Starting phenix.real_space_refine on Fri Feb 16 23:16:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oes_20036/02_2024/6oes_20036.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oes_20036/02_2024/6oes_20036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oes_20036/02_2024/6oes_20036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oes_20036/02_2024/6oes_20036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oes_20036/02_2024/6oes_20036.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oes_20036/02_2024/6oes_20036.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.008 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 126 5.49 5 S 103 5.16 5 C 10243 2.51 5 N 2954 2.21 5 O 3399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 576": "OE1" <-> "OE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A GLU 662": "OE1" <-> "OE2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "A GLU 824": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A GLU 861": "OE1" <-> "OE2" Residue "A GLU 877": "OE1" <-> "OE2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A GLU 929": "OE1" <-> "OE2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A ARG 949": "NH1" <-> "NH2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "C ARG 486": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C GLU 649": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C GLU 680": "OE1" <-> "OE2" Residue "C GLU 690": "OE1" <-> "OE2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C GLU 758": "OE1" <-> "OE2" Residue "C GLU 770": "OE1" <-> "OE2" Residue "C GLU 771": "OE1" <-> "OE2" Residue "C ARG 773": "NH1" <-> "NH2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 828": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" Residue "C ARG 848": "NH1" <-> "NH2" Residue "C GLU 983": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D ARG 349": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16829 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4411 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 548, 4405 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 522} Conformer: "B" Number of residues, atoms: 548, 4405 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 522} bond proxies already assigned to first conformer: 4495 Chain: "B" Number of atoms: 2708 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 344, 2679 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 344, 2679 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2714 Chain: "C" Number of atoms: 4397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4397 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 521} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2687 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 345, 2677 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 345, 2677 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2733 Chain: "F" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 722 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "J" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "I" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "G" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 695 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "L" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 307 Classifications: {'DNA': 15} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 14} Chain: "M" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} 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} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2074 SG CYS A 727 77.316 60.140 63.274 1.00 35.24 S ATOM 2095 SG CYS A 730 79.566 57.590 65.579 1.00 38.04 S ATOM 9193 SG CYS C 727 24.484 103.311 59.410 1.00 35.23 S ATOM 9214 SG CYS C 730 21.682 105.123 61.104 1.00 37.28 S Residues with excluded nonbonded symmetry interactions: 7 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 AASN B 268 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 268 " 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 J 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT J 15 " occ=0.85 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: 13.57, per 1000 atoms: 0.81 Number of scatterers: 16829 At special positions: 0 Unit cell: (105.93, 159.43, 119.84, 