Starting phenix.real_space_refine on Thu Sep 18 18:30:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jts_61816/09_2025/9jts_61816.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jts_61816/09_2025/9jts_61816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jts_61816/09_2025/9jts_61816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jts_61816/09_2025/9jts_61816.map" model { file = "/net/cci-nas-00/data/ceres_data/9jts_61816/09_2025/9jts_61816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jts_61816/09_2025/9jts_61816.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 P 160 5.49 5 S 106 5.16 5 C 11311 2.51 5 N 3311 2.21 5 O 3814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18706 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4969 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 618, 4963 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 591} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 618, 4963 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 591} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 5059 Chain: "B" Number of atoms: 2704 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 344, 2683 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 344, 2683 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2727 Chain: "C" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5006 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 596} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2673 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 343, 2663 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 343, 2663 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2718 Chain: "I" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 795 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "L" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 607 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "M" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 801 Classifications: {'DNA': 39} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 38} Chain: "H" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 262 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 617 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2632 SG CYS A 727 75.457 102.566 101.808 1.00 60.06 S ATOM 2653 SG CYS A 730 77.833 104.653 104.070 1.00 65.46 S ATOM 10360 SG CYS C 727 27.684 100.315 54.060 1.00 65.78 S ATOM 10381 SG CYS C 730 25.025 102.259 51.990 1.00 69.81 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N ACYS A 907 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 907 " occ=0.50 residue: pdb=" N AHIS B 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 47 " occ=0.50 residue: pdb=" N AARG B 237 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 237 " occ=0.50 residue: pdb=" N AHIS D 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 47 " occ=0.50 residue: pdb=" P DT I 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT I 15 " occ=0.85 Time building chain proxies: 6.61, per 1000 atoms: 0.35 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: 1.73 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 408 through 422 removed outlier: 4.054A pdb=" N ILE A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 443 Processing helix chain 'A' and resid 444 through 456 Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 812 Processing helix chain 'A' and resid 822 through 842 Processing helix chain 'A' and resid 850 through 858 removed outlier: 3.694A pdb=" N ALA A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.781A pdb=" N VAL A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 890 Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 902 through 924 removed outlier: 4.827A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE A 911 " --> pdb=" O ACYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.596A pdb=" N ARG A 969 " --> pdb=" O ASN A 965 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 970 " --> pdb=" O LYS A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'B' and resid 11 through 13 No H-bonds generated for 'chain 'B' and resid 11 through 13' Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.924A pdb=" N LEU C 399 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'C' and resid 410 through 423 removed outlier: 3.820A pdb=" N LYS C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 443 Processing helix chain 'C' and resid 444 through 457 Processing helix chain 'C' and resid 463 through 474 removed outlier: 3.517A pdb=" N CYS C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.707A pdb=" N LYS C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 removed outlier: 3.564A pdb=" N MET C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 581 removed outlier: 3.571A pdb=" N GLN C 581 " --> pdb=" O GLY C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 750 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 812 Processing helix chain 'C' and resid 822 through 841 