Starting phenix.real_space_refine on Wed Apr 10 11:49:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeo_20032/04_2024/6oeo_20032.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeo_20032/04_2024/6oeo_20032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeo_20032/04_2024/6oeo_20032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeo_20032/04_2024/6oeo_20032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeo_20032/04_2024/6oeo_20032.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeo_20032/04_2024/6oeo_20032.pdb" } resolution = 3.69 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 2 6.06 5 P 204 5.49 5 S 108 5.16 5 C 11687 2.51 5 N 3450 2.21 5 O 4061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A GLU 662": "OE1" <-> "OE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 838": "NH1" <-> "NH2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 915": "NH1" <-> "NH2" Residue "A ARG 927": "NH1" <-> "NH2" Residue "A ARG 969": "NH1" <-> "NH2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 446": "NH1" <-> "NH2" Residue "C ARG 471": "NH1" <-> "NH2" Residue "C ARG 494": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "C ARG 558": "NH1" <-> "NH2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C GLU 649": "OE1" <-> "OE2" Residue "C ARG 773": "NH1" <-> "NH2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" Residue "C ARG 848": "NH1" <-> "NH2" Residue "C ARG 875": "NH1" <-> "NH2" Residue "C ARG 915": "NH1" <-> "NH2" Residue "C PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 927": "NH1" <-> "NH2" Residue "C ARG 970": "NH1" <-> "NH2" Residue "C ARG 977": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19516 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 608, 4815 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 582} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Conformer: "B" Number of residues, atoms: 608, 4815 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 582} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 bond proxies already assigned to first conformer: 4912 Chain: "B" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2673 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4863 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 590} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2674 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 938 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 936 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "G" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1154 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1171 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "N" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 283 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2547 SG CYS A 727 86.774 49.596 96.475 1.00 81.65 S ATOM 2568 SG CYS A 730 89.334 47.558 97.645 1.00 85.67 S ATOM 10071 SG CYS C 727 28.937 105.793 98.885 1.00 63.74 S ATOM 10092 SG CYS C 730 26.645 107.873 100.371 1.00 63.96 S Time building chain proxies: 13.30, per 1000 atoms: 0.68 Number of scatterers: 19516 At special positions: 0 Unit cell: (117.7, 159.43, 163.71, 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 4 19.99 S 108 16.00 P 204 15.00 O 4061 8.00 N 3450 7.00 C 11687 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: 9.89 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1103 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 727 " pdb=" ZN C1103 " pdb="ZN ZN C1103 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1103 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 727 " Number of angles added : 4 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3686 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 19 sheets defined 37.6% alpha, 21.2% beta 96 base pairs and 151 stacking pairs defined. Time for finding SS restraints: 7.97 Creating SS restraints... Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 408 through 422 Processing helix chain 'A' and resid 426 through 442 removed outlier: 4.185A pdb=" N ARG A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.765A pdb=" N ALA A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.602A pdb=" N CYS A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 493 Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.656A pdb=" N ALA A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 removed outlier: 3.845A pdb=" N SER A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 removed outlier: 3.698A pdb=" N GLY A 577 " --> pdb=" O ASP A 573 " (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 708 through 716 removed outlier: 3.674A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 716 " --> pdb=" O