Starting phenix.real_space_refine on Mon Dec 11 23:54:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oet_20037/12_2023/6oet_20037.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oet_20037/12_2023/6oet_20037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oet_20037/12_2023/6oet_20037.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oet_20037/12_2023/6oet_20037.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oet_20037/12_2023/6oet_20037.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oet_20037/12_2023/6oet_20037.pdb" } resolution = 3.4 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 2 9.91 5 Zn 2 6.06 5 P 205 5.49 5 S 105 5.16 5 C 11728 2.51 5 N 3482 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 401": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 597": "OE1" <-> "OE2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "A GLU 824": "OE1" <-> "OE2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A GLU 861": "OE1" <-> "OE2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 929": "OE1" <-> "OE2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A ARG 949": "NH1" <-> "NH2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "C ARG 486": "NH1" <-> "NH2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C GLU 617": "OE1" <-> "OE2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C GLU 716": "OE1" <-> "OE2" Residue "C GLU 758": "OE1" <-> "OE2" Residue "C GLU 770": "OE1" <-> "OE2" Residue "C ARG 773": "NH1" <-> "NH2" Residue "C GLU 814": "OE1" <-> "OE2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 828": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" Residue "C ARG 848": "NH1" <-> "NH2" Residue "C GLU 873": "OE1" <-> "OE2" Residue "C GLU 877": "OE1" <-> "OE2" Residue "C GLU 904": "OE1" <-> "OE2" Residue "C GLU 945": "OE1" <-> "OE2" Residue "C GLU 948": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D GLU 301": "OE1" <-> "OE2" Residue "D ARG 349": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 19604 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4969 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 618, 4963 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 591} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 618, 4963 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 591} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 5059 Chain: "B" Number of atoms: 2691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 342, 2670 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 342, 2670 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2713 Chain: "C" Number of atoms: 5010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5010 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 596} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2673 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 343, 2663 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 343, 2663 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2718 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1030 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "I" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "J" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "G" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1205 Classifications: {'DNA': 59} Link IDs: {'rna3p': 58} Chain: "L" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 611 Classifications: {'DNA': 30} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 29} Chain: "M" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 805 Classifications: {'DNA': 39} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 38} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2632 SG CYS A 727 26.378 99.796 107.700 1.00 58.29 S ATOM 2653 SG CYS A 730 23.465 100.415 109.872 1.00 56.60 S ATOM 10347 SG CYS C 727 84.020 63.935 96.316 1.00 52.70 S ATOM 10368 SG CYS C 730 86.625 61.891 97.877 1.00 55.44 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS A 907 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 907 " occ=0.50 residue: pdb=" N AHIS B 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 47 " occ=0.50 residue: pdb=" N AARG B 237 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 237 " occ=0.50 residue: pdb=" N AHIS D 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 47 " occ=0.50 residue: pdb=" P DT I 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT I 15 " occ=0.85 residue: pdb=" P DT J 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT J 15 " occ=0.85 Time building chain proxies: 15.66, per 1000 atoms: 0.80 Number of scatterers: 19604 At special positions: 0 Unit cell: (109.14, 156.22, 162.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 105 16.00 P 205 15.00 O 4080 8.00 N 3482 7.00 C 11728 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: 9.52 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " Number of angles added : 4 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 16 sheets defined 36.7% alpha, 22.4% beta 102 base pairs and 166 stacking pairs defined. Time for finding SS restraints: 8.35 Creating SS restraints... Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.680A pdb=" N LEU A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 418 " --> pdb=" O GLN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 442 removed outlier: 3.763A pdb=" N LEU A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 456 Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.584A pdb=" N LEU A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 removed outlier: 3.744A pdb=" N LEU A 668 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 735 through 739 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 812 Processing helix chain 'A' and resid 822 through 842 removed outlier: 3.972A pdb=" N ARG A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'A' and resid 860 through 868 Processing helix chain 'A' and resid 873 through 890 Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 908 through 924 Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.569A pdb=" N ARG A 969 " --> pdb=" O ASN A 965 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A 970 " --> pdb=" O LYS A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.688A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1000 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'B' and resid 11 through 13 No H-bonds generated for 'chain 'B' and resid 11 through 13' Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.820A pdb=" N TRP B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'C' and resid 410 through 420 removed outlier: 3.713A pdb=" N ASP C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 442 removed outlier: 3.710A pdb=" N VAL C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 456 removed outlier: 3.848A pdb=" N ALA C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 removed outlier: 3.687A pdb=" N CYS C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 474 " --> pdb=" O ILE C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.697A pdb=" N LYS C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 removed outlier: 4.150A pdb=" N MET C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 580 Processing helix chain 'C' and resid 665 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 750 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 813 removed outlier: 3.518A pdb=" N CYS C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY C 813 " --> pdb=" O GLN C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 842 removed outlier: 3.640A pdb=" N ASN C 842 " --> pdb=" O ARG C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.669A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 895 Proline residue: C 891 - end of helix removed outlier: 3.526A pdb=" N SER C 895 " --> pdb=" O PRO C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 907 Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 950 removed outlier: 3.549A pdb=" N ILE C 946 " --> pdb=" O HIS C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 974 removed outlier: 4.173A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 995 removed outlier: 3.892A pdb=" N THR C 995 " --> pdb=" O HIS C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1001 Processing helix chain 'C' and resid 1002 through 1004 No H-bonds generated for 'chain 'C' and resid 1002 through 1004' Processing helix chain 'D' and resid 11 through 13 No H-bonds generated for 'chain 'D' and resid 11 through 13' Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.820A pdb=" N TRP D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 519 removed outlier: 3.584A pdb=" N THR A 705 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 519 removed outlier: 3.584A pdb=" N THR A 705 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N HIS A 633 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASN A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 24 removed outlier: 8.565A pdb=" N GLY B 18 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLN B 33 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS B 58 " --> pdb=" O AHIS B 47 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N LEU B 55 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL B 8 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N PHE B 343 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.031A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N CYS B 124 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.188A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 141 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA7, first strand: chain 'B' and resid 205 through 210 removed outlier: 5.634A pdb=" N HIS B 207 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLY B 220 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B 209 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 218 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 239 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 262 through 265 Processing sheet with id=AA9, first strand: chain 'C' and resid 517 through 519 removed outlier: 5.398A