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.881A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 870 No H-bonds generated for 'chain 'C' and resid 868 through 870' Processing helix chain 'C' and resid 872 through 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 902 through 908 removed outlier: 3.845A pdb=" N GLN C 908 " --> pdb=" O GLU C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 924 removed outlier: 3.581A pdb=" N PHE C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 950 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.949A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 995 Processing helix chain 'C' and resid 996 through 1001 Processing helix chain 'C' and resid 1002 through 1004 No H-bonds generated for 'chain 'C' and resid 1002 through 1004' Processing helix chain 'D' and resid 11 through 13 No H-bonds generated for 'chain 'D' and resid 11 through 13' Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 308 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 519 removed outlier: 6.228A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 519 removed outlier: 6.228A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.891A pdb=" N LEU B 348 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B 328 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 320 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 24 removed outlier: 8.652A pdb=" N GLY B 18 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLN B 33 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 58 " --> pdb=" O AHIS B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.554A pdb=" N TYR B 80 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN B 90 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS B 106 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS B 97 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER B 104 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.731A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS B 191 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.559A pdb=" N VAL B 208 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 239 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 246 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 267 removed outlier: 7.143A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 298 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 518 through 519 removed outlier: 6.918A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG C 628 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 519 removed outlier: 6.918A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG C 628 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 5 removed outlier: 3.754A pdb=" N PHE D 328 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D 320 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 318 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 7 through 8 removed outlier: 6.847A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS D 58 " --> pdb=" O AHIS D 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 15 through 24 removed outlier: 8.562A pdb=" N GLY D 18 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN D 33 " --> pdb=" O GLY D 18 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.451A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 77 through 78 removed outlier: 6.813A pdb=" N LYS D 106 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS D 97 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N SER D 104 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS D 127 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 109 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.354A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS D 191 " --> pdb=" O ASP D 186 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR D 193 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU D 184 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AC1, first strand: chain 'D' and resid 208 through 210 removed outlier: 4.026A pdb=" N VAL D 208 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 219 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D 210 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP D 239 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA D 246 " --> pdb=" O ASP D 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 262 through 267 removed outlier: 5.822A pdb=" N LEU D 263 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL D 274 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLN D 265 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL D 272 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N CYS D 287 " --> pdb=" O MET D 302 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET D 302 " --> pdb=" O CYS D 287 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 291 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 298 " --> pdb=" O SER D 291 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 1960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 197 hydrogen bonds 390 hydrogen bond angles 0 basepair