Starting phenix.real_space_refine on Sun Sep 13 00:30:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oen_20031/09_2026/6oen_20031.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oen_20031/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6oen_20031/09_2026/6oen_20031.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oen_20031/09_2026/6oen_20031.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oen_20031/09_2026/6oen_20031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oen_20031/09_2026/6oen_20031.map" model { file = "/net/cci-nas-00/data/ceres_data/6oen_20031/09_2026/6oen_20031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oen_20031/09_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-2.2.1-6174/lib/python3.11/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: 4.16, per 1000 atoms: 0.21 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: 1.88 Conformation dependent library (CDL) restraints added in 820.7 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: 2.82 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: 5.40 Time building geometry restraints manager: 2.47 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=" C3' DG J 37 " pdb=" O3' DG J 37 " ideal model delta sigma weight residual 1.435 1.493 -0.058 1.30e-02 5.92e+03 1.96e+01 bond pdb=" C1' DC J 43 " pdb=" N1 DC J 43 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" C3' DT J 14 " pdb=" O3' DT J 14 " ideal model delta sigma weight residual 1.435 1.482 -0.047 1.30e-02 5.92e+03 1.29e+01 bond pdb=" C1' DC G 16 " pdb=" N1 DC G 16 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" C3' DA J 45 " pdb=" O3' DA J 45 " ideal model delta sigma weight residual 1.435 1.479 -0.044 1.30e-02 5.92e+03 1.15e+01 ... (remaining 20493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 26783 1.95 - 3.91: 1640 3.91 - 5.86: 157 5.86 - 7.81: 28 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=" O4' DG J 46 " pdb=" C4' DG J 46 " pdb=" C3' DG J 46 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.48e+01 angle pdb=" O4' DG J 39 " pdb=" C1' DG J 39 " pdb=" N9 DG J 39 " ideal model delta sigma weight residual 108.00 111.48 -3.48 7.00e-01 2.04e+00 2.47e+01 angle pdb=" O4' DG F 10 " pdb=" C4' DG F 10 " pdb=" C3' DG F 10 " ideal model delta sigma weight residual 106.00 103.07 2.93 6.00e-01 2.78e+00 2.39e+01 angle pdb=" C3' DT G 25 " pdb=" C2' DT G 25 " pdb=" C1' DT G 25 " ideal model delta sigma weight residual 102.50 96.68 5.82 1.20e+00 6.94e-01 2.35e+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: 2113 0.050 - 0.100: 798 0.100 - 0.151: 211 0.151 - 0.201: 51 0.201 - 0.251: 8 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 24.600 Find NCS groups from input model: 0.490 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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= 0.522 Angle : 1.093 39.266 28629 Z= 0.709 Chirality : 0.057 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/Z covalent geometry : bond 0.00665 / 0.48 (20498) covalent geometry : angle 1.01123 / 0.70 (28625) hydrogen bonds : bond 0.15032 / 10.36 ( 965) hydrogen bonds : angle 6.47006 / 4.52 ( 2574) metal coordination : bond 0.37295 / 18.15 ( 8) metal coordination : angle 35.21477 / 19.44 ( 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 : 0.651 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: 0.8309 (tp30) REVERT: A 578 MET cc_start: 0.9118 (ttp) cc_final: 0.8673 (tpp) REVERT: A 678 GLU cc_start: 0.9036 (pp20) cc_final: 0.8807 (pp20) REVERT: A 687 LEU cc_start: 0.9043 (tp) cc_final: 0.8798 (tp) REVERT: A 889 MET cc_start: 0.8556 (mtm) cc_final: 0.8141 (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: 0.8402 (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: 0.7992 (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: 0.7896 (mmm) outliers start: 59 outliers final: 8 residues processed: 272 average time/residue: 0.1419 time to fit residues: 59.3275 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 : 0.585 ------------------------------------------------------------------------------- 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: 20.0000 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: 5.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 30.0000 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... 