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 103 16.00 P 126 15.00 O 3399 8.00 N 2954 7.00 C 10243 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 - 3.50 Amino acid : False - 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: 7.44 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " 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 942 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " Number of angles added : 4 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3350 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 17 sheets defined 34.2% alpha, 24.3% beta 61 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 5.83 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 493 removed outlier: 3.787A pdb=" N LYS A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 558 through 581 removed outlier: 5.440A pdb=" N GLU A 572 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 682 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.648A pdb=" N GLN A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) 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 841 removed outlier: 3.658A pdb=" N ARG A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'A' and resid 859 through 868 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 908 Processing helix chain 'A' and resid 908 through 923 Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.614A pdb=" N HIS A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.663A pdb=" N ARG A 969 " --> pdb=" O ASN A 965 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 970 " --> pdb=" O LYS A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.537A pdb=" N ASP A 986 " --> pdb=" O TYR A 982 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1001 removed outlier: 3.593A pdb=" N LYS A1001 " --> pdb=" O LYS A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1005 removed outlier: 3.621A pdb=" N ALA A1005 " --> pdb=" O PHE A1002 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1002 through 1005' Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.661A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 15 " --> pdb=" O ILE B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 15' Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.838A pdb=" N TRP B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.531A pdb=" N LYS C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 570 through 581 removed outlier: 3.503A pdb=" N GLN C 581 " --> pdb=" O GLY C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 813 removed outlier: 3.658A pdb=" N GLY C 813 " --> pdb=" O GLN C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 840 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.568A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 895 removed outlier: 3.630A pdb=" N HIS C 876 " --> pdb=" O SER C 872 " (cutoff:3.500A) Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 removed outlier: 3.518A pdb=" N CYS C 902 " --> pdb=" O PRO C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 908 removed outlier: 3.726A pdb=" N GLN C 908 " --> pdb=" O GLU C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.540A pdb=" N HIS C 942 " --> pdb=" O LYS C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 950 Processing helix chain 'C' and resid 958 through 975 removed outlier: 4.050A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 995 removed outlier: 3.546A pdb=" N ASP C 986 " --> pdb=" O TYR C 982 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 995 " --> pdb=" O HIS C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1001 Processing helix chain 'C' and resid 1002 through 1005 removed outlier: 3.688A pdb=" N ALA C1005 " --> pdb=" O PHE C1002 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1002 through 1005' Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.662A pdb=" N LEU D 14 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.838A pdb=" N TRP D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 520 removed outlier: 3.702A pdb=" N ILE A 694 " --> pdb=" O MET A 691 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 520 removed outlier: 3.702A pdb=" N ILE A 694 " --> pdb=" O MET A 691 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.447A 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: 3.564A pdb=" N