Starting phenix.real_space_refine on Sat Jul 4 06:56:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jts_61816/07_2026/9jts_61816.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jts_61816/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jts_61816/07_2026/9jts_61816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jts_61816/07_2026/9jts_61816.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jts_61816/07_2026/9jts_61816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jts_61816/07_2026/9jts_61816.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 4.42, per 1000 atoms: 0.24 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: 1.36 Conformation dependent library (CDL) restraints added in 967.3 milliseconds 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: 2.23 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: 3.42 Time building geometry restraints manager: 1.84 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: 961 3.16 - 4.73: 82 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.770 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.860 ------------------------------------------------------------------------------- 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= 0.328 Angle : 0.649 7.889 26992 Z= 0.480 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 0.64791 / 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 : 0.581 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: 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: 0.4628 (m-30) REVERT: C 545 VAL cc_start: 0.8341 (p) cc_final: 0.7869 (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: 0.1432 time to fit residues: 76.4408 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 : 0.457 ------------------------------------------------------------------------------- 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: 0.7980 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: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4006 r_free = 0.4006 target = 0.112878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078337 restraints weight = 128420.430| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 5.61 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (14 function evaluations) r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19462 Z= 0.160 Angle : 0.653 8.106 26992 Z= 0.368 Chirality : 0.043 0.221 2953 Planarity : 0.005 0.080 2913 Dihedral : 21.340 98.898 3904 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.89 % Allowed : 10.63 % Favored : 88.48 % 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: 0.78 (0.20), residues: 655 sheet: 0.21 (0.28), residues: 355 loop : -1.23 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 237 TYR 0.017 0.002 TYR D 138 PHE 0.035 0.002 PHE A 435 TRP 0.024 0.002 TRP B 317 HIS 0.016 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (19454) covalent geometry : angle 0.65183 / 0.37 (26988) hydrogen bonds : bond 0.04894 / 3.42 ( 858) hydrogen bonds : angle 5.06539 / 3.64 ( 2350) metal coordination : bond 0.00628 / 0.33 ( 8) metal coordination : angle 3.52345 / 1.80 ( 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 213 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 MET cc_start: 0.8519 (mtm) cc_final: 0.8265 (mtm) REVERT: A 627 MET cc_start: 0.8348 (mmm) cc_final: 0.8003 (mmm) REVERT: A 658 MET cc_start: 0.8255 (ptp) cc_final: 0.7842 (pmm) REVERT: A 858 MET cc_start: 0.8456 (mmp) cc_final: 0.8229 (mmp) REVERT: C 531 ASP cc_start: 0.7932 (p0) cc_final: 0.7605 (t0) REVERT: C 837 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8730 (mm) REVERT: C 972 ARG cc_start: 0.8622 (ttp80) cc_final: 0.8225 (ttp80) REVERT: C 984 MET cc_start: 0.8405 (mmm) cc_final: 0.8168 (mmm) REVERT: D 105 ASP cc_start: 0.8825 (p0) cc_final: 0.8447 (p0) outliers start: 13 outliers final: 9 residues processed: 210 average time/residue: 0.1402 time to fit residues: 45.4275 Evaluate side-chains 172 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 185 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 837 LEU 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: 0.7980 chunk 175 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 203 optimal weight: 40.0000 chunk 117 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 199 optimal weight: 30.