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 860 GLN C 495 GLN C 636 GLN C 795 HIS C 836 HIS C 991 HIS ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS B 282 GLN B 313 HIS D 222 HIS D 282 GLN N 134 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.065515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.047124 restraints weight = 118175.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048250 restraints weight = 65871.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048979 restraints weight = 44082.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.049450 restraints weight = 33723.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049715 restraints weight = 28311.868| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 20506 Z= 0.198 Angle : 0.714 17.258 28629 Z= 0.394 Chirality : 0.047 0.308 3181 Planarity : 0.005 0.052 2970 Dihedral : 26.360 179.715 4421 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.18 % Allowed : 5.69 % Favored : 94.13 % 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: -2.62 (0.17), residues: 1976 helix: -0.68 (0.17), residues: 728 sheet: -1.90 (0.26), residues: 308 loop : -2.55 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 446 TYR 0.021 0.001 TYR A 998 PHE 0.030 0.002 PHE A 418 TRP 0.011 0.001 TRP N 133 HIS 0.008 0.001 HIS C 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.20 (20498) covalent geometry : angle 0.70537 / 0.39 (28625) hydrogen bonds : bond 0.05016 / 3.47 ( 965) hydrogen bonds : angle 5.04449 / 3.48 ( 2574) metal coordination : bond 0.05869 / 3.29 ( 8) metal coordination : angle 9.62803 / 6.13 ( 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 176 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 173 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.2301 (ttt90) cc_final: 0.2005 (mmm160) REVERT: A 467 CYS cc_start: 0.9244 (m) cc_final: 0.8998 (m) REVERT: A 507 GLU cc_start: 0.8759 (tp30) cc_final: 0.8397 (tp30) REVERT: A 578 MET cc_start: 0.9258 (ttp) cc_final: 0.8828 (tpp) REVERT: A 687 LEU cc_start: 0.9220 (tp) cc_final: 0.8889 (tp) REVERT: A 889 MET cc_start: 0.9063 (mtm) cc_final: 0.8542 (mtm) REVERT: A 986 ASP cc_start: 0.8683 (t70) cc_final: 0.8356 (t0) REVERT: C 617 GLU cc_start: 0.8581 (tt0) cc_final: 0.8244 (tt0) REVERT: C 986 ASP cc_start: 0.9053 (t70) cc_final: 0.8794 (t0) REVERT: B 49 ASP cc_start: 0.7158 (m-30) cc_final: 0.6786 (m-30) REVERT: B 57 LEU cc_start: 0.8951 (tp) cc_final: 0.8690 (tp) REVERT: B 152 MET cc_start: 0.9016 (tpp) cc_final: 0.8584 (tpp) REVERT: D 110 MET cc_start: 0.8538 (tpp) cc_final: 0.8332 (mmm) REVERT: D 126 GLU cc_start: 0.8217 (pp20) cc_final: 0.7941 (pp20) outliers start: 3 outliers final: 2 residues processed: 176 average time/residue: 0.1303 time to fit residues: 36.7767 Evaluate side-chains 120 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 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: 6.9990 chunk 88 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 142 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 197 optimal weight: 50.0000 chunk 45 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 HIS ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN A 990 HIS C 852 ASN C 990 HIS B 33 GLN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS D 33 GLN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.064367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.045938 restraints weight = 119326.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.047096 restraints weight = 65019.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.047843 restraints weight = 42917.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048311 restraints weight = 32432.