planarities 80 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 2.25 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' DG M 37 " pdb=" O3' DG M 37 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" C LEU D 57 " pdb=" N LYS D 58 " ideal model delta sigma weight residual 1.331 1.309 0.022 2.07e-02 2.33e+03 1.08e+00 bond pdb=" CG PRO C 521 " pdb=" CD PRO C 521 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.70e-02 1.37e+03 9.73e-01 bond pdb=" O4' DG G 41 " pdb=" C1' DG G 41 " ideal model delta sigma weight residual 1.414 1.394 0.020 2.00e-02 2.50e+03 9.58e-01 bond pdb=" C3' DT F 9 " pdb=" C2' DT F 9 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 8.82e-01 ... (remaining 19449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 26261 1.58 - 3.16: 633 3.16 - 4.73: 82 4.73 - 6.31: 7 6.31 - 7.89: 5 Bond angle restraints: 26988 Sorted by residual: angle pdb=" CB LYS A 416 " pdb=" CG LYS A 416 " pdb=" CD LYS A 416 " ideal model delta sigma weight residual 111.30 118.19 -6.89 2.30e+00 1.89e-01 8.97e+00 angle pdb=" C LYS A 416 " pdb=" N GLU A 417 " pdb=" CA GLU A 417 " ideal model delta sigma weight residual 120.29 116.30 3.99 1.42e+00 4.96e-01 7.91e+00 angle pdb=" CB MET A 455 " pdb=" CG MET A 455 " pdb=" SD MET A 455 " ideal model delta sigma weight residual 112.70 120.59 -7.89 3.00e+00 1.11e-01 6.91e+00 angle pdb=" N LYS A 416 " pdb=" CA LYS A 416 " pdb=" CB LYS A 416 " ideal model delta sigma weight residual 110.16 114.05 -3.89 1.48e+00 4.57e-01 6.90e+00 angle pdb=" CB MET A 984 " pdb=" CG MET A 984 " pdb=" SD MET A 984 " ideal model delta sigma weight residual 112.70 119.91 -7.21 3.00e+00 1.11e-01 5.77e+00 ... (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 - 0.032: 1934 0.032 - 0.064: 695 0.064 - 0.095: 202 0.095 - 0.127: 112 0.127 - 0.159: 10 Chirality restraints: 2953 Sorted by residual: 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 chirality pdb=" CA LEU C 741 " pdb=" N LEU C 741 " pdb=" C LEU C 741 " pdb=" CB LEU C 741 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 2950 not shown) Planarity restraints: 2913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 179 " 0.063 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO D 180 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO D 180 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 180 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 498 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO A 499 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 317 " 0.019 2.00e-02 2.50e+03 1.44e-02 5.16e+00 pdb=" CG TRP B 317 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B 317 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 317 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 317 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 317 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 317 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 317 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 317 " 0.003 2.00e-02 2.50e+03 ... (remaining 2910 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2599 2.76 - 3.29: 17167 3.29 - 3.83: 32905 3.83 - 4.36: 37589 4.36 - 4.90: 61026 Nonbonded interactions: 151286 Sorted by model distance: nonbonded pdb=" OD2 ASP A 664 " pdb=" OG1 THR A 667 " model vdw 2.221 3.040 nonbonded pdb=" O GLY C 603 " pdb=" NH2 ARG C 969 " model vdw 2.222 3.120 nonbonded pdb=" OH TYR A 935 " pdb=" OP1 DG I 16 " model vdw 2.235 3.040 nonbonded pdb=" O LEU A 462 " pdb=" NE2 GLN A 498 " model vdw 2.243 3.120 nonbonded pdb=" OE1 GLU A 959 " pdb=" N2 DG F 30 " model vdw 2.250 3.120 ... (remaining 151281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 391 through 802 or (resid 803 and (name N or name CA or na \ me C or name O or name CB )) or resid 804 through 906 or resid 908 through 1006 \ or (resid 1007 and (name N or name CA or name C or name O or name CB )) or resid \ 1101 through 1102)) selection = (chain 'C' and (resid 391 through 392 or (resid 393 and (name N or name CA or na \ me C or name O or name CB )) or resid 394 through 457 or (resid 458 and (name N \ or name CA or name C or name O or name CB )) or resid 459 through 906 or resid 9 \ 08 through 1102)) } ncs_group { reference = (chain 'B' and (resid 1 through 46 or resid 48 through 117 or (resid 118 and (na \ me N or name CA or name C or name O or name CB )) or resid 119 through 236 or re \ sid 238 through 335 or (resid 336 and (name N or name CA or name C or name O or \ name CB )) or resid 337 or resid 340 or (resid 341 through 342 and (name N or na \ me CA or name C or name O or name CB )) or resid 343 through 350)) selection = (chain 'D' and (resid 1 through 46 or resid 48 through 236 or resid 238 through \ 350)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.060 Set scattering table: 0.040 Process input model: 26.690 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 0.003 0.044 19462 Z= 0.143 Angle : 0.580 7.889 26992 Z= 0.322 Chirality : 0.040 0.159 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 