Starting phenix.real_space_refine on Fri Aug 7 03:24:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jts_61816/08_2026/9jts_61816.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jts_61816/08_2026/9jts_61816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jts_61816/08_2026/9jts_61816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jts_61816/08_2026/9jts_61816.map" model { file = "/net/cci-nas-00/data/ceres_data/9jts_61816/08_2026/9jts_61816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jts_61816/08_2026/9jts_61816.cif" } resolution = 3.36 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= -0.000 sd= 0.022 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 2 9.91 5 Zn 2 6.06 5 P 160 5.49 5 S 106 5.16 5 C 11311 2.51 5 N 3311 2.21 5 O 3814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18706 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4969 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 618, 4963 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 591} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 618, 4963 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 591} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 5059 Chain: "B" Number of atoms: 2704 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 344, 2683 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 344, 2683 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2727 Chain: "C" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5006 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 596} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2673 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 343, 2663 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 343, 2663 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2718 Chain: "I" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 795 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "L" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 607 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "M" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 801 Classifications: {'DNA': 39} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 38} Chain: "H" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 262 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 617 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} 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: 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2632 SG CYS A 727 75.457 102.566 101.808 1.00 60.06 S ATOM 2653 SG CYS A 730 77.833 104.653 104.070 1.00 65.46 S ATOM 10360 SG CYS C 727 27.684 100.315 54.060 1.00 65.78 S ATOM 10381 SG CYS C 730 25.025 102.259 51.990 1.00 69.81 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N ACYS A 907 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 907 " occ=0.50 residue: pdb=" N AHIS B 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 47 " occ=0.50 residue: pdb=" N AARG B 237 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 237 " occ=0.50 residue: pdb=" N AHIS D 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 47 " occ=0.50 residue: pdb=" P DT I 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT I 15 " occ=0.85 Time building chain proxies: 5.62, per 1000 atoms: 0.30 Number of scatterers: 18706 At special positions: 0 Unit cell: (111.3, 153.7, 157.94, 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 2 19.99 S 106 16.00 P 160 15.00 O 3814 8.00 N 3311 7.00 C 11311 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: 1.15 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " Number of angles added : 4 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3616 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 20 sheets defined 37.4% alpha, 22.9% beta 80 base pairs and 120 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 408 through 422 removed outlier: 4.054A pdb=" N ILE A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 443 Processing helix chain 'A' and resid 444 through 456 Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 507 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 Processing helix chain 'A' and resid 733 through 741 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 Processing helix chain 'A' and resid 822 through 842 Processing helix chain 'A' and resid 850 through 858 removed outlier: 3.694A pdb=" N ALA A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.781A pdb=" N VAL A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 890 Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 902 through 924 removed outlier: 4.827A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE A 911 " --> pdb=" O ACYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.596A pdb=" N ARG A 969 " --> pdb=" O ASN A 965 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 970 " --> pdb=" O LYS A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'B' and resid 11 through 13 No H-bonds generated for 'chain 