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048552 restraints weight = 27124.743| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 20506 Z= 0.249 Angle : 0.726 18.704 28629 Z= 0.399 Chirality : 0.046 0.297 3181 Planarity : 0.005 0.051 2970 Dihedral : 26.225 178.940 4421 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.18 % Allowed : 5.02 % Favored : 94.80 % 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: -2.11 (0.18), residues: 1976 helix: -0.14 (0.19), residues: 725 sheet: -1.72 (0.28), residues: 293 loop : -2.32 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 446 TYR 0.020 0.002 TYR A 998 PHE 0.034 0.002 PHE C 641 TRP 0.013 0.002 TRP N 133 HIS 0.009 0.002 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.25 (20498) covalent geometry : angle 0.71646 / 0.40 (28625) hydrogen bonds : bond 0.05546 / 3.90 ( 965) hydrogen bonds : angle 4.96197 / 3.43 ( 2574) metal coordination : bond 0.05572 / 3.29 ( 8) metal coordination : angle 10.03145 / 6.48 ( 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 159 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.2387 (ttt90) cc_final: 0.1964 (mmm160) REVERT: A 481 TYR cc_start: 0.8945 (t80) cc_final: 0.8662 (t80) REVERT: A 578 MET cc_start: 0.9278 (ttp) cc_final: 0.8891 (tpp) REVERT: A 627 MET cc_start: 0.8497 (pmm) cc_final: 0.8023 (pmm) REVERT: A 682 MET cc_start: 0.9041 (ppp) cc_final: 0.8804 (ppp) REVERT: A 687 LEU cc_start: 0.9348 (tp) cc_final: 0.8984 (tp) REVERT: A 760 TRP cc_start: 0.9406 (t-100) cc_final: 0.9195 (t-100) REVERT: A 795 HIS cc_start: 0.8950 (m90) cc_final: 0.8703 (m90) REVERT: A 800 ASN cc_start: 0.9518 (m110) cc_final: 0.9258 (m-40) REVERT: A 889 MET cc_start: 0.9168 (mtm) cc_final: 0.8686 (mtm) REVERT: A 986 ASP cc_start: 0.8757 (t70) cc_final: 0.8439 (t0) REVERT: C 658 MET cc_start: 0.9117 (pmm) cc_final: 0.8231 (pmm) REVERT: C 852 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8579 (m110) REVERT: C 889 MET cc_start: 0.9049 (mtp) cc_final: 0.8057 (mmm) REVERT: C 986 ASP cc_start: 0.9133 (t70) cc_final: 0.8882 (t0) REVERT: B 49 ASP cc_start: 0.7255 (m-30) cc_final: 0.6999 (m-30) REVERT: B 57 LEU cc_start: 0.9002 (tp) cc_final: 0.8709 (tp) REVERT: B 152 MET cc_start: 0.9063 (tpp) cc_final: 0.8750 (tmm) REVERT: D 126 GLU cc_start: 0.8428 (pp20) cc_final: 0.8164 (pp20) REVERT: D 270 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7746 (tm-30) outliers start: 3 outliers final: 1 residues processed: 159 average time/residue: 0.1207 time to fit residues: 31.6737 Evaluate side-chains 114 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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: 0.5980 chunk 184 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 188 optimal weight: 50.0000 chunk 0 optimal weight: 30.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 HIS ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS D 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.066792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.047976 restraints weight = 122176.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.049136 restraints weight = 67909.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.049888 restraints weight = 45542.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050360 restraints weight = 34958.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.050606 restraints weight = 29611.930| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20506 Z= 0.135 Angle : 0.649 11.869 28629 Z= 0.359 Chirality : 0.046 0.319 3181 Planarity : 0.004 0.052 2970 Dihedral : 26.043 176.898 4421 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.06 % Allowed : 2.94 % Favored : 97.00 % 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: -1.68 (0.18), residues: 1976 helix: 0.21 (0.19), residues: 727 sheet: -1.38 (0.29), residues: 283 loop : -2.12 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 446 TYR 0.016 0.001 TYR A 998 PHE 0.025 0.001 PHE A 971 TRP 0.014 0.001 TRP N 133 HIS 0.007 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (20498) covalent geometry : angle 0.64711 / 0.36 (28625) hydrogen bonds : bond 0.04371 / 3.11 ( 965) hydrogen bonds : angle 4.64412 / 3.19 ( 2574) metal coordination : bond 0.01906 / 1.06 ( 8) metal coordination : angle 4.57438 / 2.83 ( 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 168 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.1921 (ttt90) cc_final: 0.1710 (mmm160) REVERT: A 455 MET cc_start: 0.8711 (mmp) cc_final: 0.8421 (mmm) REVERT: A 467 CYS cc_start: 0.9255 (m) cc_final: 0.9051 (m) REVERT: A 578 MET cc_start: 0.9285 (ttp) cc_final: 0.8819 (tpp) REVERT: A 627 MET cc_start: 0.8682 (pmm) cc_final: 0.8247 (pmm) REVERT: A 687 LEU cc_start: 0.9292 (tp) cc_final: 0.8924 (tp) REVERT: A 760 TRP cc_start: 0.9390 (t-100) cc_final: 0.9159 (t-100) REVERT: A 795 HIS cc_start: 