aren 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 covalent geometry : bond 0.00312 (19454) covalent geometry : angle 0.57843 (26988) hydrogen bonds : bond 0.14235 ( 858) hydrogen bonds : angle 6.28212 ( 2350) metal coordination : bond 0.00690 ( 8) metal coordination : angle 3.29504 ( 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 : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.7683 (mmm) cc_final: 0.7423 (mmm) REVERT: B 334 ASP cc_start: 0.5364 (m-30) cc_final: 0.4628 (m-30) REVERT: C 545 VAL cc_start: 0.8341 (p) cc_final: 0.7870 (p) REVERT: C 570 MET cc_start: 0.8546 (ptp) cc_final: 0.8264 (ptp) REVERT: C 883 MET cc_start: 0.8489 (tpp) cc_final: 0.8232 (tpt) REVERT: D 105 ASP cc_start: 0.7465 (p0) cc_final: 0.7185 (p0) REVERT: D 302 MET cc_start: 0.6876 (ppp) cc_final: 0.6615 (ppp) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.1539 time to fit residues: 81.2856 Evaluate side-chains 170 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 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: 20.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN B 173 ASN B 278 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.112163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.077461 restraints weight = 129704.080| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 5.59 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19462 Z= 0.157 Angle : 0.629 7.924 26992 Z= 0.343 Chirality : 0.041 0.196 2953 Planarity : 0.005 0.079 2913 Dihedral : 21.125 99.708 3904 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.01 % Allowed : 10.99 % Favored : 88.00 % 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 aren not related in a simple way. whole: -0.33 (0.19), residues: 1926 helix: 0.88 (0.21), residues: 656 sheet: 0.16 (0.28), residues: 337 loop : -1.17 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 703 TYR 0.017 0.002 TYR D 138 PHE 0.033 0.002 PHE A 435 TRP 0.027 0.002 TRP A 893 HIS 0.015 0.001 HIS D 10 Details of bonding type rmsd covalent geometry : bond 0.00352 (19454) covalent geometry : angle 0.62810 (26988) hydrogen bonds : bond 0.04408 ( 858) hydrogen bonds : angle 4.77625 ( 2350) metal coordination : bond 0.00709 ( 8) metal coordination : angle 3.43916 ( 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 206 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 LEU cc_start: 0.9021 (tt) cc_final: 0.8588 (tp) REVERT: A 578 MET cc_start: 0.8500 (mtm) cc_final: 0.8299 (mtm) REVERT: A 627 MET cc_start: 0.8340 (mmm) cc_final: 0.8025 (mmm) REVERT: A 858 MET cc_start: 0.8477 (mmp) cc_final: 0.8262 (mmp) REVERT: B 58 LYS cc_start: 0.8537 (mptt) cc_final: 0.8294 (mptt) REVERT: C 810 LEU cc_start: 0.8179 (tp) cc_final: 0.7946 (tp) REVERT: C 972 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8192 (ttp80) REVERT: C 984 MET cc_start: 0.8489 (mmm) cc_final: 0.8279 (mmm) REVERT: D 74 TYR cc_start: 0.8406 (m-80) cc_final: 0.8179 (m-80) REVERT: D 105 ASP cc_start: 0.8861 (p0) cc_final: 0.8507 (p0) REVERT: D 284 ARG cc_start: 0.8244 (tpt170) cc_final: 0.8027 (tpp80) outliers start: 15 outliers final: 10 residues processed: 201 average time/residue: 0.1366 time to fit residues: 42.1941 Evaluate side-chains 166 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 933 THR 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 208 VAL Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 900 LYS 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: 1.9990 chunk 175 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 94 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 HIS A 809 GLN ** A 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN B 278 GLN C 406 HIS ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.107875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.073079 restraints weight = 115387.200| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 5.19 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 19462 Z= 0.208 Angle : 0.630 9.121 26992 Z= 0.340 Chirality : 0.042 0.190 2953 Planarity : 0.005 0.070 2913 Dihedral : 21.283 99.261 3904 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.66 % Allowed : 11.64 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.19), residues: 1926 helix: 1.02 (0.21), residues: 653 sheet: 0.12 (0.27), residues: 352 loop : -1.15 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 237 TYR 0.021 0.002 TYR A 805 PHE 0.020 0.002 PHE C 435 TRP 0.030 0.002 TRP B 317 HIS 0.007 0.001 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00476 (19454) covalent geometry : angle 0.62870 (26988) hydrogen bonds : bond 0.04500 ( 858) hydrogen bonds : angle 4.50840 ( 2350) metal coordination : bond 0.00936 ( 8) metal coordination : angle 3.71096 ( 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 178 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 627 MET cc_start: 0.8316 (mmm) cc_final: 0.8000 (mmm) REVERT: A 858 MET cc_start: 0.8474 (mmp) cc_final: 0.8250 (mmp) REVERT: B 58 LYS cc_start: 0.8588 (mptt) cc_final: 0.8271 (mptt) REVERT: C 904 GLU cc_start: 0.8469 (pm20) cc_final: 0.8212 (tp30) REVERT: C 972 ARG cc_start: 0.8731 (ttp80) cc_final: 0.8344 (ttp80) REVERT: D 55 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8825 (tp) REVERT: D 105 ASP cc_start: 0.8880 (p0) cc_final: 0.8529 (p0) REVERT: D 284 ARG cc_start: 0.8342 (tpt170) cc_final: 0.8065 (tpp80) REVERT: D 302 MET cc_start: 0.6939 (ppp) cc_final: 0.6429 (ppp) REVERT: D 322 MET cc_start: 0.7018 (mmm) cc_final: 0.6775 (mmm) outliers start: 26 outliers final: 17 residues processed: 171 average time/residue: 0.1435 time to fit residues: 38.6442 Evaluate side-chains 158 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 862 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 199 optimal weight: 10.0000 chunk 107 optimal weight: 0.0040 chunk 54 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 95 optimal weight: 50.0000 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 ASN B 278 GLN ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.109529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.074293 restraints weight = 154820.777| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 6.04 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19462 Z= 0.139 Angle : 0.576 9.702 26992 Z= 0.311 Chirality : 0.040 0.156 2953 Planarity : 0.004 0.066 2913 Dihedral : 21.268 99.465 3904 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.37 % Allowed : 12.83 % Favored : 85.81 % 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 aren not related in a simple way. whole: -0.13 (0.19), residues: 1926 helix: 1.20 (0.21), residues: 646 sheet: 0.17 (0.28), residues: 350 loop : -1.11 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 442 TYR 0.017 0.001 TYR D 138 PHE 0.018 0.001 PHE B 189 TRP 0.028 0.001 TRP B 317 HIS 0.006 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00313 (19454) covalent geometry : angle 0.57402 (26988) hydrogen bonds : bond 0.03776 ( 858) hydrogen bonds : angle 4.34583 ( 2350) metal coordination : bond 0.00620 ( 8) metal coordination : angle 3.46293 ( 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 177 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.8327 (mmm) cc_final: 0.7991 (mmm) REVERT: B 58 LYS cc_start: 0.8586 (mptt) cc_final: 0.8222 (mptt) REVERT: C 972 ARG cc_start: 0.8732 (ttp80) cc_final: 0.8235 (ttp80) REVERT: C 974 MET cc_start: 0.8587 (mtt) cc_final: 0.8094 (mtm) REVERT: D 105 ASP cc_start: 0.8916 (p0) cc_final: 0.8596 (p0) REVERT: D 302 MET cc_start: 0.6916 (ppp) cc_final: 0.6351 (ppp) REVERT: D 322 MET cc_start: 0.7115 (mmm) cc_final: 0.6867 (mmm) outliers start: 20 outliers final: 18 residues processed: 169 average time/residue: 0.1389 time to fit residues: 36.6789 Evaluate side-chains 162 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 287 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 170 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 189 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 124 optimal weight: 0.0980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN A 990 HIS ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.109328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.074876 restraints weight = 117559.021| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 5.30 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19462 Z= 0.140 Angle : 0.567 10.482 26992 Z= 0.307 Chirality : 0.039 0.154 2953 Planarity : 0.004 0.063 2913 Dihedral : 21.280 100.574 3904 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.72 % Allowed : 13.18 % Favored : 85.10 % 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 aren not related in a simple way. whole: -0.11 (0.19), residues: 1926 helix: 1.21 (0.21), residues: 649 sheet: 0.08 (0.27), residues: 357 loop : -1.06 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 703 TYR 0.017 0.001 TYR A 805 PHE 0.018 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 covalent geometry : bond 0.00317 (19454) covalent geometry : angle 0.56606 (26988) hydrogen bonds : bond 0.03743 ( 858) hydrogen bonds : angle 4.29877 ( 2350) metal coordination : bond 0.00587 ( 8) metal coordination : angle 3.14565 ( 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 176 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 627 MET cc_start: 0.8351 (mmm) cc_final: 0.7999 (mmm) REVERT: A 662 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7865 (tm-30) REVERT: A 983 GLU cc_start: 0.8163 (pt0) cc_final: 0.7876 (pt0) REVERT: B 58 LYS cc_start: 0.8583 (mptt) cc_final: 0.8333 (mptt) REVERT: C 904 GLU cc_start: 0.8501 (pm20) cc_final: 0.8218 (tp30) REVERT: C 972 ARG cc_start: 0.8752 (ttp80) cc_final: 0.8365 (ttp80) REVERT: D 105 ASP cc_start: 0.8876 (p0) cc_final: 0.8572 (p0) REVERT: D 302 MET cc_start: 0.6944 (ppp) cc_final: 0.6371 (ppp) REVERT: D 322 MET cc_start: 0.7020 (mmm) cc_final: 0.6728 (mmm) outliers start: 26 outliers final: 23 residues processed: 163 average time/residue: 0.1387 time to fit residues: 36.2699 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 : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 CYS 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 651 CYS Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 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 91 TYR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 285 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 64 optimal weight: 4.9990 chunk 45 optimal weight: 0.0670 chunk 111 optimal weight: 4.9990 chunk 200 optimal weight: 30.0000 chunk 160 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 HIS ** 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 = 0.3914 r_free = 0.3914 target = 0.107799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.072867 restraints weight = 134308.087| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 5.63 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19462 Z= 0.176 Angle : 0.593 10.875 26992 Z= 0.318 Chirality : 0.040 0.180 2953 Planarity : 0.004 0.063 2913 Dihedral : 21.370 103.457 3904 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.02 % Allowed : 13.36 % Favored : 84.62 % 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 aren not related in a simple way. whole: -0.08 (0.19), residues: 1926 helix: 1.24 (0.21), residues: 650 sheet: 0.16 (0.28), residues: 353 loop : -1.09 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 970 TYR 0.018 0.001 TYR A 805 PHE 0.018 0.002 PHE B 189 TRP 0.029 0.002 TRP B 317 HIS 0.006 0.001 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00401 (19454) covalent geometry : angle 0.59172 (26988) hydrogen bonds : bond 0.04150 ( 858) hydrogen bonds : angle 4.31398 ( 2350) metal coordination : bond 0.00732 ( 8) metal coordination : angle 3.37331 ( 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 171 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.685 Fit side-chains REVERT: A 627 MET cc_start: 0.8303 (mmm) cc_final: 0.7980 (mmm) REVERT: A 662 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8015 (tm-30) REVERT: A 841 MET cc_start: 0.8231 (mmm) cc_final: 0.7896 (mtp) REVERT: A 983 GLU cc_start: 0.8257 (pt0) cc_final: 0.7937 (pt0) REVERT: B 58 LYS cc_start: 0.8637 (mptt) cc_final: 0.8389 (mptt) REVERT: B 162 MET cc_start: 0.8111 (mmm) cc_final: 0.7904 (mmp) REVERT: C 972 ARG cc_start: 0.8774 (ttp80) cc_final: 0.8391 (ttp80) REVERT: D 105 ASP cc_start: 0.8967 (p0) cc_final: 0.8669 (p0) REVERT: D 302 MET cc_start: 0.7053 (ppp) cc_final: 0.6480 (ppp) outliers start: 31 outliers final: 27 residues processed: 157 average time/residue: 0.1361 time to fit residues: 34.4676 Evaluate side-chains 164 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 CYS 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 651 CYS Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 287 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 43 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 148 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 197 optimal weight: 30.0000 chunk 125 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 515 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.110144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.075924 restraints weight = 126980.250| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 5.48 r_work (final): 0.3268 ------------------------------------------------------------------------------- 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 = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19462 Z= 0.127 Angle : 0.581 13.366 26992 Z= 0.308 Chirality : 0.039 0.199 2953 Planarity : 0.004 0.061 2913 Dihedral : 21.325 106.470 3904 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.84 % Allowed : 14.01 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.19), residues: 1926 helix: 1.27 (0.21), residues: 652 sheet: 0.16 (0.27), residues: 372 loop : -1.05 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 237 TYR 0.017 0.001 TYR A 805 PHE 0.018 0.001 PHE B 189 TRP 0.022 0.001 TRP B 317 HIS 0.005 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00284 (19454) covalent geometry : angle 0.58024 (26988) hydrogen bonds : bond 0.03638 ( 858) hydrogen bonds : angle 4.27404 ( 2350) metal coordination : bond 0.00580 ( 8) metal coordination : angle 3.13898 ( 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 172 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.729 Fit side-chains REVERT: A 627 MET cc_start: 0.8413 (mmm) cc_final: 0.8050 (mmm) REVERT: A 662 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7921 (tm-30) REVERT: A 841 MET cc_start: 0.8183 (mmm) cc_final: 0.7761 (mtp) REVERT: A 983 GLU cc_start: 0.8164 (pt0) cc_final: 0.7872 (pt0) REVERT: B 58 LYS cc_start: 0.8595 (mptt) cc_final: 0.8332 (mptt) REVERT: B 162 MET cc_start: 0.8262 (mmm) cc_final: 0.8015 (mmt) REVERT: C 399 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6712 (mm) REVERT: C 606 SER cc_start: 0.9458 (m) cc_final: 0.8364 (p) REVERT: C 972 ARG cc_start: 0.8763 (ttp80) cc_final: 0.7941 (ttt90) REVERT: D 105 ASP cc_start: 0.8963 (p0) cc_final: 0.8647 (p0) REVERT: D 302 MET