weight = 120044.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050752 restraints weight = 67043.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.051513 restraints weight = 45129.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.051939 restraints weight = 34730.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.052300 restraints weight = 29605.020| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20506 Z= 0.124 Angle : 0.598 11.691 28629 Z= 0.320 Chirality : 0.040 0.208 3181 Planarity : 0.004 0.052 2970 Dihedral : 25.220 178.749 4421 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.06 % Allowed : 0.37 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 1976 helix: 1.06 (0.20), residues: 747 sheet: -0.19 (0.30), residues: 292 loop : -1.68 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 970 TYR 0.019 0.001 TYR A 586 PHE 0.024 0.001 PHE C 557 TRP 0.018 0.001 TRP A 760 HIS 0.005 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00267 (20498) covalent geometry : angle 0.59705 (28625) hydrogen bonds : bond 0.03335 ( 965) hydrogen bonds : angle 3.87831 ( 2574) metal coordination : bond 0.00766 ( 8) metal coordination : angle 2.41281 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3102.41 seconds wall clock time: 55 minutes 31.49 seconds (3331.49 seconds total)