SER B 2 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 8 removed outlier: 6.783A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 58 " --> pdb=" O AHIS B 47 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 80 removed outlier: 4.268A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.879A 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: 6.719A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS B 191 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER B 141 " --> pdb=" O PHE B 156 " (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: 4.010A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 267 removed outlier: 3.511A pdb=" N THR B 266 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.714A 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: 3.544A pdb=" N ILE C 694 " --> pdb=" O MET C 691 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 705 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.544A pdb=" N ILE C 694 " --> pdb=" O MET C 691 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 705 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C 632 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG C 628 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 636 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 24 removed outlier: 4.189A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 58 " --> pdb=" O AHIS D 47 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LEU D 55 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 2 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL D 8 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N PHE D 343 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 318 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 80 removed outlier: 4.268A pdb=" N ILE D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.718A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS D 191 " --> pdb=" O ASP D 186 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB7, first strand: chain 'D' and resid 208 through 211 removed outlier: 4.011A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 262 through 267 removed outlier: 3.510A pdb=" N THR D 266 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU D 298 " --> pdb=" O SER D 291 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 157 hydrogen bonds 314 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 8.26 Time building geometry restraints manager: 7.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3963 1.33 - 1.45: 4431 1.45 - 1.58: 8674 1.58 - 1.70: 249 1.70 - 1.82: 157 Bond restraints: 17474 Sorted by residual: bond pdb=" N GLU B 341 " pdb=" CA GLU B 341 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.00e+01 bond pdb=" N GLU D 341 " pdb=" CA GLU D 341 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.16e+00 bond pdb=" N ASN D 335 " pdb=" CA ASN D 335 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.05e+00 bond pdb=" N LYS B 336 " pdb=" CA LYS B 336 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.68e+00 bond pdb=" O3' DC L 17 " pdb=" P DA L 18 " ideal model delta sigma weight residual 1.607 1.565 0.042 1.50e-02 4.44e+03 7.87e+00 ... (remaining 17469 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.47: 907 105.47 - 112.64: 9120 112.64 - 119.81: 5910 119.81 - 126.98: 7746 126.98 - 134.15: 495 Bond angle restraints: 24178 Sorted by residual: angle pdb=" CB GLN D 201 " pdb=" CG GLN D 201 " pdb=" CD GLN D 201 " ideal model delta sigma weight residual 112.60 122.00 -9.40 1.70e+00 3.46e-01 3.06e+01 angle pdb=" CB GLN B 201 " pdb=" CG GLN B 201 " pdb=" CD GLN B 201 " ideal model delta sigma weight residual 112.60 121.99 -9.39 1.70e+00 3.46e-01 3.05e+01 angle pdb=" C ASP C 569 " pdb=" CA ASP C 569 " pdb=" CB ASP C 569 " ideal model delta sigma weight residual 110.01 119.06 -9.05 1.80e+00 3.09e-01 2.53e+01 angle pdb=" CA GLU D 301 " pdb=" CB GLU D 301 " pdb=" CG GLU D 301 " ideal model delta sigma weight residual 114.10 123.66 -9.56 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CA GLU B 301 " pdb=" CB GLU B 301 " pdb=" CG GLU B 301 " ideal model delta sigma weight residual 114.10 123.64 -9.54 2.00e+00 2.50e-01 2.28e+01 ... (remaining 24173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8407 17.90 - 35.79: 1039 