VAL A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.658A pdb=" N ASN A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 removed outlier: 4.167A pdb=" N ASP A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 813 removed outlier: 3.975A pdb=" N GLY A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 841 Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 859 through 870 Processing helix chain 'A' and resid 873 through 890 removed outlier: 3.973A pdb=" N GLU A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 895 Processing helix chain 'A' and resid 904 through 923 removed outlier: 4.682A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE A 916 " --> pdb=" O ASN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 942 removed outlier: 4.049A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 removed outlier: 4.337A pdb=" N GLU A 948 " --> pdb=" O PRO A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 973 removed outlier: 3.663A pdb=" N ASN A 965 " --> pdb=" O ASN A 961 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 968 " --> pdb=" O GLY A 964 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 969 " --> pdb=" O ASN A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 995 Processing helix chain 'A' and resid 999 through 1004 removed outlier: 3.538A pdb=" N MET A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.859A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 402 through 423 removed outlier: 4.920A pdb=" N GLU C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 441 Processing helix chain 'C' and resid 444 through 455 removed outlier: 3.763A pdb=" N ALA C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 500 through 508 removed outlier: 4.216A pdb=" N ALA C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 664 through 682 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 715 Processing helix chain 'C' and resid 733 through 740 removed outlier: 3.711A pdb=" N SER C 738 " --> pdb=" O ARG C 734 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 814 Processing helix chain 'C' and resid 824 through 842 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 868 removed outlier: 4.047A pdb=" N GLU C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 902 through 923 removed outlier: 3.503A pdb=" N LEU C 906 " --> pdb=" O CYS C 902 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE C 911 " --> pdb=" O CYS C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.781A pdb=" N HIS C 937 " --> pdb=" O THR C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.685A pdb=" N ALA C 957 " --> pdb=" O GLY C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 963 removed outlier: 3.645A pdb=" N SER C 963 " --> pdb=" O GLU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 975 removed outlier: 4.381A pdb=" N LEU C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 995 Processing helix chain 'C' and resid 999 through 1004 removed outlier: 4.375A pdb=" N MET C1003 " --> pdb=" O LEU C 999 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.997A pdb=" N LEU D 14 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 334 through 338 Processing helix chain 'N' and resid 102 through 117 Proline residue: N 111 - end of helix removed outlier: 3.893A pdb=" N HIS N 117 " --> pdb=" O ILE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 135 Processing helix chain 'N' and resid 141 through 155 removed outlier: 3.728A pdb=" N GLU N 145 " --> pdb=" O LYS N 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 520 removed outlier: 7.058A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR A 707 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU A 632 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 628 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS A 596 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL A 626 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER A 598 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE A 624 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 520 removed outlier: 7.058A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR A 707 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU A 632 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 628 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS A 596 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL A 626 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER A 598 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE A 624 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.448A 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 6 removed outlier: 3.584A pdb=" N VAL B 6 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 24 removed