'B' and resid 11 through 13' Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.924A pdb=" N LEU C 399 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'C' and resid 410 through 423 removed outlier: 3.820A pdb=" N LYS C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 443 Processing helix chain 'C' and resid 444 through 457 Processing helix chain 'C' and resid 463 through 474 removed outlier: 3.517A 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 508 removed outlier: 3.707A pdb=" N LYS C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 removed outlier: 3.564A pdb=" N MET C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 581 removed outlier: 3.571A pdb=" N GLN C 581 " --> pdb=" O GLY C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 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 750 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 812 Processing helix chain 'C' and resid 822 through 841 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.881A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 870 No H-bonds generated for 'chain 'C' and resid 868 through 870' Processing helix chain 'C' and resid 872 through 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 902 through 908 removed outlier: 3.845A pdb=" N GLN C 908 " --> pdb=" O GLU C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 924 removed outlier: 3.581A pdb=" N PHE C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 950 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.949A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 995 Processing helix chain 'C' and resid 996 through 1001 Processing helix chain 'C' and resid 1002 through 1004 No H-bonds generated for 'chain 'C' and resid 1002 through 1004' Processing helix chain 'D' and resid 11 through 13 No H-bonds generated for 'chain 'D' and resid 11 through 13' Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 308 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 519 removed outlier: 6.228A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 519 removed outlier: 6.228A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.891A pdb=" N LEU B 348 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B 328 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 320 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 24 removed outlier: 8.652A pdb=" N GLY B 18 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLN B 33 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 58 " --> pdb=" O AHIS B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.554A pdb=" N TYR B 80 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN B 90 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS B 106 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS B 97 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER B 104 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.731A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS B 191 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.559A pdb=" N VAL B 208 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 239 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 246 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 267 removed outlier: 7.143A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 298 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 518 through 519 removed outlier: 6.918A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG C 628 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 519 removed outlier: 6.918A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG C 628 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 5 removed outlier: 3.754A pdb=" N PHE D 328 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D 320 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 318 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 7 through 8 removed outlier: 6.847A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS D 58 " --> pdb=" O AHIS D 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 15 through 24 removed outlier: 8.562A pdb=" N GLY D 18 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN D 33 " --> pdb=" O GLY D 18 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.451A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 77 through 78 removed outlier: 6.813A pdb=" N LYS D 106 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS D 97 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N SER D 104 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS D 127 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 109 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.354A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS D 191 " --> pdb=" O ASP D 186 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR D 193 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU D 184 " --> pdb=" O THR D 193 " (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 210 removed outlier: 4.026A pdb=" N