35.79 - 53.69: 571 53.69 - 71.58: 110 71.58 - 89.48: 15 Dihedral angle restraints: 10142 sinusoidal: 4936 harmonic: 5206 Sorted by residual: dihedral pdb=" C ASP C 569 " pdb=" N ASP C 569 " pdb=" CA ASP C 569 " pdb=" CB ASP C 569 " ideal model delta harmonic sigma weight residual -122.60 -136.16 13.56 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" C ASN D 335 " pdb=" N ASN D 335 " pdb=" CA ASN D 335 " pdb=" CB ASN D 335 " ideal model delta harmonic sigma weight residual -122.60 -133.49 10.89 0 2.50e+00 1.60e-01 1.90e+01 dihedral pdb=" N ASN D 335 " pdb=" C ASN D 335 " pdb=" CA ASN D 335 " pdb=" CB ASN D 335 " ideal model delta harmonic sigma weight residual 122.80 133.37 -10.57 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 10139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2375 0.083 - 0.165: 251 0.165 - 0.248: 13 0.248 - 0.330: 0 0.330 - 0.413: 2 Chirality restraints: 2641 Sorted by residual: chirality pdb=" CA ASP C 569 " pdb=" N ASP C 569 " pdb=" C ASP C 569 " pdb=" CB ASP C 569 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA ASN D 335 " pdb=" N ASN D 335 " pdb=" C ASN D 335 " pdb=" CB ASN D 335 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA LYS D 336 " pdb=" N LYS D 336 " pdb=" C LYS D 336 " pdb=" CB LYS D 336 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 2638 not shown) Planarity restraints: 2672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 317 " 0.018 2.00e-02 2.50e+03 1.68e-02 7.08e+00 pdb=" CG TRP D 317 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP D 317 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 317 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 317 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 317 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 317 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 317 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 317 " 0.018 2.00e-02 2.50e+03 1.67e-02 6.97e+00 pdb=" CG TRP B 317 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 317 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 317 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 317 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 317 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 317 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 317 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 317 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 331 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C ILE D 331 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE D 331 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO D 332 " 0.013 2.00e-02 2.50e+03 ... (remaining 2669 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2485 2.76 - 3.30: 13805 3.30 - 3.83: 29361 3.83 - 4.37: 35133 4.37 - 4.90: 58523 Nonbonded interactions: 139307 Sorted by model distance: nonbonded pdb=" O SER B 340 " pdb=" OG SER B 340 " model vdw 2.226 2.440 nonbonded pdb=" N GLY B 333 " pdb=" O ALA B 342 " model vdw 2.263 2.520 nonbonded pdb=" OD1 ASP B 143 " pdb=" OG SER B 209 " model vdw 2.275 2.440 nonbonded pdb=" OD1 ASP D 143 " pdb=" OG SER D 209 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR C 805 " pdb=" OD1 ASP C 834 " model vdw 2.314 2.440 ... (remaining 139302 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 461 through 906 or resid 908 through 1006 or (resid 1007 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1101 through 11 \ 02)) selection = (chain 'C' and (resid 461 through 906 or resid 908 through 1007 or resid 1101 th \ rough 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 267 or resid 269 through 333 or (resid 334 and (name N or name C \ A or name C or name O or name CB )) or resid 335 through 350)) selection = (chain 'D' and (resid 1 through 46 or resid 48 through 236 or resid 238 through \ 267 or resid 269 through 350)) } ncs_group { reference = (chain 'F' and (resid 19 through 20 or resid 22 through 32 or resid 34 through 5 \ 0)) selection = (chain 'G' and (resid 30 through 31 or resid 33 through 43 or resid 45 through 6 \ 1)) } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 1.890 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: 5.300 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 61.830 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.005 