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 HIS ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.110794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.076055 restraints weight = 113404.967| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 5.28 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (11 function evaluations) r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19462 Z= 0.168 Angle : 0.617 9.369 26992 Z= 0.345 Chirality : 0.043 0.356 2953 Planarity : 0.005 0.072 2913 Dihedral : 21.480 98.441 3904 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.07 % Allowed : 11.76 % Favored : 87.17 % 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: -0.29 (0.19), residues: 1926 helix: 0.91 (0.21), residues: 656 sheet: 0.20 (0.28), residues: 333 loop : -1.14 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 167 TYR 0.018 0.002 TYR A 805 PHE 0.026 0.002 PHE A 435 TRP 0.033 0.002 TRP B 317 HIS 0.007 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (19454) covalent geometry : angle 0.61543 / 0.35 (26988) hydrogen bonds : bond 0.04569 / 3.24 ( 858) hydrogen bonds : angle 4.67677 / 3.36 ( 2350) metal coordination : bond 0.00761 / 0.38 ( 8) metal coordination : angle 3.15620 / 1.60 ( 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 180 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8525 (t80) cc_final: 0.8248 (t80) REVERT: A 442 ARG cc_start: 0.8156 (tpt90) cc_final: 0.7914 (tpt90) REVERT: A 578 MET cc_start: 0.8511 (mtm) cc_final: 0.8308 (mtm) REVERT: A 627 MET cc_start: 0.8335 (mmm) cc_final: 0.8041 (mmm) REVERT: A 658 MET cc_start: 0.8442 (ptp) cc_final: 0.8026 (pmm) REVERT: B 58 LYS cc_start: 0.8569 (mptt) cc_final: 0.8343 (mptt) REVERT: C 972 ARG cc_start: 0.8764 (ttp80) cc_final: 0.8325 (ttp80) REVERT: D 105 ASP cc_start: 0.8874 (p0) cc_final: 0.8526 (p0) REVERT: D 302 MET cc_start: 0.6847 (ppp) cc_final: 0.6364 (ppp) outliers start: 16 outliers final: 12 residues processed: 175 average time/residue: 0.1223 time to fit residues: 33.6258 Evaluate side-chains 161 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 900 LYS 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: 0.0370 chunk 54 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 133 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 95 optimal weight: 50.0000 overall best weight: 0.7860 ------------------------------------------------------------------------------- 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 842 ASN B 33 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.111260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.076099 restraints weight = 153934.792| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 6.05 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19462 Z= 0.133 Angle : 0.590 10.445 26992 Z= 0.328 Chirality : 0.042 0.205 2953 Planarity : 0.004 0.067 2913 Dihedral : 21.547 98.088 3904 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.48 % Allowed : 12.89 % Favored : 85.63 % 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: -0.21 (0.19), residues: 1926 helix: 1.03 (0.21), residues: 653 sheet: 0.12 (0.28), residues: 359 loop : -1.10 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 703 TYR 0.019 0.001 TYR A 805 PHE 0.020 0.001 PHE B 189 TRP 0.025 0.001 TRP B 317 HIS 0.006 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (19454) covalent geometry : angle 0.58860 / 0.33 (26988) hydrogen bonds : bond 0.04126 / 2.92 ( 858) hydrogen bonds : angle 4.50867 / 3.24 ( 2350) metal coordination : bond 0.00586 / 0.32 ( 8) metal coordination : angle 3.54265 / 1.80 ( 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 184 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8646 (t80) cc_final: 0.8400 (t80) REVERT: A 627 MET cc_start: 0.8305 (mmm) cc_final: 0.8027 (mmm) REVERT: A 658 MET cc_start: 0.8451 (ptp) cc_final: 0.8037 (pmm) REVERT: B 58 LYS cc_start: 0.8520 (mptt) cc_final: 0.8237 (mptt) REVERT: C 841 MET cc_start: 0.8763 (mmm) cc_final: 0.8175 (mmt) REVERT: C 972 ARG cc_start: 0.8778 (ttp80) cc_final: 0.8371 (ttp80) REVERT: D 105 ASP cc_start: 0.8908 (p0) cc_final: 0.8555 (p0) REVERT: D 302 MET cc_start: 0.6948 (ppp) cc_final: 0.6367 (ppp) outliers start: 22 outliers final: 13 residues processed: 176 average time/residue: 0.1193 time to fit residues: 33.5709 Evaluate side-chains 165 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 837 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 263 