outlier: 4.980A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.368A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (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 212 Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 267 removed outlier: 5.535A pdb=" N GLN B 265 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 272 " --> pdb=" O GLN B 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 277 through 279 Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 520 removed outlier: 6.731A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP C 600 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG C 621 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 518 through 520 removed outlier: 6.731A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP C 600 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG C 621 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.690A pdb=" N VAL D 6 " --> pdb=" O PHE D 345 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 20 through 24 removed outlier: 5.385A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS D 58 " --> pdb=" O HIS D 47 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 80 removed outlier: 7.009A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB9, first strand: chain 'D' and resid 207 through 212 removed outlier: 4.421A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 262 through 267 removed outlier: 4.030A pdb=" N ILE D 262 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) 721 hydrogen bonds defined for protein. 1997 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 239 hydrogen bonds 478 hydrogen bond angles 0 basepair planarities 96 basepair parallelities 151 stacking parallelities Total time for adding SS restraints: 11.12 Time building geometry restraints manager: 10.02 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: 4740 1.33 - 1.45: 5074 1.45 - 1.57: 9977 1.57 - 1.69: 405 1.69 - 1.82: 164 Bond restraints: 20360 Sorted by residual: bond pdb=" O3' DC J 19 " pdb=" P DA J 20 " ideal model delta sigma weight residual 1.607 1.553 0.054 1.50e-02 4.44e+03 1.30e+01 bond pdb=" N ASN A 850 " pdb=" CA ASN A 850 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.16e+00 bond pdb=" N ASP C 600 " pdb=" CA ASP C 600 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.24e-02 6.50e+03 6.33e+00 bond pdb=" N ARG C 713 " pdb=" CA ARG C 713 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.33e-02 5.65e+03 5.89e+00 bond pdb=" N ARG A 848 " pdb=" CA ARG A 848 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.50e+00 ... (remaining 20355 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.53: 1245 105.53 - 112.65: 10955 112.65 - 119.78: 6593 119.78 - 126.91: 8935 126.91 - 134.04: 711 Bond angle restraints: 28439 Sorted by residual: angle pdb=" N ILE A 953 " pdb=" CA ILE A 953 " pdb=" C ILE A 953 " ideal model delta sigma weight residual 113.71 107.34 6.37 9.50e-01 1.11e+00 4.50e+01 angle pdb=" C4' DC I 19 " pdb=" C3' DC I 19 " pdb=" O3' DC I 19 " ideal model delta sigma weight residual 110.00 101.69 8.31 1.50e+00 4.44e-01 3.07e+01 angle pdb=" C4' DA J 18 " pdb=" C3' DA J 18 " pdb=" O3' DA J 18 " ideal model delta sigma weight residual 110.00 118.30 -8.30 1.50e+00 4.44e-01 3.06e+01 angle pdb=" C4' DT F 29 " pdb=" C3' DT F 29 " pdb=" O3' DT F 29 " ideal model delta sigma weight residual 110.00 118.11 -8.11 1.50e+00 4.44e-01 2.92e+01 angle pdb=" C2' DC I 19 " pdb=" C1' DC I 19 " pdb=" N1 DC I 19 " ideal model delta sigma weight residual 113.50 121.03 -7.53 1.50e+00 4.44e-01 2.52e+01 ... (remaining 28434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 10720 35.68 - 71.35: 951 71.35 - 107.03: 14 107.03 - 142.70: 0 142.70 - 178.38: 9 Dihedral angle restraints: 11694 sinusoidal: 5976 harmonic: 5718 Sorted by residual: dihedral pdb=" CA ARG D 212 " pdb=" C ARG D 212 " pdb=" N ASN D 213 " pdb=" CA ASN D 213 " ideal model delta harmonic sigma weight residual 180.00 153.10 26.90 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ARG B 212 " pdb=" C ARG B 212 " pdb=" N ASN B 213 " pdb=" CA ASN B 213 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA PHE B 46 " pdb=" C PHE B 46 " pdb=" N HIS B 47 " pdb=" CA HIS B 47 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 11691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2910 0.083 - 0.167: 234 0.167 - 0.250: 8 0.250 - 0.333: 0 0.333 - 0.416: 1 Chirality restraints: 3153 Sorted by residual: chirality pdb=" C3' DT F 29 " pdb=" C4' DT F 29 " pdb=" O3' DT F 29 " pdb=" C2' DT F 29 " both_signs ideal model delta sigma weight residual False -2.66 -2.24 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C3' DG F 30 " pdb=" C4' DG F 30 " pdb=" O3' DG