0.8813 (m90) cc_final: 0.8608 (m90) REVERT: A 881 GLU cc_start: 0.8951 (pt0) cc_final: 0.8588 (pp20) REVERT: A 886 TYR cc_start: 0.8643 (t80) cc_final: 0.8388 (t80) REVERT: A 889 MET cc_start: 0.9134 (mtm) cc_final: 0.8699 (mtm) REVERT: A 986 ASP cc_start: 0.8643 (t70) cc_final: 0.8306 (t0) REVERT: A 1003 MET cc_start: 0.8109 (tpp) cc_final: 0.7680 (tmm) REVERT: C 504 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.8219 (mtm180) REVERT: C 507 GLU cc_start: 0.8682 (pt0) cc_final: 0.8240 (pp20) REVERT: C 511 LEU cc_start: 0.9582 (mm) cc_final: 0.9368 (mt) REVERT: C 658 MET cc_start: 0.9025 (pmm) cc_final: 0.8364 (pmm) REVERT: C 889 MET cc_start: 0.9042 (mtp) cc_final: 0.8068 (mmm) REVERT: C 986 ASP cc_start: 0.9028 (t70) cc_final: 0.8815 (t0) REVERT: B 5 MET cc_start: 0.7883 (tpt) cc_final: 0.7597 (tpt) REVERT: B 67 CYS cc_start: 0.8746 (t) cc_final: 0.7877 (p) REVERT: B 152 MET cc_start: 0.9175 (tpp) cc_final: 0.8924 (mmm) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.1201 time to fit residues: 33.4874 Evaluate side-chains 125 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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: 7.9990 chunk 99 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 197 optimal weight: 50.0000 chunk 141 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 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 = 0.3478 r_free = 0.3478 target = 0.065366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046478 restraints weight = 123570.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047624 restraints weight = 67681.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048367 restraints weight = 45097.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.048841 restraints weight = 34586.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049139 restraints weight = 29261.817| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20506 Z= 0.181 Angle : 0.663 13.320 28629 Z= 0.364 Chirality : 0.045 0.298 3181 Planarity : 0.004 0.065 2970 Dihedral : 26.002 178.175 4421 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: -1.51 (0.18), residues: 1976 helix: 0.37 (0.19), residues: 732 sheet: -1.23 (0.30), residues: 281 loop : -2.05 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 446 TYR 0.018 0.001 TYR A 998 PHE 0.020 0.002 PHE C 641 TRP 0.013 0.001 TRP A 519 HIS 0.007 0.001 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (20498) covalent geometry : angle 0.65843 / 0.36 (28625) hydrogen bonds : bond 0.04840 / 3.47 ( 965) hydrogen bonds : angle 4.59543 / 3.16 ( 2574) metal coordination : bond 0.03261 / 1.85 ( 8) metal coordination : angle 6.82909 / 4.22 ( 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 150 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.508 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: 0.8744 (mmp) cc_final: 0.8454 (mmm) REVERT: A 578 MET cc_start: 0.9272 (ttp) cc_final: 0.8856 (tpp) REVERT: A 627 MET cc_start: 0.8632 (pmm) cc_final: 0.8324 (pmm) REVERT: A 687 LEU cc_start: 0.9362 (tp) cc_final: 0.9090 (tp) REVERT: A 795 HIS cc_start: 0.8791 (m90) cc_final: 0.8585 (m90) REVERT: A 800 ASN cc_start: 0.9449 (m110) cc_final: 0.9213 (m-40) REVERT: A 881 GLU cc_start: 0.8938 (pt0) cc_final: 0.8564 (pp20) REVERT: A 889 MET cc_start: 0.9104 (mtm) cc_final: 0.8680 (mtm) REVERT: A 986 ASP cc_start: 0.8690 (t70) cc_final: 0.8372 (t0) REVERT: C 504 ARG cc_start: 0.8665 (mtm-85) cc_final: 0.8259 (mtm-85) REVERT: C 507 GLU cc_start: 0.8750 (pt0) cc_final: 0.8208 (pp20) REVERT: C 602 MET cc_start: 0.9205 (mpp) cc_final: 0.8997 (mpp) REVERT: C 658 MET cc_start: 0.9028 (pmm) cc_final: 0.8189 (pmm) REVERT: C 889 MET cc_start: 0.9051 (mtp) cc_final: 0.8104 (mmm) REVERT: C 986 ASP cc_start: 0.9060 (t70) cc_final: 0.8833 (t0) REVERT: B 5 MET cc_start: 0.7794 (tpt) cc_final: 0.7429 (tpt) REVERT: B 22 MET cc_start: 0.8454 (mtp) cc_final: 0.8036 (ttm) REVERT: B 152 MET cc_start: 0.9121 (tpp) cc_final: 0.8899 (mmm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1162 time to fit residues: 28.6942 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 : 0.575 ------------------------------------------------------------------------------- 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: 0.9990 chunk 150 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 85 optimal weight: 0.0470 chunk 124 optimal weight: 7.9990 chunk 151 optimal weight: 0.0970 chunk 91 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN B 89 HIS B 282 GLN B 313 HIS D 201 GLN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.066610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.048234 restraints weight = 116864.