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 900 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 170 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 63 optimal weight: 0.3980 chunk 101 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 124 optimal weight: 0.5980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 GLN A 975 ASN A 990 HIS ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3975 r_free = 0.3975 target = 0.110636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.076237 restraints weight = 114586.363| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 5.22 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 = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19462 Z= 0.166 Angle : 0.600 10.928 26992 Z= 0.330 Chirality : 0.042 0.191 2953 Planarity : 0.004 0.067 2913 Dihedral : 21.644 98.113 3904 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.84 % Allowed : 12.83 % Favored : 85.33 % 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: -0.22 (0.19), residues: 1926 helix: 1.11 (0.21), residues: 654 sheet: 0.07 (0.28), residues: 333 loop : -1.13 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 237 TYR 0.018 0.001 TYR A 805 PHE 0.018 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 0.00350 / 0.17 (19454) covalent geometry : angle 0.59835 / 0.33 (26988) hydrogen bonds : bond 0.04248 / 3.00 ( 858) hydrogen bonds : angle 4.46178 / 3.21 ( 2350) metal coordination : bond 0.00778 / 0.39 ( 8) metal coordination : angle 3.14999 / 1.59 ( 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 183 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8706 (t80) cc_final: 0.8492 (t80) REVERT: A 627 MET cc_start: 0.8293 (mmm) cc_final: 0.8031 (mmm) REVERT: A 658 MET cc_start: 0.8508 (ptp) cc_final: 0.8165 (pmm) REVERT: A 662 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7836 (tm-30) REVERT: A 841 MET cc_start: 0.8322 (mmm) cc_final: 0.7984 (mtp) REVERT: C 841 MET cc_start: 0.8848 (mmm) cc_final: 0.8253 (mmt) REVERT: C 904 GLU cc_start: 0.8450 (pm20) cc_final: 0.8234 (tp30) REVERT: C 972 ARG cc_start: 0.8823 (ttp80) cc_final: 0.8302 (ttp80) REVERT: C 974 MET cc_start: 0.8671 (mtt) cc_final: 0.8101 (mtm) REVERT: D 105 ASP cc_start: 0.8888 (p0) cc_final: 0.8527 (p0) REVERT: D 302 MET cc_start: 0.6925 (ppp) cc_final: 0.6366 (ppp) outliers start: 28 outliers final: 22 residues processed: 170 average time/residue: 0.1172 time to fit residues: 32.0061 Evaluate side-chains 170 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 12 ILE Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 114 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 B residue 264 THR Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 249 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 64 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 200 optimal weight: 50.0000 chunk 160 optimal weight: 1.9990 chunk 203 optimal weight: 30.0000 chunk 43 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.110117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.075437 restraints weight = 132912.556| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 5.62 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19462 Z= 0.150 Angle : 0.586 11.839 26992 Z= 0.322 Chirality : 0.041 0.220 2953 Planarity : 0.004 0.064 2913 Dihedral : 21.658 98.234 3904 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.84 % Allowed : 13.00 % Favored : 85.15 % 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: -0.15 (0.19), residues: 1926 helix: 1.17 (0.21), residues: 655 sheet: 0.05 (0.28), residues: 353 loop : -1.10 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 703 TYR 0.018 0.001 TYR D 138 PHE 0.019 0.001 PHE B 189 TRP 0.025 0.001 TRP B 317 HIS 0.005 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (19454) covalent geometry : angle 0.58449 / 0.32 (26988) hydrogen bonds : bond 0.04162 / 2.97 ( 858) hydrogen bonds : angle 4.35128 / 3.12 ( 2350) metal coordination : bond 0.00683 / 0.36 ( 8) metal coordination : angle 3.42714 / 1.73 ( 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 178 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8794 (t80) cc_final: 0.8553 (t80) REVERT: A 627 MET cc_start: 0.8357 (mmm) cc_final: 0.8009 (mmm) REVERT: A 658 MET cc_start: 0.8554 (ptp) cc_final: 0.8223 (pmm) REVERT: A 662 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7774 (tm-30) REVERT: A 