F 30 " pdb=" C2' DG F 30 " both_signs ideal model delta sigma weight residual False -2.66 -2.87 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' DC I 17 " pdb=" C4' DC I 17 " pdb=" O3' DC I 17 " pdb=" C2' DC I 17 " both_signs ideal model delta sigma weight residual False -2.66 -2.47 -0.19 2.00e-01 2.50e+01 9.20e-01 ... (remaining 3150 not shown) Planarity restraints: 2952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 212 " -0.014 2.00e-02 2.50e+03 2.72e-02 7.41e+00 pdb=" C ARG B 212 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG B 212 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN B 213 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT G 40 " 0.035 2.00e-02 2.50e+03 1.50e-02 5.65e+00 pdb=" N1 DT G 40 " -0.019 2.00e-02 2.50e+03 pdb=" C2 DT G 40 " -0.008 2.00e-02 2.50e+03 pdb=" O2 DT G 40 " -0.011 2.00e-02 2.50e+03 pdb=" N3 DT G 40 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT G 40 " 0.006 2.00e-02 2.50e+03 pdb=" O4 DT G 40 " 0.015 2.00e-02 2.50e+03 pdb=" C5 DT G 40 " -0.004 2.00e-02 2.50e+03 pdb=" C7 DT G 40 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT G 40 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 317 " 0.018 2.00e-02 2.50e+03 1.48e-02 5.48e+00 pdb=" CG TRP D 317 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP D 317 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP D 317 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 317 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 317 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 317 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 317 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 317 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 317 " 0.004 2.00e-02 2.50e+03 ... (remaining 2949 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 121 2.49 - 3.10: 14196 3.10 - 3.70: 31373 3.70 - 4.30: 43179 4.30 - 4.90: 67298 Nonbonded interactions: 156167 Sorted by model distance: nonbonded pdb=" OD1 ASP C 600 " pdb="CA CA C1101 " model vdw 1.892 2.510 nonbonded pdb=" OD2 ASP C 600 " pdb="CA CA C1102 " model vdw 1.916 2.510 nonbonded pdb=" OD1 ASP A 600 " pdb="CA CA A1101 " model vdw 1.936 2.510 nonbonded pdb=" OE1 GLN C 962 " pdb="CA CA C1102 " model vdw 1.977 2.510 nonbonded pdb=" OP1 DC I 17 " pdb="CA CA A1102 " model vdw 1.993 2.510 ... (remaining 156162 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 401 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB )) or resid 408 through 427 or (resid 428 through 429 \ and (name N or name CA or name C or name O or name CB )) or resid 430 or resid 4 \ 32 through 451 or (resid 452 through 453 and (name N or name CA or name C or nam \ e O or name CB )) or resid 454 through 455 or (resid 456 and (name N or name CA \ or name C or name O or name CB )) or resid 457 or (resid 458 and (name N or name \ CA or name C or name O or name CB )) or resid 459 through 879 or (resid 880 and \ (name N or name CA or name C or name O or name CB )) or resid 881 through 1008 \ or resid 1101 through 1103)) selection = (chain 'C' and (resid 401 through 430 or resid 432 through 843 or (resid 844 and \ (name N or name CA or name C or name O or name CB )) or resid 845 through 854 o \ r (resid 855 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 56 through 860 or (resid 861 and (name N or name CA or name C or name O or name \ CB )) or resid 862 through 867 or (resid 868 and (name N or name CA or name C or \ name O or name CB )) or resid 869 through 1008 or resid 1101 through 1103)) } ncs_group { reference = (chain 'B' and (resid 1 through 334 or (resid 335 through 338 and (name N or nam \ e CA or name C or name O or name CB )) or resid 339 through 351)) selection = (chain 'D' and (resid 1 through 116 or (resid 117 and (name N or name CA or name \ C or name O or name CB )) or resid 118 through 339 or (resid 340 through 342 an \ d (name N or name CA or name C or name O or name CB )) or resid 343 through 351) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 5.950 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 71.250 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.120 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 0.054 20360 Z= 0.332 Angle : 0.721 10.459 28439 Z= 0.425 Chirality : 0.045 0.416 3153 Planarity : 0.004 0.050 2952 Dihedral : 21.769 178.376 8008 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.19 % Favored : 91.66 % Rotamer: Outliers : 0.12 % Allowed : 6.61 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -4.21 (0.16), residues: 1955 helix: -2.29 (0.16), residues: 674 sheet: -2.01 (0.26), residues: 362 loop : -3.54 (0.16), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 317 HIS 0.006 0.001 