VAL D 208 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 219 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D 210 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP D 239 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA D 246 " --> pdb=" O ASP D 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 262 through 267 removed outlier: 5.822A pdb=" N LEU D 263 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL D 274 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLN D 265 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL D 272 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N CYS D 287 " --> pdb=" O MET D 302 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET D 302 " --> pdb=" O CYS D 287 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 291 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 298 " --> pdb=" O SER D 291 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 1960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 197 hydrogen bonds 390 hydrogen bond angles 0 basepair planarities 80 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5327 1.34 - 1.46: 4256 1.46 - 1.58: 9392 1.58 - 1.70: 318 1.70 - 1.81: 161 Bond restraints: 19454 Sorted by residual: bond pdb=" C3' DT F 9 " pdb=" C2' DT F 9 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DG M 37 " pdb=" C2' DG M 37 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DA L 36 " pdb=" C2' DA L 36 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT G 24 " pdb=" C2' DT G 24 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA M 40 " pdb=" C2' DA M 40 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.58e+00 ... (remaining 19449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 25933 1.58 - 3.16: 960 3.16 - 4.73: 83 4.73 - 6.31: 7 6.31 - 7.89: 5 Bond angle restraints: 26988 Sorted by residual: angle pdb=" O4' DC I 14 " pdb=" C4' DC I 14 " pdb=" C3' DC I 14 " ideal model delta sigma weight residual 106.00 102.88 3.12 6.00e-01 2.78e+00 2.71e+01 angle pdb=" N3 DT L 22 " pdb=" C4 DT L 22 " pdb=" O4 DT L 22 " ideal model delta sigma weight residual 119.90 122.75 -2.85 6.00e-01 2.78e+00 2.25e+01 angle pdb=" O4' DA L 18 " pdb=" C4' DA L 18 " pdb=" C3' DA L 18 " ideal model delta sigma weight residual 106.00 103.27 2.73 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT F 27 " pdb=" C4 DT F 27 " pdb=" O4 DT F 27 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT G 34 " pdb=" C4 DT G 34 " pdb=" O4 DT G 34 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 26983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.21: 9512 20.21 - 40.42: 1200 40.42 - 60.62: 556 60.62 - 80.83: 27 80.83 - 101.04: 5 Dihedral angle restraints: 11300 sinusoidal: 5687 harmonic: 5613 Sorted by residual: dihedral pdb=" CA ILE D 316 " pdb=" C ILE D 316 " pdb=" N TRP D 317 " pdb=" CA TRP D 317 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LYS C 608 " pdb=" C LYS C 608 " pdb=" N HIS C 609 " pdb=" CA HIS C 609 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLY C 717 " pdb=" C GLY C 717 " pdb=" N LEU C 718 " pdb=" CA LEU C 718 " ideal model delta harmonic sigma weight residual -180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 11297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2042 0.040 - 0.081: 649 0.081 - 0.121: 235 0.121 - 0.161: 26 0.161 - 0.202: 1 Chirality restraints: 2953 Sorted by residual: chirality pdb=" C3' DT L 22 " pdb=" C4' DT L 22 " pdb=" O3' DT L 22 " pdb=" C2' DT L 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LYS A 416 " pdb=" N LYS A 416 " pdb=" C LYS A 416 " pdb=" CB LYS A 416 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA ILE B 331 " pdb=" N ILE B 331 " pdb=" C ILE B 331 " pdb=" CB ILE B 331 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 2950 not shown) Planarity restraints: 2913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 179 " 0.063 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO D 180 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO D 180 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 180 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 498 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO A 499 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 317 " 0.019 2.00e-02 2.50e+03 1.44e-02 5.16e+00 pdb=" CG TRP B 317 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B 317 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 317 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 317 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 317 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 317 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 317 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 317 " 0.003 2.00e-02 2.50e+03 ... (remaining 2910 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2599 2.76 - 3.29: 17167 3.29 - 3.83: 32905 3.83 - 4.36: 37589 4.36 - 4.90: 61026 Nonbonded interactions: 151286 Sorted by model distance: nonbonded pdb=" OD2 ASP A 664 " pdb=" OG1 THR A 667 " model vdw 2.221 3.040 nonbonded pdb=" O GLY C 603 " pdb=" NH2 ARG C 969 " model vdw 2.222 3.120 nonbonded pdb=" OH TYR A 935 " pdb=" OP1 DG I 16 " model vdw 2.235 3.040 nonbonded pdb=" O LEU A 462 " pdb=" NE2 GLN A 498 " model vdw 2.243 3.120 nonbonded pdb=" OE1 GLU A 959 " pdb=" N2 DG F 30 " model vdw 2.250 3.120 ... (remaining 151281 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 391 through 802 or (resid 803 and (name N or name CA or na \ me C or name O or name CB )) or resid 804 through 906 or resid 908 through 1006 \ or (resid 1007 and (name N or name CA or name C or name O or name CB )) or resid \ 1101 through 1102)) selection = (chain 'C' and (resid 391 through 392 or (resid 393 and (name N or name CA or na \ me C or name O or name CB )) or resid 394 through 457 or (resid 458 and (name N \ or name CA or name C or name O or name CB )) or resid 459 through 906 or resid 9 \ 08 through 1102)) } ncs_group { reference = (chain 'B' and (resid 1 through 46 or resid 48 through 117 or (resid 118 and (na \ me N or name CA or name C or name O or name CB )) or resid 119 through 236 or re \ sid 238 through 335 or (resid 336 and (name N or name CA or name C or name O or \ name CB )) or resid 337 or resid 340 or (resid 341 through 342 and (name N or na \ me CA or name C or name O or name CB )) or resid 343 through 350)) selection = (chain 'D' and (resid 1 through 46 or resid 48 through 236 or resid 238 through \ 350)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 23.210 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.004 0.044 19462 Z= 0.329 Angle : 0.651 7.889 26992 Z= 0.482 Chirality : 0.044 0.202 2953 Planarity : 0.004 0.096 2913 Dihedral : 19.473 101.039 7684 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.18 % Allowed : 0.59 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.40 (0.19), residues: 1926 helix: 0.84 (0.21), residues: 650 sheet: 0.18 (0.28), residues: 362 loop : -1.27 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 703 TYR 0.021 0.001 TYR A 805 PHE 0.023 0.002 PHE C 936 TRP 0.039 0.002 TRP B 317 HIS 0.010 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.33 (19454) covalent geometry : angle 0.64962 / 0.48 (26988) hydrogen bonds : bond 0.14235 / 9.58 ( 858) hydrogen bonds : angle 6.28212 / 4.50 ( 2350) metal coordination : bond 0.00690 / 0.39 ( 8) metal coordination : angle 3.29504 / 1.68 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.7683 (mmm) cc_final: 0.7423 (mmm) REVERT: B 334 ASP cc_start: 0.5364 (m-30) cc_final: 0.4629 (m-30) REVERT: C 545 VAL cc_start: 0.8341 (p) cc_final: 0.7870 (p) REVERT: C 570 MET cc_start: 0.8546 (ptp) cc_final: 0.8264 (ptp) REVERT: C 883 MET cc_start: 0.8489 (tpp) cc_final: 0.8232 (tpt) REVERT: D 105 ASP cc_start: 0.7465 (p0) cc_final: 0.7185 (p0) REVERT: D 302 MET cc_start: 0.6876 (ppp) cc_final: 0.6615 (ppp) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.1404 time to fit residues: 74.8912 Evaluate side-chains 171 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 50.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN B 278 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 HIS ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN D 173 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.112311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.077346 restraints weight = 128844.245| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 5.67 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (12 function evaluations) r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19462 Z= 0.169 Angle : 0.656 8.324 26992 Z= 0.369 Chirality : 0.043 0.218 2953 Planarity : 0.005 0.082 2913 Dihedral : 21.348 98.157 3904 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.83 % Allowed : 10.51 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.40 (0.19), residues: 1926 helix: 0.77 (0.21), residues: 656 sheet: 0.19 (0.28), residues: 355 loop : -1.22 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 237 TYR 0.018 0.002 TYR D 138 PHE 0.032 0.002 PHE A 435 TRP 0.025 0.002 TRP B 317 HIS 0.017 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (19454) covalent geometry : angle 0.65501 / 0.37 (26988) hydrogen bonds : bond 0.04945 / 3.47 ( 858) hydrogen bonds : angle 5.02880 / 3.61 ( 2350) metal coordination : bond 0.00698 / 0.35 ( 8) metal coordination : angle 3.46014 / 1.76 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 MET cc_start: 0.8533 (mtm) cc_final: 0.8289 (mtm) REVERT: A 627 MET cc_start: 0.8355 (mmm) cc_final: 0.8018 (mmm) REVERT: A 658 MET cc_start: 0.8296 (ptp) cc_final: 0.7932 (ptp) REVERT: A 858 MET cc_start: 0.8497 (mmp) cc_final: 0.8258 (mmp) REVERT: C 972 ARG cc_start: 0.8626 (ttp80) cc_final: 0.8164 (ttp80) REVERT: C 984 MET cc_start: 0.8422 (mmm) cc_final: 0.8032 (mmm) REVERT: D 105 ASP cc_start: 0.8826 (p0) cc_final: 0.8453 (p0) outliers start: 11 outliers final: 10 residues