828 ARG cc_start: 0.8530 (ttt180) cc_final: 0.8285 (ttt180) REVERT: A 841 MET cc_start: 0.8351 (mmm) cc_final: 0.8005 (mtp) REVERT: B 162 MET cc_start: 0.8053 (mmm) cc_final: 0.7794 (mmp) REVERT: C 841 MET cc_start: 0.8893 (mmm) cc_final: 0.8122 (mmt) REVERT: C 972 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8339 (ttp80) REVERT: C 974 MET cc_start: 0.8688 (mtt) cc_final: 0.8441 (mtp) REVERT: D 105 ASP cc_start: 0.8886 (p0) cc_final: 0.8544 (p0) REVERT: D 302 MET cc_start: 0.6916 (ppp) cc_final: 0.6338 (ppp) REVERT: D 344 TYR cc_start: 0.8418 (m-10) cc_final: 0.7998 (m-10) outliers start: 28 outliers final: 24 residues processed: 167 average time/residue: 0.1271 time to fit residues: 33.9447 Evaluate side-chains 168 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 550 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 114 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 B residue 264 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 145 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 43 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 chunk 148 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 150 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 197 optimal weight: 50.0000 chunk 125 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.110791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.076054 restraints weight = 127639.041| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 5.59 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19462 Z= 0.122 Angle : 0.569 12.116 26992 Z= 0.313 Chirality : 0.040 0.168 2953 Planarity : 0.004 0.062 2913 Dihedral : 21.601 98.403 3904 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.37 % Allowed : 13.66 % 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: -0.06 (0.19), residues: 1926 helix: 1.26 (0.21), residues: 651 sheet: 0.11 (0.28), residues: 364 loop : -1.06 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 442 TYR 0.016 0.001 TYR D 138 PHE 0.021 0.001 PHE B 189 TRP 0.021 0.001 TRP B 317 HIS 0.006 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (19454) covalent geometry : angle 0.56762 / 0.31 (26988) hydrogen bonds : bond 0.03806 / 2.68 ( 858) hydrogen bonds : angle 4.29647 / 3.07 ( 2350) metal coordination : bond 0.00562 / 0.31 ( 8) metal coordination : angle 3.25648 / 1.65 ( 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 175 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 627 MET cc_start: 0.8323 (mmm) cc_final: 0.7980 (mmm) REVERT: A 658 MET cc_start: 0.8480 (ptp) cc_final: 0.8180 (pmm) REVERT: A 662 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7755 (tm-30) REVERT: A 828 ARG cc_start: 0.8552 (ttt180) cc_final: 0.8301 (ttt180) REVERT: A 841 MET cc_start: 0.8245 (mmm) cc_final: 0.7895 (mtp) REVERT: B 162 MET cc_start: 0.8249 (mmm) cc_final: 0.7978 (mmp) REVERT: C 904 GLU cc_start: 0.8415 (pm20) cc_final: 0.8200 (tp30) REVERT: C 972 ARG cc_start: 0.8793 (ttp80) cc_final: 0.8308 (ttp80) REVERT: D 105 ASP cc_start: 0.8867 (p0) cc_final: 0.8517 (p0) REVERT: D 302 MET cc_start: 0.6925 (ppp) cc_final: 0.6251 (ppp) REVERT: D 328 PHE cc_start: 0.8016 (t80) cc_final: 0.7581 (t80) REVERT: D 344 TYR cc_start: 0.8374 (m-10) cc_final: 0.8057 (m-10) outliers start: 20 outliers final: 17 residues processed: 167 average time/residue: 0.1279 time to fit residues: 34.1778 Evaluate side-chains 162 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 534 ILE Chi-restraints excluded: chain A residue 573 ASP 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 B residue 264 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 107 ILE 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: 9.9990 chunk 179 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 176 optimal weight: 0.1980 chunk 82 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 HIS ** 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 = 0.3902 r_free = 0.3902 target = 0.107239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.071990 restraints weight = 155026.370| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 5.98 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 19462 Z= 0.226 Angle : 0.639 12.532 26992 Z= 0.348 Chirality : 0.043 0.224 2953 Planarity : 0.005 0.061 2913 Dihedral : 21.757 99.231 3904 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.54 % Allowed : 13.78 % Favored : 84.68 % 