HIS D 222 PHE 0.016 0.002 PHE A 916 TYR 0.026 0.002 TYR D 91 ARG 0.005 0.001 ARG C 977 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7919 (pp20) cc_final: 0.7396 (pp20) REVERT: A 691 MET cc_start: 0.9095 (tpp) cc_final: 0.8807 (tpp) REVERT: A 883 MET cc_start: 0.8208 (tpp) cc_final: 0.7806 (tpt) REVERT: B 270 GLU cc_start: 0.8881 (tt0) cc_final: 0.8632 (tm-30) REVERT: C 401 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8001 (tpt90) REVERT: C 418 PHE cc_start: 0.8094 (t80) cc_final: 0.7817 (t80) REVERT: C 847 MET cc_start: 0.8042 (mpp) cc_final: 0.7758 (mpp) REVERT: C 883 MET cc_start: 0.9245 (tpp) cc_final: 0.8788 (tpp) REVERT: D 339 MET cc_start: 0.7061 (mmm) cc_final: 0.5300 (pmm) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.3383 time to fit residues: 77.1143 Evaluate side-chains 108 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 108 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS A 850 ASN ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 HIS B 4 GLN B 23 ASN B 33 GLN B 53 ASN B 248 ASN C 395 HIS C 414 GLN C 581 GLN C 820 ASN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20360 Z= 0.203 Angle : 0.632 9.819 28439 Z= 0.344 Chirality : 0.041 0.194 3153 Planarity : 0.004 0.056 2952 Dihedral : 25.450 178.725 4401 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.70 % Favored : 93.19 % Rotamer: Outliers : 0.98 % Allowed : 10.90 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -2.77 (0.18), residues: 1955 helix: -0.77 (0.19), residues: 684 sheet: -1.60 (0.27), residues: 353 loop : -2.81 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 317 HIS 0.005 0.001 HIS A 818 PHE 0.026 0.001 PHE A 804 TYR 0.014 0.001 TYR C 928 ARG 0.006 0.000 ARG C 713 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7800 (pp20) cc_final: 0.7420 (pp20) REVERT: A 691 MET cc_start: 0.9020 (tpp) cc_final: 0.8750 (tpp) REVERT: A 883 MET cc_start: 0.8274 (tpp) cc_final: 0.7869 (tpt) REVERT: B 270 GLU cc_start: 0.8851 (tt0) cc_final: 0.8615 (tm-30) REVERT: C 401 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.7878 (tpt90) REVERT: C 418 PHE cc_start: 0.8119 (t80) cc_final: 0.7824 (t80) REVERT: D 339 MET cc_start: 0.6906 (mmm) cc_final: 0.5268 (pmm) REVERT: D 349 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7355 (ttp-170) outliers start: 16 outliers final: 5 residues processed: 141 average time/residue: 0.3219 time to fit residues: 72.9533 Evaluate side-chains 123 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 0.0070 chunk 59 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 192 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 overall best weight: 2.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN A 750 HIS ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 89 HIS C 495 GLN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 282 GLN D 313 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20360 Z= 0.279 Angle : 0.646 12.776 28439 Z= 0.350 Chirality : 0.042 0.184 3153 Planarity : 0.004 0.050 2952 Dihedral : 25.399 179.938 4401 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.32 % Favored : 92.58 % Rotamer: Outliers : 1.53 % Allowed : 13.23 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -2.17 (0.18), residues: 1955 helix: -0.18 (0.20), residues: 687 sheet: -1.26 (0.27), residues: 361 loop : -2.55 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 317 HIS 0.004 0.001 HIS C1006 PHE 0.025 0.002 PHE A 804 TYR 0.016 0.001 TYR C 928 ARG 0.004 0.000 ARG C 713 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 883 MET cc_start: 0.8165 (tpp) cc_final: 0.7639 (tpt) REVERT: B 270 GLU cc_start: 0.8873 (tt0) cc_final: 0.8555 (tm-30) REVERT: C 401 ARG cc_start: 0.8424 (mmm-85) cc_final: 0.7916 (tpt90) REVERT: C 418 PHE cc_start: 0.8137 (t80) cc_final: 0.7838 (t80) REVERT: D 232 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.8108 (p0) REVERT: D 339 MET cc_start: 0.6692 (mmm) cc_final: 0.5164 (pmm) REVERT: D 349 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7435 (ttp-170) outliers start: 25 outliers final: 14 residues processed: 147 average time/residue: 0.2931 time to fit residues: 69.4855 Evaluate side-chains 129 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS D 313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 20360 Z= 0.368 Angle : 0.685 9.923 28439 Z= 0.369 Chirality : 0.043 0.180 3153 Planarity : 0.004 0.052 2952 Dihedral : 25.407 179.486 4401 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.93 % Favored : 91.97 % Rotamer: Outliers : 2.51 % Allowed : 14.64 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -2.03 (0.19), residues: 1955 helix: -0.08 (0.20), residues: 686 sheet: -1.06 (0.27), residues: 364 loop : -2.52 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 317 HIS 0.005 0.001 HIS C1006 PHE 0.024 0.002 PHE A 804 TYR 0.016 0.002 TYR A 548 ARG 0.007 0.000 ARG C 894 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 657 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8336 (pp) REVERT: A 883 MET cc_start: 0.8264 (tpp) cc_final: 0.7791 (tpt) REVERT: A 973 LYS cc_start: 0.8958 (tppt) cc_final: 0.8739 (mmmt) REVERT: B 270 GLU cc_start: 0.8947 (tt0) cc_final: 0.8561 (tm-30) REVERT: B 292 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8122 (tp) REVERT: C 401 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.7855 (tpt90) REVERT: C 418 PHE cc_start: 0.8149 (t80) cc_final: 0.7841 (t80) REVERT: D 299 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8694 (mm) REVERT: D 339 MET cc_start: 0.6704 (mmm) cc_final: 0.5184 (pmm) REVERT: D 349 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7439 (ttp-170) outliers start: 41 outliers final: 21 residues processed: 148 average time/residue: 0.3025 time to fit residues: 72.0405 Evaluate side-chains 137 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 141 optimal weight: 0.0770 chunk 0 optimal weight: 30.0000 chunk 104 optimal weight: 0.2980 chunk 183 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20360 Z= 0.187 Angle : 0.607 12.949 28439 Z= 0.329 Chirality : 0.040 0.190 3153 Planarity : 0.004 0.047 2952 Dihedral : 25.201 179.971 4401 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.58 % Favored : 94.32 % Rotamer: Outliers : 1.90 % Allowed : 16.23 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.57 (0.19), residues: 1955 helix: 0.32 (0.21), residues: 679 sheet: -0.75 (0.27), residues: 381 loop : -2.28 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 317 HIS 0.005 0.001 HIS A 818 PHE 0.025 0.001 PHE A 804 TYR 0.016 0.001 TYR C 481 ARG 0.008 0.000 ARG C 894 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 883 MET cc_start: 0.8360 (tpp) cc_final: 0.7858 (tpt) REVERT: A 973 LYS cc_start: 0.8834 (tppt) cc_final: 0.8624 (mmmt) REVERT: B 5 MET cc_start: 0.8471 (tpp) cc_final: 0.8035 (tpp) REVERT: B 270 GLU cc_start: 0.8914 (tt0) cc_final: 0.8536 (tm-30) REVERT: C 401 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.7832 (tpt90) REVERT: C 418 PHE cc_start: 0.8051 (t80) cc_final: 0.7772 (t80) REVERT: D 47 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.7963 (t-90) REVERT: D 299 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8626 (mm) REVERT: D 339 MET cc_start: 0.6745 (mmm) cc_final: 0.5362 (pmm) REVERT: D 349 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7412 (ttp-170) outliers start: 31 outliers final: 13 residues processed: 155 average time/residue: 0.2994 time to fit residues: 74.7982 Evaluate side-chains 136 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 ASN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20360 Z= 0.212 Angle : 0.624 13.094 28439 Z= 0.333 Chirality : 0.040 0.181 3153 Planarity : 0.004 0.048 2952 Dihedral : 25.099 178.940 4401 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.50 % Favored : 93.40 % Rotamer: Outliers : 2.39 % Allowed : 16.60 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.37 (0.19), residues: 1955 helix: 0.39 (0.21), residues: 683 sheet: -0.46 (0.29), residues: 363 loop : -2.16 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 317 HIS 0.005 0.001 HIS A 515 PHE 0.024 0.001 PHE A 804 TYR 0.012 0.001 TYR C 928 ARG 0.008 0.000 ARG C 894 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 2.049 Fit side-chains revert: symmetry clash REVERT: A 883 MET cc_start: 0.8362 (tpp) cc_final: 0.7886 (tpt) REVERT: A 973 LYS cc_start: 0.8706 (tppt) cc_final: 0.8321 (tppt) REVERT: B 5 MET cc_start: 0.8534 (tpp) cc_final: 0.8124 (tpp) REVERT: B 266 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.6894 (t) REVERT: B 270 GLU cc_start: 0.8925 (tt0) cc_final: 0.8572 (tm-30) REVERT: B 292 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8170 (tp) REVERT: C 401 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.7813 (tpt90) REVERT: C 418 PHE cc_start: 0.8043 (t80) cc_final: 0.7773 (t80) REVERT: C 494 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7824 (mtt-85) REVERT: D 47 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.7982 (t-90) REVERT: D 280 GLU cc_start: 0.7695 (pm20) cc_final: 0.7381 (pm20) REVERT: D 302 MET cc_start: 0.6974 (mmm) cc_final: 0.6752 (mmm) REVERT: D 339 MET cc_start: 0.6631 (mmm) cc_final: 0.5192 (pmm) REVERT: D 349 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7404 (ttp-170) outliers start: 39 outliers final: 22 residues processed: 156 average time/residue: 0.3092 time to fit residues: 76.3295 Evaluate side-chains 