processed: 203 average time/residue: 0.1259 time to fit residues: 39.2550 Evaluate side-chains 167 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 287 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 142 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 203 optimal weight: 40.0000 chunk 117 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 199 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 GLN B 33 GLN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 HIS C 809 GLN ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.107942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.073093 restraints weight = 115330.940| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 5.18 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 19462 Z= 0.234 Angle : 0.672 9.437 26992 Z= 0.369 Chirality : 0.045 0.385 2953 Planarity : 0.005 0.072 2913 Dihedral : 21.583 97.918 3904 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.48 % Allowed : 11.82 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.42 (0.19), residues: 1926 helix: 0.82 (0.20), residues: 655 sheet: 0.04 (0.28), residues: 338 loop : -1.20 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 167 TYR 0.022 0.002 TYR D 138 PHE 0.028 0.002 PHE A 435 TRP 0.041 0.002 TRP B 317 HIS 0.008 0.002 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.23 (19454) covalent geometry : angle 0.67076 / 0.37 (26988) hydrogen bonds : bond 0.05022 / 3.57 ( 858) hydrogen bonds : angle 4.68399 / 3.36 ( 2350) metal coordination : bond 0.01240 / 0.61 ( 8) metal coordination : angle 3.24420 / 1.63 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8588 (t80) cc_final: 0.8326 (t80) REVERT: A 442 ARG cc_start: 0.8261 (tpt90) cc_final: 0.7987 (tpt90) REVERT: A 627 MET cc_start: 0.8298 (mmm) cc_final: 0.8009 (mmm) REVERT: A 658 MET cc_start: 0.8451 (ptp) cc_final: 0.8017 (pmm) REVERT: B 58 LYS cc_start: 0.8609 (mptt) cc_final: 0.8377 (mptt) REVERT: C 972 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8234 (ttp80) REVERT: D 105 ASP cc_start: 0.8901 (p0) cc_final: 0.8586 (p0) REVERT: D 284 ARG cc_start: 0.8345 (tpt170) cc_final: 0.8118 (tpp80) REVERT: D 302 MET cc_start: 0.6859 (ppp) cc_final: 0.6305 (ppp) REVERT: D 322 MET cc_start: 0.7061 (mmm) cc_final: 0.6753 (mmm) outliers start: 23 outliers final: 14 residues processed: 176 average time/residue: 0.1174 time to fit residues: 32.8192 Evaluate side-chains 159 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 287 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 199 optimal weight: 30.0000 chunk 107 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 95 optimal weight: 40.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.109781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.074532 restraints weight = 154209.658| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 6.00 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19462 Z= 0.136 Angle : 0.602 10.017 26992 Z= 0.334 Chirality : 0.042 0.212 2953 Planarity : 0.004 0.067 2913 Dihedral : 21.565 97.581 3904 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.25 % Allowed : 13.06 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.30 (0.19), residues: 1926 helix: 0.98 (0.21), residues: 654 sheet: 0.08 (0.28), residues: 338 loop : -1.16 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 703 TYR 0.017 0.001 TYR D 138 PHE 0.019 0.001 PHE B 189 TRP 0.027 0.001 TRP B 317 HIS 0.006 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (19454) covalent geometry : angle 0.60074 / 0.33 (26988) hydrogen bonds : bond 0.04324 / 3.08 ( 858) hydrogen bonds : angle 4.54138 / 3.27 ( 2350) metal coordination : bond 0.00634 / 0.35 ( 8) metal coordination : angle 3.61162 / 1.83 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8605 (t80) cc_final: 0.8389 (t80) REVERT: A 627 MET cc_start: 0.8252 (mmm) cc_final: 0.7981 (mmm) REVERT: A 658 MET cc_start: 0.8511 (ptp) cc_final: 0.8131 (pmm) REVERT: B 58 LYS cc_start: 0.8542 (mptt) cc_final: 0.8277 (mptt) REVERT: C 972 ARG cc_start: 0.8728 (ttp80) cc_final: 0.8294 (ttp80) REVERT: C 974 MET cc_start: 0.8625 (mtt) cc_final: 0.8412 (mtm) REVERT: C 984 MET cc_start: 0.8397 (mmm) cc_final: 0.8156 (mmm) REVERT: D 105 ASP cc_start: 0.8899 (p0) cc_final: 0.8575 (p0) REVERT: D 284 ARG cc_start: 0.8231 (tpt170) cc_final: 0.7989 (tpp80) REVERT: D 302 MET cc_start: 0.6903 (ppp) cc_final: 0.6304 (ppp) outliers start: 18 outliers final: 14 residues processed: 173 average time/residue: 0.1218 time to fit residues: 33.1199 Evaluate side-chains 164 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 287 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 170 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 63 optimal weight: 0.3980 chunk 101 optimal weight: 8.9990 chunk 190 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.109851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.075288 restraints weight = 114346.244| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 