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.049413 restraints weight = 64187.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050176 restraints weight = 42465.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.050666 restraints weight = 32127.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.050970 restraints weight = 26790.262| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 20506 Z= 0.125 Angle : 0.629 12.431 28629 Z= 0.344 Chirality : 0.045 0.323 3181 Planarity : 0.004 0.051 2970 Dihedral : 25.885 176.808 4421 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % 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: -1.32 (0.19), residues: 1976 helix: 0.52 (0.19), residues: 742 sheet: -1.03 (0.29), residues: 305 loop : -2.02 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 446 TYR 0.012 0.001 TYR B 217 PHE 0.016 0.001 PHE A 971 TRP 0.019 0.001 TRP B 317 HIS 0.006 0.001 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (20498) covalent geometry : angle 0.62792 / 0.34 (28625) hydrogen bonds : bond 0.04023 / 2.89 ( 965) hydrogen bonds : angle 4.42358 / 3.03 ( 2574) metal coordination : bond 0.00760 / 0.42 ( 8) metal coordination : angle 2.98433 / 1.79 ( 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 165 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.694 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: 0.8681 (mmp) cc_final: 0.8444 (mmm) REVERT: A 467 CYS cc_start: 0.9183 (m) cc_final: 0.8610 (t) REVERT: A 481 TYR cc_start: 0.8975 (t80) cc_final: 0.8433 (t80) REVERT: A 576 GLU cc_start: 0.9303 (tm-30) cc_final: 0.9016 (tm-30) REVERT: A 578 MET cc_start: 0.9267 (ttp) cc_final: 0.8853 (tpp) REVERT: A 627 MET cc_start: 0.8608 (pmm) cc_final: 0.8306 (pmm) REVERT: A 687 LEU cc_start: 0.9270 (tp) cc_final: 0.9003 (tp) REVERT: A 760 TRP cc_start: 0.9407 (t-100) cc_final: 0.9121 (t-100) REVERT: A 795 HIS cc_start: 0.8764 (m90) cc_final: 0.8542 (m90) REVERT: A 800 ASN cc_start: 0.9406 (m110) cc_final: 0.9147 (m-40) REVERT: A 889 MET cc_start: 0.9049 (mtm) cc_final: 0.8602 (mtm) REVERT: A 986 ASP cc_start: 0.8597 (t70) cc_final: 0.8287 (t0) REVERT: A 999 LEU cc_start: 0.9482 (mp) cc_final: 0.9274 (mp) REVERT: C 504 ARG cc_start: 0.8599 (mtm-85) cc_final: 0.8006 (mtm-85) REVERT: C 507 GLU cc_start: 0.8586 (pt0) cc_final: 0.8053 (pp20) REVERT: C 658 MET cc_start: 0.8947 (pmm) cc_final: 0.8599 (pmm) REVERT: C 889 MET cc_start: 0.9030 (mtp) cc_final: 0.8068 (mmm) REVERT: C 986 ASP cc_start: 0.9047 (t70) cc_final: 0.8828 (t0) REVERT: B 5 MET cc_start: 0.7871 (tpt) cc_final: 0.7508 (tpt) REVERT: B 67 CYS cc_start: 0.8636 (t) cc_final: 0.7802 (p) REVERT: B 172 TRP cc_start: 0.9174 (t-100) cc_final: 0.8737 (t-100) REVERT: D 110 MET cc_start: 0.8565 (tpp) cc_final: 0.8048 (tpp) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1284 time to fit residues: 35.3250 Evaluate side-chains 126 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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: 0.9990 chunk 174 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 192 optimal weight: 50.0000 chunk 84 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS D 94 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 = 0.3500 r_free = 0.3500 target = 0.066091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.047712 restraints weight = 117071.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.048862 restraints weight = 65124.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049614 restraints weight = 43463.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.050081 restraints weight = 32927.