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: 1.26 (0.21), residues: 649 sheet: -0.08 (0.28), residues: 347 loop : -1.06 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 123 TYR 0.019 0.002 TYR D 138 PHE 0.023 0.002 PHE A 435 TRP 0.027 0.002 TRP B 317 HIS 0.010 0.002 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (19454) covalent geometry : angle 0.63842 / 0.35 (26988) hydrogen bonds : bond 0.04822 / 3.44 ( 858) hydrogen bonds : angle 4.35511 / 3.10 ( 2350) metal coordination : bond 0.01207 / 0.59 ( 8) metal coordination : angle 3.08496 / 1.55 ( 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 165 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 627 MET cc_start: 0.8294 (mmm) cc_final: 0.8033 (mmm) REVERT: A 658 MET cc_start: 0.8633 (ptp) cc_final: 0.8356 (pmm) REVERT: A 662 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7874 (tm-30) REVERT: A 828 ARG cc_start: 0.8527 (ttt180) cc_final: 0.8260 (ttt180) REVERT: A 841 MET cc_start: 0.8322 (mmm) cc_final: 0.7973 (mtp) REVERT: A 983 GLU cc_start: 0.8356 (pt0) cc_final: 0.8006 (pt0) REVERT: B 162 MET cc_start: 0.8256 (mmm) cc_final: 0.8012 (mmp) REVERT: C 904 GLU cc_start: 0.8557 (pm20) cc_final: 0.8293 (tp30) REVERT: C 972 ARG cc_start: 0.8784 (ttp80) cc_final: 0.8361 (ttp80) REVERT: D 105 ASP cc_start: 0.8978 (p0) cc_final: 0.8657 (p0) REVERT: D 302 MET cc_start: 0.6941 (ppp) cc_final: 0.6247 (ppp) REVERT: D 344 TYR cc_start: 0.8539 (m-10) cc_final: 0.8108 (m-10) outliers start: 23 outliers final: 20 residues processed: 156 average time/residue: 0.1341 time to fit residues: 33.3705 Evaluate side-chains 154 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 837 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 114 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 263 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 107 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 180 optimal weight: 0.0770 chunk 59 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 202 optimal weight: 50.0000 chunk 173 optimal weight: 0.7980 chunk 85 optimal weight: 40.0000 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.109370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.074678 restraints weight = 120283.429| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 5.40 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (15 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19462 Z= 0.128 Angle : 0.588 11.442 26992 Z= 0.321 Chirality : 0.041 0.185 2953 Planarity : 0.004 0.060 2913 Dihedral : 21.660 99.742 3904 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.31 % Allowed : 14.19 % Favored : 84.50 % 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: -0.06 (0.19), residues: 1926 helix: 1.33 (0.21), residues: 650 sheet: -0.03 (0.27), residues: 359 loop : -1.05 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 237 TYR 0.017 0.001 TYR D 138 PHE 0.037 0.001 PHE A 435 TRP 0.022 0.001 TRP B 317 HIS 0.009 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (19454) covalent geometry : angle 0.58687 / 0.32 (26988) hydrogen bonds : bond 0.04019 / 2.86 ( 858) hydrogen bonds : angle 4.31336 / 3.07 ( 2350) metal coordination : bond 0.00618 / 0.34 ( 8) metal coordination : angle 3.44018 / 1.75 ( 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 162 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 597 GLU cc_start: 0.9058 (pm20) cc_final: 0.8783 (pm20) REVERT: A 627 MET cc_start: 0.8305 (mmm) cc_final: 0.7984 (mmm) REVERT: A 658 MET cc_start: 0.8535 (ptp) cc_final: 0.8284 (pmm) REVERT: A 662 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 828 ARG cc_start: 0.8552 (ttt180) cc_final: 0.8301 (ttt180) REVERT: A 841 MET cc_start: 0.8254 (mmm) cc_final: 0.7841 (mtp) REVERT: A 983 GLU cc_start: 0.8171 (pt0) cc_final: 0.7871 (pt0) REVERT: B 162 MET cc_start: 0.8254 (mmm) cc_final: 0.8009 (mmp) REVERT: C 531 ASP cc_start: 0.8177 (p0) cc_final: 0.7700 (t0) REVERT: C 972 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8340 (ttp80) REVERT: D 105 ASP cc_start: 0.8943 (p0) cc_final: 0.8588 (p0) REVERT: D 302 MET cc_start: 0.6929 (ppp) cc_final: 0.6240 (ppp) REVERT: D 344 TYR cc_start: 0.8468 (m-10) cc_final: 0.8107 (m-10) outliers start: 19 outliers final: 15 residues processed: 155 average time/residue: 0.1325 time to fit residues: 33.3553 Evaluate side-chains 156 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 