0.074 17474 Z= 0.336 Angle : 0.768 9.700 24178 Z= 0.446 Chirality : 0.050 0.413 2641 Planarity : 0.006 0.055 2672 Dihedral : 19.675 89.477 6792 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.39 % Favored : 96.44 % Rotamer: Outliers : 2.87 % Allowed : 4.47 % Favored : 92.66 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.16), residues: 1787 helix: -2.15 (0.15), residues: 558 sheet: -1.02 (0.26), residues: 349 loop : -2.43 (0.17), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP D 317 HIS 0.005 0.001 HIS A 836 PHE 0.016 0.002 PHE A 916 TYR 0.019 0.002 TYR A 757 ARG 0.004 0.000 ARG C 734 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 253 time to evaluate : 2.054 Fit side-chains REVERT: A 602 MET cc_start: 0.8385 (mtp) cc_final: 0.8082 (mtp) REVERT: A 970 ARG cc_start: 0.8261 (ttt180) cc_final: 0.8056 (ttt180) REVERT: B 22 MET cc_start: 0.8383 (ptp) cc_final: 0.8134 (ptp) REVERT: B 223 SER cc_start: 0.8891 (OUTLIER) cc_final: 0.8529 (m) REVERT: B 347 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8177 (m) REVERT: C 568 MET cc_start: 0.8205 (mmm) cc_final: 0.7989 (tpt) REVERT: C 617 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7490 (mt-10) REVERT: C 649 GLU cc_start: 0.7847 (pm20) cc_final: 0.7613 (pm20) REVERT: C 889 MET cc_start: 0.8490 (mtp) cc_final: 0.8137 (mtp) REVERT: D 22 MET cc_start: 0.8876 (ptp) cc_final: 0.8649 (ptp) REVERT: D 114 CYS cc_start: 0.7703 (p) cc_final: 0.7457 (p) REVERT: D 300 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7837 (m) outliers start: 43 outliers final: 11 residues processed: 282 average time/residue: 0.3366 time to fit residues: 137.1838 Evaluate side-chains 176 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 335 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 95 optimal weight: 0.0370 chunk 75 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 750 HIS A 753 ASN A 961 ASN B 54 HIS B 101 ASN B 181 HIS ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 HIS C 820 ASN C 961 ASN C 965 ASN C1004 ASN D 54 HIS D 181 HIS D 268 ASN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17474 Z= 0.183 Angle : 0.536 7.407 24178 Z= 0.299 Chirality : 0.041 0.173 2641 Planarity : 0.005 0.050 2672 Dihedral : 21.033 67.047 3334 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.82 % Favored : 97.01 % Rotamer: Outliers : 1.53 % Allowed : 9.58 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.19), residues: 1787 helix: 0.19 (0.21), residues: 567 sheet: -0.16 (0.28), residues: 334 loop : -1.71 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 317 HIS 0.003 0.001 HIS C 990 PHE 0.026 0.001 PHE A 911 TYR 0.017 0.001 TYR A 559 ARG 0.008 0.000 ARG C 494 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 1.618 Fit side-chains REVERT: A 602 MET cc_start: 0.8445 (mtp) cc_final: 0.8180 (mtp) REVERT: A 828 ARG cc_start: 0.7052 (tpp80) cc_final: 0.6844 (mmm160) REVERT: B 339 MET cc_start: 0.5502 (OUTLIER) cc_final: 0.5296 (mtp) REVERT: C 649 GLU cc_start: 0.7827 (pm20) cc_final: 0.7594 (pm20) REVERT: C 858 MET cc_start: 0.8458 (mmt) cc_final: 0.8164 (mmp) REVERT: C 889 MET cc_start: 0.8476 (mtp) cc_final: 0.8056 (mtt) REVERT: D 22 MET cc_start: 0.8745 (ptp) cc_final: 0.8470 (ptm) REVERT: D 278 GLN cc_start: 0.7914 (mt0) cc_final: 0.7468 (mm-40) outliers start: 22 outliers final: 14 residues processed: 196 average time/residue: 0.3125 time to fit residues: 90.7163 Evaluate side-chains 164 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 317 TRP Chi-restraints excluded: chain D residue 326 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.0060 chunk 52 optimal weight: 2.9990 chunk 140 optimal weight: 0.0980 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN A 766 HIS ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN D 52 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17474 Z= 0.226 Angle : 0.535 7.994 24178 Z= 0.295 Chirality : 0.041 0.173 2641 Planarity : 0.004 0.042 2672 Dihedral : 21.076 72.210 3323 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 1.85 % Allowed : 11.75 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 1787 helix: 0.92 (0.22), residues: 568 sheet: 0.02 (0.27), residues: 349 loop : -1.43 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 317 HIS 