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050367 restraints weight = 27584.885| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20506 Z= 0.136 Angle : 0.624 11.881 28629 Z= 0.342 Chirality : 0.044 0.314 3181 Planarity : 0.004 0.040 2970 Dihedral : 25.859 178.041 4421 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -1.23 (0.19), residues: 1976 helix: 0.62 (0.19), residues: 743 sheet: -1.10 (0.29), residues: 321 loop : -1.95 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 875 TYR 0.020 0.001 TYR C 998 PHE 0.019 0.001 PHE A 418 TRP 0.012 0.001 TRP B 317 HIS 0.005 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (20498) covalent geometry : angle 0.62168 / 0.34 (28625) hydrogen bonds : bond 0.04200 / 3.02 ( 965) hydrogen bonds : angle 4.37301 / 2.99 ( 2574) metal coordination : bond 0.01683 / 0.97 ( 8) metal coordination : angle 4.24616 / 2.57 ( 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 155 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8766 (mmp) cc_final: 0.8516 (mmm) REVERT: A 467 CYS cc_start: 0.9221 (m) cc_final: 0.8639 (t) REVERT: A 578 MET cc_start: 0.9279 (ttp) cc_final: 0.8863 (tpp) REVERT: A 627 MET cc_start: 0.8593 (pmm) cc_final: 0.8324 (pmm) REVERT: A 687 LEU cc_start: 0.9282 (tp) cc_final: 0.9014 (tp) REVERT: A 795 HIS cc_start: 0.8787 (m90) cc_final: 0.8580 (m-70) REVERT: A 889 MET cc_start: 0.9027 (mtm) cc_final: 0.8654 (mtm) REVERT: A 986 ASP cc_start: 0.8630 (t70) cc_final: 0.8347 (t0) REVERT: C 504 ARG cc_start: 0.8668 (mtm-85) cc_final: 0.8064 (mtm-85) REVERT: C 507 GLU cc_start: 0.8679 (pt0) cc_final: 0.8087 (pp20) REVERT: C 602 MET cc_start: 0.9246 (mpp) cc_final: 0.9022 (mpp) REVERT: C 658 MET cc_start: 0.8986 (pmm) cc_final: 0.8574 (pmm) REVERT: C 889 MET cc_start: 0.9071 (mtp) cc_final: 0.8128 (mmm) REVERT: C 986 ASP cc_start: 0.9062 (t70) cc_final: 0.8817 (t0) REVERT: B 5 MET cc_start: 0.7915 (tpt) cc_final: 0.7496 (tpt) REVERT: B 67 CYS cc_start: 0.8647 (t) cc_final: 0.7783 (p) REVERT: B 172 TRP cc_start: 0.9185 (t-100) cc_final: 0.8732 (t-100) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1288 time to fit residues: 33.1104 Evaluate side-chains 123 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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: 7.9990 chunk 189 optimal weight: 50.0000 chunk 178 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 12 optimal weight: 0.1980 chunk 83 optimal weight: 5.9990 chunk 6 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 overall best weight: 1.6524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** 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 = 0.3509 r_free = 0.3509 target = 0.066548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047515 restraints weight = 115587.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048724 restraints weight = 63096.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.049498 restraints weight = 41829.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.049993 restraints weight = 31629.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050313 restraints weight = 26403.121| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20506 Z= 0.131 Angle : 0.620 11.236 28629 Z= 0.340 Chirality : 0.044 0.324 3181 Planarity : 0.004 0.074 2970 Dihedral : 25.811 178.461 4421 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -1.14 (0.19), residues: 1976 helix: 0.65 (0.19), residues: 746 sheet: -0.96 (0.29), residues: 321 loop : -1.91 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 446 TYR 0.022 0.001 TYR A 481 PHE 0.031 0.001 PHE C 557 TRP 0.012 0.001 TRP B 317 HIS 0.006 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (20498) covalent geometry : angle 0.61872 / 0.34 (28625) hydrogen bonds : bond 0.04043 / 2.90 ( 965) hydrogen bonds : angle 4.32590 / 2.95 ( 2574) metal coordination : bond 0.01311 / 0.75 ( 8) metal coordination : angle 3.69135 / 2.19 ( 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 154 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8658 (mmp) cc_final: 0.8450 (mmm) REVERT: A 467 CYS cc_start: 0.9288 (m) cc_final: 0.8704 (t) REVERT: A 576 GLU cc_start: 0.9370 (tm-30) cc_final: 0.9047 (tm-30) REVERT: A 578 MET cc_start: 0.9336 (ttp) cc_final: 0.8896 (tpp) REVERT: A 627 MET cc_start: 0.8549 (pmm) cc_final: 0.8298 (pmm) REVERT: A 687 LEU cc_start: 0.9331 (tp) cc_final: 0.9052 (tp) REVERT: A 795 HIS cc_start: 0.8891 (m90) cc_final: 0.8634 (m90) REVERT: A 889 MET cc_start: 0.9057 (mtm) cc_final: 0.8717 (mtm) REVERT: A 986 ASP cc_start: 0.8696 (t70) cc_final: 0.8396 (t0) REVERT: C 504 ARG cc_start: 