5.25 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19462 Z= 0.136 Angle : 0.584 11.210 26992 Z= 0.324 Chirality : 0.041 0.185 2953 Planarity : 0.004 0.064 2913 Dihedral : 21.611 97.141 3904 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.48 % Allowed : 13.54 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.24 (0.19), residues: 1926 helix: 1.07 (0.21), residues: 653 sheet: 0.09 (0.28), residues: 339 loop : -1.14 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 703 TYR 0.015 0.001 TYR D 138 PHE 0.019 0.001 PHE B 189 TRP 0.023 0.001 TRP B 317 HIS 0.005 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (19454) covalent geometry : angle 0.58285 / 0.32 (26988) hydrogen bonds : bond 0.04103 / 2.89 ( 858) hydrogen bonds : angle 4.43498 / 3.18 ( 2350) metal coordination : bond 0.00568 / 0.31 ( 8) metal coordination : angle 3.23784 / 1.64 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8696 (t80) cc_final: 0.8454 (t80) REVERT: A 444 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8011 (mm-30) REVERT: A 627 MET cc_start: 0.8280 (mmm) cc_final: 0.7989 (mmm) REVERT: A 658 MET cc_start: 0.8498 (ptp) cc_final: 0.8191 (pmm) REVERT: C 972 ARG cc_start: 0.8746 (ttp80) cc_final: 0.8238 (ttp80) REVERT: C 974 MET cc_start: 0.8671 (mtt) cc_final: 0.8107 (mtm) REVERT: D 105 ASP cc_start: 0.8872 (p0) cc_final: 0.8534 (p0) REVERT: D 302 MET cc_start: 0.6947 (ppp) cc_final: 0.6381 (ppp) REVERT: D 322 MET cc_start: 0.6950 (mmm) cc_final: 0.6748 (mmm) outliers start: 22 outliers final: 19 residues processed: 166 average time/residue: 0.1131 time to fit residues: 30.1708 Evaluate side-chains 167 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 249 CYS Chi-restraints excluded: chain D residue 287 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 200 optimal weight: 50.0000 chunk 160 optimal weight: 0.9990 chunk 203 optimal weight: 40.0000 chunk 43 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 HIS ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 525 ASN ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.107664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.072711 restraints weight = 132825.797| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 5.57 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19462 Z= 0.213 Angle : 0.631 12.293 26992 Z= 0.342 Chirality : 0.043 0.194 2953 Planarity : 0.004 0.061 2913 Dihedral : 21.697 97.045 3904 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.66 % Allowed : 13.54 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.27 (0.19), residues: 1926 helix: 1.08 (0.21), residues: 654 sheet: -0.05 (0.28), residues: 340 loop : -1.14 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 970 TYR 0.018 0.002 TYR A 805 PHE 0.020 0.002 PHE B 189 TRP 0.026 0.002 TRP B 317 HIS 0.007 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (19454) covalent geometry : angle 0.62944 / 0.34 (26988) hydrogen bonds : bond 0.04623 / 3.29 ( 858) hydrogen bonds : angle 4.42159 / 3.16 ( 2350) metal coordination : bond 0.01071 / 0.54 ( 8) metal coordination : angle 3.25265 / 1.64 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8729 (t80) cc_final: 0.8521 (t80) REVERT: A 478 CYS cc_start: 0.8471 (m) cc_final: 0.8010 (t) REVERT: A 627 MET cc_start: 0.8323 (mmm) cc_final: 0.8014 (mmm) REVERT: A 658 MET cc_start: 0.8605 (ptp) cc_final: 0.8303 (pmm) REVERT: A 662 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7877 (tm-30) REVERT: A 828 ARG cc_start: 0.8546 (ttt180) cc_final: 0.8266 (ttt180) REVERT: B 162 MET cc_start: 0.8085 (mmm) cc_final: 0.7802 (mmp) REVERT: C 523 LEU cc_start: 0.8526 (mt) cc_final: 0.8184 (mm) REVERT: C 972 ARG cc_start: 0.8709 (ttp80) cc_final: 0.8270 (ttp80) REVERT: C 974 MET cc_start: 0.8603 (mtt) cc_final: 0.8251 (mtm) REVERT: D 105 ASP cc_start: 0.8880 (p0) cc_final: 0.8551 (p0) REVERT: D 302 MET cc_start: 0.6983 (ppp) cc_final: 0.6433 (ppp) outliers start: 25 outliers final: 21 residues processed: 160 average time/residue: 0.1266 time to fit residues: 32.3132 Evaluate side-chains 165 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 249 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 43 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 197 optimal weight: 50.0000 chunk 125 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.108872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.074083 restraints weight = 127428.524| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 5.50 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19462 Z= 0.146 Angle : 0.599 12.112 26992 Z= 0.327 Chirality : 0.041 0.198 2953 Planarity : 0.004 0.060 2913 Dihedral : 21.660 96.834 3904 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.43 % Allowed : 13.84 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.16 (0.19), residues: 1926 helix: 1.21 (0.21), residues: 647 sheet: 0.06 (0.28), residues: 344 loop : -1.12 