cc_start: 0.7051 (ppp) cc_final: 0.6454 (ppp) outliers start: 28 outliers final: 23 residues processed: 162 average time/residue: 0.1399 time to fit residues: 36.1772 Evaluate side-chains 161 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 CYS 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 651 CYS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 399 LEU 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 779 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 TYR 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: 7.9990 chunk 179 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 164 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.110197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.075617 restraints weight = 152142.163| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 5.93 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19462 Z= 0.130 Angle : 0.571 12.129 26992 Z= 0.304 Chirality : 0.039 0.198 2953 Planarity : 0.004 0.060 2913 Dihedral : 21.324 110.944 3904 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.14 % Allowed : 13.95 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.19), residues: 1926 helix: 1.33 (0.21), residues: 649 sheet: 0.21 (0.27), residues: 370 loop : -0.98 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 237 TYR 0.017 0.001 TYR A 805 PHE 0.022 0.001 PHE B 189 TRP 0.022 0.001 TRP B 317 HIS 0.007 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00293 (19454) covalent geometry : angle 0.57016 (26988) hydrogen bonds : bond 0.03626 ( 858) hydrogen bonds : angle 4.26506 ( 2350) metal coordination : bond 0.00556 ( 8) metal coordination : angle 2.91620 ( 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 174 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 627 MET cc_start: 0.8362 (mmm) cc_final: 0.8062 (mmm) REVERT: A 662 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 841 MET cc_start: 0.8167 (mmm) cc_final: 0.7855 (mtp) REVERT: A 983 GLU cc_start: 0.8214 (pt0) cc_final: 0.7863 (pt0) REVERT: B 58 LYS cc_start: 0.8587 (mptt) cc_final: 0.8316 (mptt) REVERT: B 162 MET cc_start: 0.8251 (mmm) cc_final: 0.8048 (mmp) REVERT: C 399 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6666 (mm) REVERT: C 606 SER cc_start: 0.9463 (m) cc_final: 0.8916 (p) REVERT: C 841 MET cc_start: 0.8625 (mmt) cc_final: 0.8297 (mmt) REVERT: C 972 ARG cc_start: 0.8795 (ttp80) cc_final: 0.8146 (ttp80) REVERT: D 105 ASP cc_start: 0.8987 (p0) cc_final: 0.8696 (p0) REVERT: D 302 MET cc_start: 0.7179 (ppp) cc_final: 0.6575 (ppp) outliers start: 33 outliers final: 25 residues processed: 160 average time/residue: 0.1414 time to fit residues: 35.9812 Evaluate side-chains 164 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 72 LEU 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 C residue 399 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 101 ASN 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: 9.9990 chunk 59 optimal weight: 0.7980 chunk 149 optimal weight: 0.0070 chunk 202 optimal weight: 30.0000 chunk 173 optimal weight: 0.9980 chunk 85 optimal weight: 40.0000 chunk 78 optimal weight: 7.9990 chunk 62 optimal weight: 0.0050 chunk 98 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 overall best weight: 0.7614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** 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 = 0.3991 r_free = 0.3991 target = 0.111355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.077387 restraints weight = 119873.434| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 5.46 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19462 Z= 0.122 Angle : 0.573 11.774 26992 Z= 0.303 Chirality : 0.039 0.199 2953 Planarity : 0.004 0.059 2913 Dihedral : 21.305 117.392 3904 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.90 % Allowed : 14.13 % Favored : 83.97 % 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 aren not related in a simple way. whole: 0.12 (0.19), residues: 1926 helix: 1.38 (0.21), residues: 649 sheet: 0.28 (0.27), residues: 370 loop : -0.95 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 458 TYR 0.017 0.001 TYR A 805 PHE 0.021 0.001 PHE B 189 TRP 0.020 0.001 TRP B 317 HIS 0.006 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00273 (19454) covalent geometry : angle 0.57228 (26988) hydrogen bonds : bond 0.03427 ( 858) hydrogen bonds : angle 4.21637 ( 2350) metal coordination : bond 0.00560 ( 8) metal coordination : angle 2.80512 ( 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 173 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 627 MET cc_start: 0.8402 (mmm) cc_final: 0.8089 (mmm) REVERT: A 662 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7925 (tm-30) REVERT: A 841 MET cc_start: 0.8136 (mmm) cc_final: 0.7688 (mtp) REVERT: A 983 GLU cc_start: 0.8213 (pt0) cc_final: 0.7857 (pt0) REVERT: B 58 LYS cc_start: 0.8573 (mptt) cc_final: 0.8328 (mttm) REVERT: C 399 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6607 (mm) REVERT: C 606 SER cc_start: 0.9414 (m) cc_final: 