0.8728 (mtm-85) cc_final: 0.8078 (mtm-85) REVERT: C 507 GLU cc_start: 0.8700 (pt0) cc_final: 0.8076 (pp20) REVERT: C 602 MET cc_start: 0.9262 (mpp) cc_final: 0.9001 (mpp) REVERT: C 889 MET cc_start: 0.9099 (mtp) cc_final: 0.8150 (mmm) REVERT: C 986 ASP cc_start: 0.9091 (t70) cc_final: 0.8831 (t0) REVERT: B 5 MET cc_start: 0.7951 (tpt) cc_final: 0.7518 (tpt) REVERT: B 67 CYS cc_start: 0.8657 (t) cc_final: 0.7764 (p) REVERT: B 172 TRP cc_start: 0.9184 (t-100) cc_final: 0.8714 (t-100) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1309 time to fit residues: 33.2484 Evaluate side-chains 121 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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: 0.0670 chunk 135 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 193 optimal weight: 50.0000 chunk 29 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 120 optimal weight: 0.4980 overall best weight: 1.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** 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 = 0.3520 r_free = 0.3520 target = 0.067093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.047969 restraints weight = 114432.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.049196 restraints weight = 61985.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.049993 restraints weight = 40764.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.050496 restraints weight = 30695.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050765 restraints weight = 25542.534| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 20506 Z= 0.131 Angle : 0.624 11.361 28629 Z= 0.340 Chirality : 0.044 0.327 3181 Planarity : 0.004 0.041 2970 Dihedral : 25.787 179.312 4421 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -1.06 (0.19), residues: 1976 helix: 0.70 (0.19), residues: 745 sheet: -0.90 (0.29), residues: 321 loop : -1.85 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 446 TYR 0.018 0.001 TYR A 481 PHE 0.030 0.001 PHE C 557 TRP 0.011 0.001 TRP B 317 HIS 0.005 0.001 HIS A1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (20498) covalent geometry : angle 0.62236 / 0.34 (28625) hydrogen bonds : bond 0.04011 / 2.89 ( 965) hydrogen bonds : angle 4.32464 / 2.94 ( 2574) metal coordination : bond 0.01135 / 0.66 ( 8) metal coordination : angle 3.45115 / 2.04 ( 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 : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 CYS cc_start: 0.9224 (m) cc_final: 0.8606 (t) REVERT: A 576 GLU cc_start: 0.9296 (tm-30) cc_final: 0.8975 (tm-30) REVERT: A 578 MET cc_start: 0.9307 (ttp) cc_final: 0.8847 (tpp) REVERT: A 687 LEU cc_start: 0.9265 (tp) cc_final: 0.8983 (tp) REVERT: A 889 MET cc_start: 0.8969 (mtm) cc_final: 0.8609 (mtm) REVERT: A 986 ASP cc_start: 0.8537 (t70) cc_final: 0.8263 (t0) REVERT: C 504 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.7963 (mtm-85) REVERT: C 507 GLU cc_start: 0.8588 (pt0) cc_final: 0.8003 (pp20) REVERT: C 658 MET cc_start: 0.9026 (pmm) cc_final: 0.7679 (pmm) REVERT: C 889 MET cc_start: 0.9052 (mtp) cc_final: 0.8115 (mmm) REVERT: C 986 ASP cc_start: 0.8936 (t70) cc_final: 0.8716 (t0) REVERT: B 5 MET cc_start: 0.7875 (tpt) cc_final: 0.7477 (tpt) REVERT: B 67 CYS cc_start: 0.8594 (t) cc_final: 0.7678 (p) REVERT: B 152 MET cc_start: 0.8758 (tpp) cc_final: 0.8280 (tpp) REVERT: B 172 TRP cc_start: 0.9126 (t-100) cc_final: 0.8695 (t-100) REVERT: D 242 LEU cc_start: 0.9339 (mt) cc_final: 0.8948 (tt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1275 time to fit residues: 34.0257 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 : 0.661 ------------------------------------------------------------------------------- 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: 0.7980 chunk 209 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 201 optimal weight: 50.0000 chunk 168 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 193 optimal weight: 50.0000 chunk 51 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 HIS ** A 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 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 = 0.3526 r_free = 0.3526 target = 0.067264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.048107 restraints weight = 115374.