147 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 chunk 172 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 94 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 ASN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20360 Z= 0.213 Angle : 0.622 13.503 28439 Z= 0.331 Chirality : 0.040 0.214 3153 Planarity : 0.004 0.049 2952 Dihedral : 25.030 178.809 4401 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.04 % Favored : 93.86 % Rotamer: Outliers : 2.20 % Allowed : 17.09 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.26 (0.19), residues: 1955 helix: 0.46 (0.21), residues: 684 sheet: -0.43 (0.29), residues: 368 loop : -2.08 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 317 HIS 0.004 0.001 HIS A 515 PHE 0.027 0.001 PHE A 804 TYR 0.012 0.001 TYR C 928 ARG 0.009 0.000 ARG C 894 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 129 time to evaluate : 2.297 Fit side-chains revert: symmetry clash REVERT: A 883 MET cc_start: 0.8340 (tpp) cc_final: 0.7865 (tpt) REVERT: A 973 LYS cc_start: 0.8600 (tppt) cc_final: 0.8246 (tppt) REVERT: B 5 MET cc_start: 0.8537 (tpp) cc_final: 0.8142 (tpp) REVERT: B 270 GLU cc_start: 0.8911 (tt0) cc_final: 0.8597 (tm-30) REVERT: B 292 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8151 (tp) REVERT: C 401 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.7782 (tpt90) REVERT: C 418 PHE cc_start: 0.8055 (t80) cc_final: 0.7793 (t80) REVERT: C 494 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7743 (mtt-85) REVERT: C 602 MET cc_start: 0.7808 (ttm) cc_final: 0.7414 (mtt) REVERT: D 47 HIS cc_start: 0.8670 (OUTLIER) cc_final: 0.7958 (t-90) REVERT: D 264 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8385 (p) REVERT: D 280 GLU cc_start: 0.7662 (pm20) cc_final: 0.7357 (pm20) REVERT: D 339 MET cc_start: 0.6579 (mmm) cc_final: 0.5191 (pmm) REVERT: D 349 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7313 (ttp-170) outliers start: 36 outliers final: 20 residues processed: 157 average time/residue: 0.3357 time to fit residues: 84.2188 Evaluate side-chains 147 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 ASN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20360 Z= 0.254 Angle : 0.645 13.784 28439 Z= 0.340 Chirality : 0.041 0.198 3153 Planarity : 0.004 0.048 2952 Dihedral : 25.021 178.462 4401 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.70 % Favored : 93.19 % Rotamer: Outliers : 2.45 % Allowed : 17.58 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.27 (0.19), residues: 1955 helix: 0.43 (0.21), residues: 685 sheet: -0.31 (0.31), residues: 326 loop : -2.07 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 317 HIS 0.005 0.001 HIS A 515 PHE 0.026 0.001 PHE A 804 TYR 0.012 0.001 TYR C 928 ARG 0.009 0.000 ARG C 894 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 122 time to evaluate : 2.072 Fit side-chains revert: symmetry clash REVERT: A 883 MET cc_start: 0.8337 (tpp) cc_final: 0.7891 (tpt) REVERT: B 5 MET cc_start: 0.8552 (tpp) cc_final: 0.8133 (tpp) REVERT: B 266 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.6925 (t) REVERT: B 270 GLU cc_start: 0.8920 (tt0) cc_final: 0.8579 (tm-30) REVERT: B 292 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8136 (tp) REVERT: C 401 ARG cc_start: 0.8311 (mmm-85) cc_final: 0.7773 (tpt90) REVERT: C 418 PHE cc_start: 0.8059 (t80) cc_final: 0.7797 (t80) REVERT: C 494 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7629 (mtt-85) REVERT: C 894 ARG cc_start: 0.8750 (mmm160) cc_final: 0.8418 (mmm-85) REVERT: D 47 HIS cc_start: 0.8684 (OUTLIER) cc_final: 0.7978 (t-90) REVERT: D 264 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8399 (p) REVERT: D 280 GLU cc_start: 0.7731 (pm20) cc_final: 0.7443 (pm20) REVERT: D 339 MET cc_start: 0.6515 (mmm) cc_final: 0.5117 (pmm) REVERT: D 349 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7304 (ttp-170) outliers start: 40 outliers final: 26 residues processed: 153 average time/residue: 0.2932 time to fit residues: 72.2396 Evaluate side-chains 150 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 118 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 172 optimal weight: 0.0980 chunk 180 optimal weight: 10.0000 chunk 189 optimal weight: 20.0000 chunk 125 optimal weight: 0.6980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 852 ASN ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 ASN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20360 Z= 0.220 Angle : 0.636 13.563 28439 Z= 0.336 Chirality : 0.040 0.208 3153 Planarity : 0.004 0.049 2952 Dihedral : 24.978 178.575 4401 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.63 % Favored : 94.27 % Rotamer: Outliers : 2.20 % Allowed : 17.88 