0.005 0.001 HIS C 990 PHE 0.027 0.001 PHE A 911 TYR 0.015 0.001 TYR A 757 ARG 0.005 0.000 ARG C 494 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.676 Fit side-chains REVERT: A 602 MET cc_start: 0.8408 (mtp) cc_final: 0.8076 (mtp) REVERT: A 828 ARG cc_start: 0.7129 (tpp80) cc_final: 0.6904 (mmm160) REVERT: A 1003 MET cc_start: 0.8821 (mmm) cc_final: 0.8107 (mmm) REVERT: B 339 MET cc_start: 0.5941 (OUTLIER) cc_final: 0.5626 (mtp) REVERT: C 649 GLU cc_start: 0.7851 (pm20) cc_final: 0.7624 (pm20) REVERT: C 889 MET cc_start: 0.8512 (mtp) cc_final: 0.8095 (mtt) outliers start: 27 outliers final: 18 residues processed: 179 average time/residue: 0.3003 time to fit residues: 80.7040 Evaluate side-chains 168 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.0570 chunk 127 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8500 ------------------------------------------------------------------------------- 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** B 4 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN D 101 ASN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17474 Z= 0.197 Angle : 0.518 8.924 24178 Z= 0.285 Chirality : 0.040 0.169 2641 Planarity : 0.004 0.041 2672 Dihedral : 21.011 75.001 3320 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.56 % Rotamer: Outliers : 1.92 % Allowed : 12.39 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1787 helix: 1.24 (0.22), residues: 568 sheet: 0.30 (0.28), residues: 334 loop : -1.30 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 317 HIS 0.004 0.001 HIS C 990 PHE 0.028 0.001 PHE A 911 TYR 0.015 0.001 TYR A 757 ARG 0.006 0.000 ARG C 494 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 1.708 Fit side-chains REVERT: A 602 MET cc_start: 0.8369 (mtp) cc_final: 0.8041 (mtp) REVERT: A 828 ARG cc_start: 0.7063 (tpp80) cc_final: 0.6849 (mmm160) REVERT: B 49 ASP cc_start: 0.7049 (t70) cc_final: 0.6549 (t70) REVERT: B 148 ARG cc_start: 0.7502 (mmt90) cc_final: 0.7256 (mmt90) REVERT: B 339 MET cc_start: 0.6067 (mtt) cc_final: 0.5762 (mtp) REVERT: C 649 GLU cc_start: 0.7822 (pm20) cc_final: 0.7592 (pm20) REVERT: C 889 MET cc_start: 0.8486 (mtp) cc_final: 0.8078 (mtt) REVERT: D 186 ASP cc_start: 0.7921 (t70) cc_final: 0.7574 (t70) REVERT: D 188 GLU cc_start: 0.7446 (mp0) cc_final: 0.7244 (mp0) outliers start: 28 outliers final: 21 residues processed: 177 average time/residue: 0.3218 time to fit residues: 84.2198 Evaluate side-chains 173 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 161 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** C 961 ASN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17474 Z= 0.221 Angle : 0.522 9.452 24178 Z= 0.286 Chirality : 0.041 0.169 2641 Planarity : 0.004 0.040 2672 Dihedral : 20.991 76.131 3316 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 1.85 % Allowed : 13.09 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1787 helix: 1.45 (0.23), residues: 562 sheet: 0.44 (0.28), residues: 338 loop : -1.19 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 317 HIS 0.004 0.001 HIS C 990 PHE 0.028 0.001 PHE A 911 TYR 0.015 0.001 TYR A 757 ARG 0.009 0.000 ARG C 494 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.874 Fit side-chains REVERT: A 602 MET cc_start: 0.8439 (mtp) cc_final: 0.8140 (mtp) REVERT: B 51 LYS cc_start: 0.7560 (ptpp) cc_final: 0.7294 (mtpp) REVERT: B 55 LEU cc_start: 0.9104 (tp) cc_final: 0.8866 (tp) REVERT: B 148 ARG cc_start: 0.7526 (mmt90) cc_final: 0.7294 (mmt90) REVERT: B 339 MET cc_start: 0.6034 (mtt) cc_final: 0.5729 (mtp) REVERT: C 649 GLU cc_start: 0.7819 (pm20) cc_final: 0.7598 (pm20) REVERT: C 889 MET cc_start: 0.8461 (mtp) cc_final: 0.8080 (mtt) REVERT: C 968 PHE cc_start: 0.8818 (t80) cc_final: 0.8567 (t80) REVERT: D 186 ASP cc_start: 0.7890 (t70) cc_final: 0.7477 (t70) REVERT: D 278 GLN cc_start: 0.7978 (mt0) cc_final: 0.7569 (mm-40) outliers start: 27 outliers final: 23 residues processed: 182 average time/residue: 0.3193 time to fit residues: 86.0340 Evaluate side-chains 175 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.1980 chunk 94 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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** C 961 ASN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17474 Z= 0.159 Angle : 0.493 