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.049345 restraints weight = 62365.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050142 restraints weight = 40954.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.050647 restraints weight = 30848.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050986 restraints weight = 25728.945| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 20506 Z= 0.122 Angle : 0.612 11.426 28629 Z= 0.334 Chirality : 0.044 0.328 3181 Planarity : 0.004 0.041 2970 Dihedral : 25.731 179.847 4421 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -0.98 (0.19), residues: 1976 helix: 0.79 (0.19), residues: 744 sheet: -0.81 (0.29), residues: 321 loop : -1.84 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 471 TYR 0.015 0.001 TYR A 481 PHE 0.030 0.001 PHE A 475 TRP 0.011 0.001 TRP N 133 HIS 0.005 0.001 HIS A1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (20498) covalent geometry : angle 0.61144 / 0.33 (28625) hydrogen bonds : bond 0.03813 / 2.73 ( 965) hydrogen bonds : angle 4.24238 / 2.89 ( 2574) metal coordination : bond 0.00638 / 0.38 ( 8) metal coordination : angle 2.65309 / 1.52 ( 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 : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8723 (mmp) cc_final: 0.8471 (mmm) REVERT: A 467 CYS cc_start: 0.9287 (m) cc_final: 0.8648 (t) REVERT: A 576 GLU cc_start: 0.9323 (tm-30) cc_final: 0.9029 (tm-30) REVERT: A 578 MET cc_start: 0.9336 (ttp) cc_final: 0.8638 (tpp) REVERT: A 658 MET cc_start: 0.8641 (ptp) cc_final: 0.8219 (pmm) REVERT: A 687 LEU cc_start: 0.9281 (tp) cc_final: 0.8996 (tp) REVERT: A 777 LYS cc_start: 0.9306 (mttt) cc_final: 0.9032 (mmmt) REVERT: A 889 MET cc_start: 0.9001 (mtm) cc_final: 0.8624 (mtm) REVERT: A 986 ASP cc_start: 0.8689 (t70) cc_final: 0.8392 (t0) REVERT: C 504 ARG cc_start: 0.8649 (mtm-85) cc_final: 0.8417 (mtm180) REVERT: C 507 GLU cc_start: 0.8551 (pt0) cc_final: 0.8040 (pp20) REVERT: C 602 MET cc_start: 0.9113 (mpp) cc_final: 0.8582 (mpp) REVERT: C 658 MET cc_start: 0.8952 (pmm) cc_final: 0.7645 (pmm) REVERT: C 889 MET cc_start: 0.9066 (mtp) cc_final: 0.8110 (mmm) REVERT: C 986 ASP cc_start: 0.9015 (t70) cc_final: 0.8755 (t0) REVERT: B 5 MET cc_start: 0.7912 (tpt) cc_final: 0.7495 (tpt) REVERT: B 67 CYS cc_start: 0.8576 (t) cc_final: 0.7529 (p) REVERT: B 152 MET cc_start: 0.8704 (tpp) cc_final: 0.8180 (tpp) REVERT: B 172 TRP cc_start: 0.9131 (t-100) cc_final: 0.8636 (t-100) REVERT: D 242 LEU cc_start: 0.9312 (mt) cc_final: 0.8936 (tt) REVERT: D 329 LEU cc_start: 0.9349 (pp) cc_final: 0.9145 (tt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1303 time to fit residues: 34.6131 Evaluate side-chains 132 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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: 6.9990 chunk 55 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 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 = 0.3506 r_free = 0.3506 target = 0.066594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.047572 restraints weight = 122341.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048720 restraints weight = 68521.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.049456 restraints weight = 46190.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049928 restraints weight = 35618.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050223 restraints weight = 30212.738| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20506 Z= 0.155 Angle : 0.634 13.189 28629 Z= 0.344 Chirality : 0.043 0.319 3181 Planarity : 0.004 0.039 2970 Dihedral : 25.722 179.479 4421 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.92 (0.19), residues: 1976 helix: 0.85 (0.19), residues: 743 sheet: -0.79 (0.29), residues: 321 loop : -1.81 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 284 TYR 0.016 0.001 TYR A 481 PHE 0.027 0.001 PHE C 557 TRP 0.012 0.001 TRP B 317 HIS 0.006 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (20498) covalent geometry : angle 0.63121 / 0.34 (28625) hydrogen bonds : bond 0.04212 / 3.02 ( 965) hydrogen bonds : angle 4.22803 / 2.89 ( 2574) metal coordination : bond 0.01937 / 1.13 ( 8) metal coordination : angle 4.92000 / 2.82 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3304.92 seconds wall clock time: 58 minutes 5.62 seconds (3485.62 seconds total)