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.20 (0.19), residues: 1955 helix: 0.52 (0.21), residues: 683 sheet: -0.37 (0.30), residues: 336 loop : -2.00 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 317 HIS 0.004 0.001 HIS A 818 PHE 0.022 0.001 PHE A 804 TYR 0.017 0.001 TYR C 481 ARG 0.008 0.000 ARG C 894 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 124 time to evaluate : 1.586 Fit side-chains revert: symmetry clash REVERT: A 883 MET cc_start: 0.8316 (tpp) cc_final: 0.7853 (tpt) REVERT: A 973 LYS cc_start: 0.8456 (tppt) cc_final: 0.7839 (tptt) REVERT: B 5 MET cc_start: 0.8535 (tpp) cc_final: 0.8106 (tpp) REVERT: B 266 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.6895 (t) REVERT: B 270 GLU cc_start: 0.8929 (tt0) cc_final: 0.8613 (tm-30) REVERT: B 292 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8131 (tp) REVERT: C 401 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.7758 (tpt90) REVERT: C 418 PHE cc_start: 0.8062 (t80) cc_final: 0.7801 (t80) REVERT: C 494 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7582 (mtt-85) REVERT: C 602 MET cc_start: 0.7835 (ttm) cc_final: 0.7420 (mtt) REVERT: D 47 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.7957 (t-90) REVERT: D 264 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8381 (p) REVERT: D 280 GLU cc_start: 0.7708 (pm20) cc_final: 0.7489 (pm20) REVERT: D 339 MET cc_start: 0.6448 (mmm) cc_final: 0.5058 (pmm) REVERT: D 349 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7288 (ttp-170) outliers start: 36 outliers final: 25 residues processed: 153 average time/residue: 0.2989 time to fit residues: 72.7667 Evaluate side-chains 153 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 ASN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20360 Z= 0.209 Angle : 0.645 12.777 28439 Z= 0.336 Chirality : 0.040 0.224 3153 Planarity : 0.004 0.049 2952 Dihedral : 24.920 178.541 4401 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.04 % Favored : 93.86 % Rotamer: Outliers : 1.96 % Allowed : 18.37 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.14 (0.19), residues: 1955 helix: 0.55 (0.21), residues: 683 sheet: -0.31 (0.30), residues: 338 loop : -1.98 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 317 HIS 0.004 0.001 HIS C 836 PHE 0.016 0.001 PHE B 48 TYR 0.015 0.001 TYR C 481 ARG 0.011 0.000 ARG C 894 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 2.141 Fit side-chains revert: symmetry clash REVERT: A 883 MET cc_start: 0.8232 (tpp) cc_final: 0.7922 (tpt) REVERT: A 973 LYS cc_start: 0.8422 (tppt) cc_final: 0.7788 (tptt) REVERT: B 5 MET cc_start: 0.8533 (tpp) cc_final: 0.8094 (tpp) REVERT: B 266 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.6891 (t) REVERT: B 270 GLU cc_start: 0.8919 (tt0) cc_final: 0.8597 (tm-30) REVERT: B 292 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8091 (tp) REVERT: C 401 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.7755 (tpt90) REVERT: C 418 PHE cc_start: 0.8049 (t80) cc_final: 0.7793 (t80) REVERT: C 494 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7684 (mtt-85) REVERT: C 894 ARG cc_start: 0.8742 (mmm160) cc_final: 0.8401 (mmm-85) REVERT: D 47 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.8020 (t-90) REVERT: D 264 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8348 (p) REVERT: D 339 MET cc_start: 0.6618 (mmm) cc_final: 0.5072 (pmm) REVERT: D 349 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7254 (ttp-170) outliers start: 32 outliers final: 23 residues processed: 150 average time/residue: 0.3077 time to fit residues: 74.1283 Evaluate side-chains 149 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.100840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.068106 restraints weight = 58196.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.069652 restraints weight = 32796.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.070597 restraints weight = 23713.933| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20360 Z= 0.247 Angle : 0.658 13.103 28439 Z= 0.344 Chirality : 0.041 0.189 3153 Planarity : 0.004 0.048 2952 Dihedral : 24.912 178.236 4401 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.45 % Favored : 93.45 % Rotamer: Outliers : 2.20 % Allowed : 18.49 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.15 (0.19), residues: 1955 helix: 0.48 (0.20), residues: 691 sheet: -0.21 (0.31), residues: 326 loop : -1.97 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 317 HIS 0.004 0.001 HIS A 515 PHE 0.016 0.001 PHE B 48 TYR 0.015 0.001 TYR C 481 ARG 0.010 0.000 ARG C 894 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3321.45 seconds wall clock time: 62 minutes 8.24 seconds (3728.24 seconds total)