10.321 24178 Z= 0.271 Chirality : 0.039 0.163 2641 Planarity : 0.004 0.039 2672 Dihedral : 20.846 77.400 3316 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 1.72 % Allowed : 13.86 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1787 helix: 1.65 (0.23), residues: 562 sheet: 0.64 (0.29), residues: 331 loop : -1.08 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 317 HIS 0.003 0.001 HIS C 990 PHE 0.030 0.001 PHE A 911 TYR 0.015 0.001 TYR A 757 ARG 0.009 0.000 ARG C 494 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.901 Fit side-chains REVERT: A 520 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7372 (mt0) REVERT: A 602 MET cc_start: 0.8488 (mtp) cc_final: 0.8204 (mtp) REVERT: B 51 LYS cc_start: 0.7559 (ptpp) cc_final: 0.7351 (mtpp) REVERT: B 55 LEU cc_start: 0.9084 (tp) cc_final: 0.8835 (tp) REVERT: B 148 ARG cc_start: 0.7522 (mmt90) cc_final: 0.7294 (mmt90) REVERT: B 339 MET cc_start: 0.5851 (mtt) cc_final: 0.5514 (mtp) REVERT: C 649 GLU cc_start: 0.7760 (pm20) cc_final: 0.7527 (pm20) REVERT: C 889 MET cc_start: 0.8376 (mtp) cc_final: 0.8007 (mtt) REVERT: C 968 PHE cc_start: 0.8750 (t80) cc_final: 0.8506 (t80) REVERT: D 186 ASP cc_start: 0.7752 (t70) cc_final: 0.7509 (t70) outliers start: 24 outliers final: 15 residues processed: 187 average time/residue: 0.3125 time to fit residues: 87.0449 Evaluate side-chains 165 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN A 800 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17474 Z= 0.199 Angle : 0.512 10.181 24178 Z= 0.280 Chirality : 0.040 0.167 2641 Planarity : 0.004 0.039 2672 Dihedral : 20.876 78.511 3315 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 2.17 % Allowed : 13.92 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1787 helix: 1.69 (0.23), residues: 562 sheet: 0.74 (0.29), residues: 324 loop : -1.01 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 317 HIS 0.004 0.001 HIS C 990 PHE 0.029 0.001 PHE A 911 TYR 0.014 0.001 TYR A 757 ARG 0.008 0.000 ARG C 494 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 1.751 Fit side-chains REVERT: A 520 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7385 (mt0) REVERT: A 602 MET cc_start: 0.8491 (mtp) cc_final: 0.8215 (mtp) REVERT: B 55 LEU cc_start: 0.9105 (tp) cc_final: 0.8842 (tp) REVERT: B 148 ARG cc_start: 0.7520 (mmt90) cc_final: 0.7278 (mmt90) REVERT: B 339 MET cc_start: 0.5826 (mtt) cc_final: 0.5547 (mtp) REVERT: C 617 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7475 (mt-10) REVERT: C 649 GLU cc_start: 0.7744 (pm20) cc_final: 0.7514 (pm20) REVERT: C 848 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7816 (mtt180) REVERT: C 889 MET cc_start: 0.8385 (mtp) cc_final: 0.8040 (mtt) REVERT: D 186 ASP cc_start: 0.7789 (t70) cc_final: 0.7532 (t70) outliers start: 31 outliers final: 27 residues processed: 180 average time/residue: 0.3165 time to fit residues: 84.5894 Evaluate side-chains 177 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** C 961 ASN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17474 Z= 0.171 Angle : 0.500 10.626 24178 Z= 0.274 Chirality : 0.040 0.165 2641 Planarity : 0.004 0.039 2672 Dihedral : 20.842 79.284 3315 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 1.92 % Allowed : 14.18 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1787 helix: 1.77 (0.23), residues: 562 sheet: 0.81 (0.28), residues: 336 loop : -0.92 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 317 HIS 0.003 0.001 HIS C 990 PHE 0.028 0.001 PHE A 911 TYR 0.015 0.001 TYR A 757 ARG 0.007 0.000 ARG C 529 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 1.908 Fit side-chains REVERT: A 520 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7377 (mt0) REVERT: A 602 MET cc_start: 0.8488 (mtp) cc_final: 0.8226 (mtp) REVERT: B 55 LEU cc_start: 0.9101 (tp) cc_final: 0.8810 (tp) REVERT: B 148 ARG cc_start: 0.7519 (mmt90) cc_final: 0.7279 (mmt90) REVERT: B 339 MET cc_start: 0.5788 (mtt) cc_final: 0.5508 (mtp) REVERT: C 617 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7441 (mt-10) REVERT: C 649 GLU cc_start: 0.7740 (pm20) cc_final: 0.7504 (pm20) REVERT: C 889 MET cc_start: 0.8374 (mtp) cc_final: 0.8037 (mtt) REVERT: D 186 ASP cc_start: 0.7766 (t70) cc_final: 0.7491 (t70) outliers start: 27 outliers final: 24 residues