573 ASP 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 B residue 320 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 107 ILE 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: 2.9990 chunk 183 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 201 optimal weight: 20.0000 chunk 175 optimal weight: 8.9990 chunk 156 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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** C 800 ASN ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.108313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.073171 restraints weight = 154204.215| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 5.96 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19462 Z= 0.170 Angle : 0.603 11.402 26992 Z= 0.329 Chirality : 0.042 0.289 2953 Planarity : 0.004 0.059 2913 Dihedral : 21.715 100.795 3904 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.31 % Allowed : 14.37 % 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: -0.07 (0.19), residues: 1926 helix: 1.30 (0.21), residues: 647 sheet: 0.12 (0.28), residues: 344 loop : -1.09 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 237 TYR 0.018 0.001 TYR D 138 PHE 0.032 0.002 PHE A 435 TRP 0.024 0.002 TRP D 317 HIS 0.008 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (19454) covalent geometry : angle 0.60209 / 0.33 (26988) hydrogen bonds : bond 0.04409 / 3.15 ( 858) hydrogen bonds : angle 4.34063 / 3.08 ( 2350) metal coordination : bond 0.00757 / 0.39 ( 8) metal coordination : angle 3.08423 / 1.56 ( 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 159 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 597 GLU cc_start: 0.9052 (pm20) cc_final: 0.8769 (pm20) REVERT: A 627 MET cc_start: 0.8290 (mmm) cc_final: 0.7996 (mmm) REVERT: A 658 MET cc_start: 0.8535 (ptp) cc_final: 0.8296 (pmm) REVERT: A 662 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7808 (tm-30) REVERT: A 828 ARG cc_start: 0.8565 (ttt180) cc_final: 0.8300 (ttt180) REVERT: A 841 MET cc_start: 0.8252 (mmm) cc_final: 0.7856 (mtp) REVERT: A 983 GLU cc_start: 0.8255 (pt0) cc_final: 0.7968 (pt0) REVERT: B 162 MET cc_start: 0.8264 (mmm) cc_final: 0.7966 (mmp) REVERT: C 972 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8372 (ttp80) REVERT: D 105 ASP cc_start: 0.8997 (p0) cc_final: 0.8699 (p0) REVERT: D 302 MET cc_start: 0.6986 (ppp) cc_final: 0.6285 (ppp) REVERT: D 344 TYR cc_start: 0.8500 (m-10) cc_final: 0.8123 (m-10) outliers start: 19 outliers final: 17 residues processed: 154 average time/residue: 0.1186 time to fit residues: 29.3523 Evaluate side-chains 152 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 573 ASP Chi-restraints excluded: chain A residue 947 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 263 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 107 ILE 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: 4.9990 chunk 103 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 140 optimal weight: 0.0980 chunk 193 optimal weight: 50.0000 chunk 109 optimal weight: 8.9990 chunk 1 optimal weight: 0.3980 chunk 160 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN C 473 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.109944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.074724 restraints weight = 167632.420| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 6.30 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19462 Z= 0.124 Angle : 0.593 12.348 26992 Z= 0.321 Chirality : 0.041 0.221 2953 Planarity : 0.004 0.059 2913 Dihedral : 21.641 101.840 3904 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.25 % Allowed : 14.31 % Favored : 84.44 % 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: -0.04 (0.19), residues: 1926 helix: 1.30 (0.21), residues: 648 sheet: -0.01 (0.27), residues: 374 loop : -1.00 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 579 TYR 0.017 0.001 TYR D 138 PHE 0.029 0.001 PHE A 435 TRP 0.022 0.001 TRP D 317 HIS 0.009 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (19454) covalent geometry : angle 0.59155 / 0.32 (26988) hydrogen bonds : bond 0.03853 / 2.73 ( 858) hydrogen bonds : angle 4.32150 / 3.07 ( 2350) metal coordination : bond 0.00704 / 0.38 ( 8) metal coordination : angle 3.50065 / 1.79 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3851.64 seconds wall clock time: 66 minutes 54.80 seconds (4014.80 seconds total)