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 703 TYR 0.017 0.001 TYR D 138 PHE 0.022 0.001 PHE B 189 TRP 0.023 0.001 TRP B 317 HIS 0.005 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (19454) covalent geometry : angle 0.59776 / 0.33 (26988) hydrogen bonds : bond 0.04186 / 2.97 ( 858) hydrogen bonds : angle 4.37571 / 3.13 ( 2350) metal coordination : bond 0.00632 / 0.34 ( 8) metal coordination : angle 3.38604 / 1.72 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8767 (t80) cc_final: 0.8532 (t80) REVERT: A 444 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7965 (mm-30) REVERT: A 627 MET cc_start: 0.8310 (mmm) cc_final: 0.7994 (mmm) REVERT: A 658 MET cc_start: 0.8563 (ptp) cc_final: 0.8287 (pmm) REVERT: A 662 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 828 ARG cc_start: 0.8544 (ttt180) cc_final: 0.8315 (ttt180) REVERT: B 162 MET cc_start: 0.8228 (mmm) cc_final: 0.7956 (mmp) REVERT: C 972 ARG cc_start: 0.8689 (ttp80) cc_final: 0.8314 (ttp80) REVERT: C 974 MET cc_start: 0.8669 (mtt) cc_final: 0.8293 (mtm) REVERT: D 105 ASP cc_start: 0.8884 (p0) cc_final: 0.8576 (p0) REVERT: D 302 MET cc_start: 0.7031 (ppp) cc_final: 0.6383 (ppp) outliers start: 21 outliers final: 18 residues processed: 163 average time/residue: 0.1127 time to fit residues: 30.1756 Evaluate side-chains 162 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 249 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 0 optimal weight: 40.0000 chunk 175 optimal weight: 8.9990 chunk 179 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 186 optimal weight: 30.0000 chunk 164 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.109056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.074156 restraints weight = 154028.732| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 5.97 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19462 Z= 0.150 Angle : 0.596 10.829 26992 Z= 0.326 Chirality : 0.041 0.187 2953 Planarity : 0.004 0.061 2913 Dihedral : 21.660 96.761 3904 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.60 % Allowed : 14.07 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.13 (0.19), residues: 1926 helix: 1.24 (0.21), residues: 647 sheet: 0.05 (0.28), residues: 339 loop : -1.09 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 442 TYR 0.017 0.001 TYR D 138 PHE 0.022 0.001 PHE B 189 TRP 0.023 0.001 TRP B 317 HIS 0.005 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (19454) covalent geometry : angle 0.59477 / 0.33 (26988) hydrogen bonds : bond 0.04222 / 3.00 ( 858) hydrogen bonds : angle 4.32746 / 3.09 ( 2350) metal coordination : bond 0.00659 / 0.35 ( 8) metal coordination : angle 3.16643 / 1.61 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8809 (t80) cc_final: 0.8586 (t80) REVERT: A 478 CYS cc_start: 0.8389 (m) cc_final: 0.7927 (t) REVERT: A 627 MET cc_start: 0.8312 (mmm) cc_final: 0.8017 (mmm) REVERT: A 658 MET cc_start: 0.8601 (ptp) cc_final: 0.8321 (pmm) REVERT: A 662 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7834 (tm-30) REVERT: A 828 ARG cc_start: 0.8549 (ttt180) cc_final: 0.8323 (ttt180) REVERT: A 983 GLU cc_start: 0.8228 (pt0) cc_final: 0.7882 (pt0) REVERT: B 162 MET cc_start: 0.8249 (mmm) cc_final: 0.8001 (mmp) REVERT: C 972 ARG cc_start: 0.8741 (ttp80) cc_final: 0.8318 (ttp80) REVERT: C 974 MET cc_start: 0.8621 (mtt) cc_final: 0.8258 (mtm) REVERT: D 105 ASP cc_start: 0.8908 (p0) cc_final: 0.8612 (p0) REVERT: D 302 MET cc_start: 0.7005 (ppp) cc_final: 0.6329 (ppp) outliers start: 24 outliers final: 18 residues processed: 166 average time/residue: 0.1115 time to fit residues: 29.6305 Evaluate side-chains 161 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 249 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 180 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 202 optimal weight: 50.0000 chunk 173 optimal weight: 4.9990 chunk 85 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.6988 > 50:) chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 19 optimal weight: 0.0050 chunk 4 optimal weight: 6.9990 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN A 990 HIS ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.107472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.072782 restraints weight = 118341.554| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 5.25 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19462 Z= 0.180 Angle : 0.616 13.028 26992 Z= 0.337 Chirality : 0.042 0.207 2953 Planarity : 0.004 0.060 2913 Dihedral : 21.713 96.974 3904 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.43 % Allowed : 14.43 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.14 (0.19), residues: 1926 helix: 1.24 (0.21), residues: 648 sheet: 0.08 (0.28), residues: 344 loop : -1.12 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 237 TYR 0.017 0.001 TYR D 138 PHE 0.023 0.002 PHE B 189 TRP 0.025 0.002 TRP B 317 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (19454) covalent geometry : angle 0.61530 / 0.34 (26988) hydrogen bonds : bond 0.04470 / 3.17 ( 858) hydrogen bonds : angle 4.36029 / 3.11 ( 2350) metal coordination : bond 0.00756 / 0.41 ( 8) metal coordination : angle 2.83145 / 1.46 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 CYS cc_start: 0.8435 (m) cc_final: 0.8002 (t) REVERT: A 597 GLU cc_start: 0.9072 (pm20) cc_final: 0.8806 (pm20) REVERT: A 627 MET cc_start: 0.8273 (mmm) cc_final: 0.8008 (mmm) REVERT: A 658 MET cc_start: 0.8482 (ptp) cc_final: 0.8255 (pmm) REVERT: A 662 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7919 (tm-30) REVERT: A 828 ARG cc_start: 0.8543 (ttt180) cc_final: 0.8302 (ttt180) REVERT: A 983 GLU cc_start: 0.8303 (pt0) cc_final: 0.7980 (pt0) REVERT: B 162 MET cc_start: 0.8259 (mmm) cc_final: 0.8019 (mmp) REVERT: C 972 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8321 (ttp80) REVERT: C 974 MET cc_start: 0.8615 (mtt) cc_final: 0.8259 (mtm) REVERT: D 105 ASP cc_start: 0.8955 (p0) cc_final: 0.8642 (p0) REVERT: D 302 MET cc_start: 0.7030 (ppp) cc_final: 0.6351 (ppp) REVERT: D 322 MET cc_start: 0.6809 (mmm) cc_final: 0.6590 (mmm) outliers start: 21 outliers final: 20 residues processed: 157 average time/residue: 0.1128 time to fit residues: 28.3891 Evaluate side-chains 160 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 249 CYS Chi-restraints excluded: chain D residue 287 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 30 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 201 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.108444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.073379 restraints weight = 150364.510| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 5.93 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19462 Z= 0.140 Angle : 0.595 12.053 26992 Z= 0.325 Chirality : 0.041 0.312 2953 Planarity : 0.004 0.060 2913 Dihedral : 21.664 97.258 3904 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.37 % Allowed : 14.73 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.07 (0.19), residues: 1926 helix: 1.32 (0.21), residues: 647 sheet: 0.00 (0.27), residues: 369 loop : -1.06 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 237 TYR 0.017 0.001 TYR A 805 PHE 0.025 0.001 PHE B 189 TRP 0.024 0.001 TRP B 317 HIS 0.005 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (19454) covalent geometry : angle 0.59390 / 0.32 (26988) hydrogen bonds : bond 0.04144 / 2.95 ( 858) hydrogen bonds : angle 4.35023 / 3.10 ( 2350) metal coordination : bond 0.00628 / 0.35 ( 8) metal coordination : angle 3.27855 / 1.66 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 478 CYS cc_start: 0.8345 (m) cc_final: 0.7904 (t) REVERT: A 627 MET cc_start: 0.8312 (mmm) cc_final: 0.8026 (mmm) REVERT: A 662 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 828 ARG cc_start: 0.8589 (ttt180) cc_final: 0.8369 (ttt180) REVERT: A 849 MET cc_start: 0.6728 (ptm) cc_final: 0.6507 (ptm) REVERT: A 983 GLU cc_start: 0.8168 (pt0) cc_final: 0.7902 (pt0) REVERT: B 162 MET cc_start: 0.8251 (mmm) cc_final: 0.8008 (mmp) REVERT: C 972 ARG cc_start: 0.8743 (ttp80) cc_final: 0.8327 (ttp80) REVERT: C 974 MET cc_start: 0.8607 (mtt) cc_final: 0.8252 (mtm) REVERT: D 105 ASP cc_start: 0.8979 (p0) cc_final: 0.8690 (p0) REVERT: D 302 MET cc_start: 0.7035 (ppp) cc_final: 0.6356 (ppp) outliers start: 20 outliers final: 18 residues processed: 161 average time/residue: 0.1085 time to fit residues: 28.3520 Evaluate side-chains 158 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 287 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 40.0000 chunk 46 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 193 optimal weight: 50.0000 chunk 109 optimal weight: 6.9990 chunk 1 optimal weight: 0.0980 chunk 160 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.107856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.072572 restraints weight = 166182.564| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 6.14 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19462 Z= 0.160 Angle : 0.605 12.001 26992 Z= 0.329 Chirality : 0.042 0.246 2953 Planarity : 0.004 0.060 2913 Dihedral : 21.693 97.716 3904 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.43 % Allowed : 14.96 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.09 (0.19), residues: 1926 helix: 1.30 (0.21), residues: 647 sheet: 0.02 (0.28), residues: 353 loop : -1.08 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 237 TYR 0.016 0.001 TYR A 805 PHE 0.032 0.001 PHE A 435 TRP 0.024 0.001 TRP B 317 HIS 0.005 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (19454) covalent geometry : angle 0.60342 / 0.33 (26988) hydrogen bonds : bond 0.04237 / 3.00 ( 858) hydrogen bonds : angle 4.36390 / 3.11 ( 2350) metal coordination : bond 0.00656 / 0.35 ( 8) metal coordination : angle 3.11739 / 1.58 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3603.41 seconds wall clock time: 62 minutes 42.98 seconds (3762.98 seconds total)