processed: 173 average time/residue: 0.3073 time to fit residues: 79.5181 Evaluate side-chains 173 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 158 optimal weight: 0.3980 chunk 166 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 800 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17474 Z= 0.177 Angle : 0.497 10.642 24178 Z= 0.272 Chirality : 0.040 0.164 2641 Planarity : 0.004 0.039 2672 Dihedral : 20.826 80.819 3315 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 2.11 % Allowed : 13.98 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1787 helix: 1.75 (0.23), residues: 568 sheet: 0.92 (0.29), residues: 324 loop : -0.86 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 317 HIS 0.003 0.001 HIS C 990 PHE 0.030 0.001 PHE A 911 TYR 0.014 0.001 TYR A 757 ARG 0.008 0.000 ARG C 529 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 1.798 Fit side-chains REVERT: A 520 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7381 (mt0) REVERT: A 602 MET cc_start: 0.8484 (mtp) cc_final: 0.8246 (mtp) REVERT: B 148 ARG cc_start: 0.7532 (mmt90) cc_final: 0.7290 (mmt90) REVERT: C 617 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7453 (mt-10) REVERT: C 649 GLU cc_start: 0.7738 (pm20) cc_final: 0.7500 (pm20) REVERT: C 889 MET cc_start: 0.8364 (mtp) cc_final: 0.8039 (mtt) REVERT: D 186 ASP cc_start: 0.7746 (t70) cc_final: 0.7473 (t70) outliers start: 30 outliers final: 26 residues processed: 183 average time/residue: 0.3167 time to fit residues: 86.3235 Evaluate side-chains 175 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 122 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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** C 961 ASN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17474 Z= 0.190 Angle : 0.507 10.627 24178 Z= 0.277 Chirality : 0.040 0.165 2641 Planarity : 0.004 0.039 2672 Dihedral : 20.863 81.678 3315 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.44 % Favored : 96.50 % Rotamer: Outliers : 2.04 % Allowed : 14.24 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1787 helix: 1.73 (0.23), residues: 568 sheet: 0.92 (0.29), residues: 336 loop : -0.84 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 317 HIS 0.004 0.001 HIS C 990 PHE 0.030 0.001 PHE A 911 TYR 0.014 0.001 TYR A 757 ARG 0.010 0.000 ARG C 529 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.795 Fit side-chains REVERT: A 520 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7376 (mt0) REVERT: A 602 MET cc_start: 0.8483 (mtp) cc_final: 0.8257 (mtp) REVERT: A 636 GLN cc_start: 0.7851 (mp10) cc_final: 0.7558 (mp10) REVERT: B 148 ARG cc_start: 0.7543 (mmt90) cc_final: 0.7298 (mmt90) REVERT: C 617 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7466 (mt-10) REVERT: C 649 GLU cc_start: 0.7703 (pm20) cc_final: 0.7477 (pm20) REVERT: C 889 MET cc_start: 0.8367 (mtp) cc_final: 0.8047 (mtt) REVERT: D 186 ASP cc_start: 0.7762 (t70) cc_final: 0.7366 (t70) outliers start: 29 outliers final: 27 residues processed: 176 average time/residue: 0.3070 time to fit residues: 80.6003 Evaluate side-chains 180 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 151 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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** C 961 ASN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 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 = 0.3645 r_free = 0.3645 target = 0.134051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.107200 restraints weight = 56264.286| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.55 r_work: 0.3068 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17474 Z= 0.171 Angle : 0.502 10.993 24178 Z= 0.274 Chirality : 0.040 0.164 2641 Planarity : 0.004 0.039 2672 Dihedral : 20.851 81.922 3315 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 1.98 % Allowed : 14.30 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1787 helix: 1.76 (0.23), residues: 568 sheet: 0.89 (0.28), residues: 347 loop : -0.78 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 317 HIS 0.003 0.001 HIS C 990 PHE 0.030 0.001 PHE A 911 TYR 0.014 0.001 TYR A 757 ARG 0.009 0.000 ARG C 529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3411.56 seconds wall clock time: 62 minutes 49.59 seconds (3769.59 seconds total)