0.8424 (p) REVERT: C 841 MET cc_start: 0.8558 (mmt) cc_final: 0.8280 (mmt) REVERT: C 904 GLU cc_start: 0.8516 (pm20) cc_final: 0.8110 (tp30) REVERT: C 972 ARG cc_start: 0.8796 (ttp80) cc_final: 0.8030 (ttt90) REVERT: D 105 ASP cc_start: 0.8952 (p0) cc_final: 0.8675 (p0) REVERT: D 110 MET cc_start: 0.8071 (mmp) cc_final: 0.7810 (mmp) REVERT: D 302 MET cc_start: 0.7154 (ppp) cc_final: 0.6537 (ppp) REVERT: D 320 SER cc_start: 0.8033 (t) cc_final: 0.7612 (t) outliers start: 29 outliers final: 24 residues processed: 160 average time/residue: 0.1412 time to fit residues: 36.4195 Evaluate side-chains 165 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 72 LEU 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 C residue 399 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 101 ASN 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: 0.3980 chunk 132 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 45 optimal weight: 0.0470 chunk 93 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 201 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** 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 = 0.3960 r_free = 0.3960 target = 0.110659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.075797 restraints weight = 156664.413| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 6.16 r_work (final): 0.3282 ------------------------------------------------------------------------------- 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 = 0.23 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 = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19462 Z= 0.120 Angle : 0.576 11.619 26992 Z= 0.304 Chirality : 0.039 0.205 2953 Planarity : 0.004 0.059 2913 Dihedral : 21.307 122.889 3904 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.60 % Allowed : 14.79 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.19), residues: 1926 helix: 1.39 (0.21), residues: 652 sheet: 0.33 (0.28), residues: 370 loop : -0.98 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 442 TYR 0.017 0.001 TYR D 138 PHE 0.024 0.001 PHE B 189 TRP 0.019 0.001 TRP B 317 HIS 0.005 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00269 (19454) covalent geometry : angle 0.57537 (26988) hydrogen bonds : bond 0.03378 ( 858) hydrogen bonds : angle 4.20678 ( 2350) metal coordination : bond 0.00545 ( 8) metal coordination : angle 2.67775 ( 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 168 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 627 MET cc_start: 0.8360 (mmm) cc_final: 0.8057 (mmm) REVERT: A 662 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 841 MET cc_start: 0.8139 (mmm) cc_final: 0.7732 (mtp) REVERT: A 983 GLU cc_start: 0.8203 (pt0) cc_final: 0.7869 (pt0) REVERT: B 58 LYS cc_start: 0.8588 (mptt) cc_final: 0.8338 (mttm) REVERT: C 399 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6648 (mm) REVERT: C 606 SER cc_start: 0.9415 (m) cc_final: 0.8967 (p) REVERT: C 841 MET cc_start: 0.8556 (mmt) cc_final: 0.7863 (mmt) REVERT: C 904 GLU cc_start: 0.8547 (pm20) cc_final: 0.8225 (tp30) REVERT: D 105 ASP cc_start: 0.8919 (p0) cc_final: 0.8662 (p0) REVERT: D 302 MET cc_start: 0.7148 (ppp) cc_final: 0.6516 (ppp) REVERT: D 320 SER cc_start: 0.8143 (t) cc_final: 0.7720 (t) outliers start: 24 outliers final: 22 residues processed: 157 average time/residue: 0.1393 time to fit residues: 35.3864 Evaluate side-chains 161 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 72 LEU 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 C residue 399 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 101 ASN 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 191 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 103 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 193 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3919 r_free = 0.3919 target = 0.108372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.073292 restraints weight = 168364.709| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 6.20 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19462 Z= 0.164 Angle : 0.598 11.438 26992 Z= 0.317 Chirality : 0.040 0.208 2953 Planarity : 0.004 0.059 2913 Dihedral : 21.392 127.798 3904 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.84 % Allowed : 14.79 % Favored : 83.37 % 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 aren not related in a simple way. whole: 0.19 (0.19), residues: 1926 helix: 1.44 (0.21), residues: 647 sheet: 0.35 (0.28), residues: 364 loop : -0.91 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 237 TYR 0.018 0.001 TYR D 138 PHE 0.024 0.001 PHE B 189 TRP 0.025 0.002 TRP B 317 HIS 0.007 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00375 (19454) covalent geometry : angle 0.59660 (26988) hydrogen bonds : bond 0.03842 ( 858) hydrogen bonds : angle 4.24353 ( 2350) metal coordination : bond 0.00639 ( 8) metal coordination : angle 3.02039 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4384.79 seconds wall clock time: 76 minutes 13.23 seconds (4573.23 seconds total)