pdb=" N ILE C 631 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 621 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 619 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 534 through 536 removed outlier: 7.078A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 619 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 621 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE C 631 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 15 through 24 removed outlier: 8.565A pdb=" N GLY D 18 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLN D 33 " --> pdb=" O GLY D 18 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS D 58 " --> pdb=" O AHIS D 47 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N LEU D 55 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL D 8 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N PHE D 343 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.031A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS D 124 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.188A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB6, first strand: chain 'D' and resid 205 through 210 removed outlier: 5.633A pdb=" N HIS D 207 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLY D 220 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER D 209 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE D 218 " --> pdb=" O SER D 209 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP D 239 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 262 through 265 688 hydrogen bonds defined for protein. 1932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 257 hydrogen bonds 510 hydrogen bond angles 0 basepair planarities 102 basepair parallelities 166 stacking parallelities Total time for adding SS restraints: 10.26 Time building geometry restraints manager: 10.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3324 1.32 - 1.44: 6148 1.44 - 1.56: 10423 1.56 - 1.68: 407 1.68 - 1.80: 159 Bond restraints: 20461 Sorted by residual: bond pdb=" N ASN D 335 " pdb=" CA ASN D 335 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.31e-02 5.83e+03 5.68e+00 bond pdb=" N ASN B 335 " pdb=" CA ASN B 335 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.28e-02 6.10e+03 5.54e+00 bond pdb=" N ASP D 334 " pdb=" CA ASP D 334 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.39e+00 bond pdb=" N TYR B 68 " pdb=" CA TYR B 68 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.24e-02 6.50e+03 4.81e+00 bond pdb=" C1' DT M 22 " pdb=" N1 DT M 22 " ideal model delta sigma weight residual 1.490 1.425 0.065 3.00e-02 1.11e+03 4.66e+00 ... (remaining 20456 not shown) Histogram of bond angle deviations from ideal: 97.37 - 104.97: 1163 104.97 - 112.58: 10972 112.58 - 120.19: 8343 120.19 - 127.80: 7625 127.80 - 135.40: 442 Bond angle restraints: 28545 Sorted by residual: angle pdb=" N LYS D 336 " pdb=" CA LYS D 336 " pdb=" C LYS D 336 " ideal model delta sigma weight residual 111.28 117.09 -5.81 1.09e+00 8.42e-01 2.84e+01 angle pdb=" O3' DG L 21 " pdb=" C3' DG L 21 " pdb=" C2' DG L 21 " ideal model delta sigma weight residual 111.50 104.03 7.47 1.50e+00 4.44e-01 2.48e+01 angle pdb=" N LYS B 336 " pdb=" CA LYS B 336 " pdb=" C LYS B 336 " ideal model delta sigma weight residual 111.33 117.02 -5.69 1.21e+00 6.83e-01 2.21e+01 angle pdb=" N ASP A 585 " pdb=" CA ASP A 585 " pdb=" C ASP A 585 " ideal model delta sigma weight residual 113.55 107.84 5.71 1.26e+00 6.30e-01 2.05e+01 angle pdb=" N VAL C 943 " pdb=" CA VAL C 943 " pdb=" C VAL C 943 " ideal model delta sigma weight residual 108.88 118.38 -9.50 2.16e+00 2.14e-01 1.94e+01 ... (remaining 28540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.92: 10070 26.92 - 53.84: 1469 53.84 - 80.77: 207 80.77 - 107.69: 7 107.69 - 134.61: 1 Dihedral angle restraints: 11754 sinusoidal: 6148 harmonic: 5606 Sorted by residual: dihedral pdb=" CA GLN A 520 " pdb=" C GLN A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA GLN C 463 " pdb=" C GLN C 463 " pdb=" N PRO C 464 " pdb=" CA PRO C 464 " ideal model delta harmonic sigma weight residual 180.00 -154.25 -25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ILE D 316 " pdb=" C ILE D 316 " pdb=" N TRP D 317 " pdb=" CA TRP D 317 " ideal model delta harmonic sigma weight residual 180.00 155.07 24.93 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 11751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2281 0.058 - 0.116: 710 0.116 - 0.174: 121 0.174 - 0.232: 13 0.232 - 0.290: 3 Chirality restraints: 3128 Sorted by residual: chirality pdb=" CB VAL C 943 " pdb=" CA VAL C 943 " pdb=" CG1 VAL C 943 " pdb=" CG2 VAL C 943 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB VAL C 545 " pdb=" CA VAL C 545 " pdb=" CG1 VAL C 545 " pdb=" CG2 VAL C 545 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL C 776 " pdb=" CA VAL C 776 " pdb=" CG1 VAL C 776 " pdb=" CG2 VAL C 776 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3125 not shown) Planarity restraints: 2955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO B 99 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 788 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.06e+00 pdb=" N PRO C 789 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 789 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 789 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO D 99 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " -0.042 5.00e-02 4.00e+02 ... (remaining 2952 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 4845 2.78 - 3.31: 16128 3.31 - 3.84: 35670 3.84 - 4.37: 40821 4.37 - 4.90: 65751 Nonbonded interactions: 163215 Sorted by model distance: nonbonded pdb=" OD2 ASP A 546 " pdb=" OG SER B 259 " model vdw 2.256 2.440 nonbonded pdb=" OE2 GLU A 803 " pdb=" OH TYR A 928 " model vdw 2.260 2.440 nonbonded pdb=" O TYR A 935 " pdb=" OG1 THR A 939 " model vdw 2.272 2.440 nonbonded pdb=" O SER C 543 " pdb=" OG SER C 543 " model vdw 2.292 2.440 nonbonded pdb=" OH TYR C 805 " pdb=" OD1 ASP C 834 " model vdw 2.295 2.440 ... (remaining 163210 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 391 through 906 or resid 908 through 1006 or (resid 1007 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1101 through 11 \ 02)) selection = (chain 'C' and (resid 391 through 392 or (resid 393 and (name N or name CA or na \ me C or name O or name CB )) or resid 394 through 457 or (resid 458 and (name N \ or name CA or name C or name O or name CB )) or resid 459 through 906 or resid 9 \ 08 through 1007 or resid 1101 through 1102)) } ncs_group { reference = (chain 'B' and (resid 1 through 46 or resid 48 through 117 or (resid 118 and (na \ me N or name CA or name C or name O or name CB )) or resid 119 through 236 or re \ sid 238 through 335 or (resid 336 and (name N or name CA or name C or name O or \ name CB )) or resid 337 through 340 or (resid 341 through 342 and (name N or nam \ e CA or name C or name O or name CB )) or resid 343 through 350)) selection = (chain 'D' and (resid 1 through 46 or resid 48 through 236 or resid 238 through \ 350)) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.020 Extract box with map and model: 5.550 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 73.900 Find NCS groups from input model: 0.980 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: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 0.010 0.104 20461 Z= 0.626 Angle : 0.920 9.778 28545 Z= 0.519 Chirality : 0.056 0.290 3128 Planarity : 0.007 0.075 2955 Dihedral : 22.107 134.610 8142 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.81 % Favored : 94.08 % Rotamer: Outliers : 3.50 % Allowed : 7.66 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.15), residues: 1922 helix: -2.49 (0.14), residues: 647 sheet: -1.46 (0.27), residues: 340 loop : -2.57 (0.17), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 893 HIS 0.014 0.002 HIS A 991 PHE 0.024 0.003 PHE A 916 TYR 0.019 0.002 TYR A 757 ARG 0.016 0.001 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 172 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 9 residues processed: 219 average time/residue: 0.3315 time to fit residues: 110.1742 Evaluate side-chains 116 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 2.067 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1712 time to fit residues: 5.5774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 176 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 106 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 445 HIS ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN A 990 HIS A1000 GLN B 33 GLN B 90 GLN B 101 ASN B 181 HIS B 337 GLN C 443 ASN C 473 ASN C 965 ASN C1004 ASN D 33 GLN D 53 ASN D 181 HIS D 335 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20461 Z= 0.177 Angle : 0.576 9.205 28545 Z= 0.320 Chirality : 0.039 0.191 3128 Planarity : 0.005 0.060 2955 Dihedral : 23.438 118.168 4362 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.31 % Allowed : 12.95 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -1.79 (0.18), residues: 1922 helix: -0.42 (0.19), residues: 660 sheet: -0.67 (0.29), residues: 332 loop : -1.95 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 317 HIS 0.006 0.001 HIS A 990 PHE 0.017 0.001 PHE B 48 TYR 0.013 0.001 TYR A 757 ARG 0.004 0.000 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 162 average time/residue: 0.3252 time to fit residues: 82.7704 Evaluate side-chains 137 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 2.089 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1816 time to fit residues: 7.5036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 HIS B 54 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS C 991 HIS ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 20461 Z= 0.375 Angle : 0.663 10.579 28545 Z= 0.362 Chirality : 0.043 0.181 3128 Planarity : 0.005 0.054 2955 Dihedral : 23.734 110.322 4362 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.13 % Allowed : 14.90 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.24 (0.19), residues: 1922 helix: 0.24 (0.20), residues: 656 sheet: -0.57 (0.29), residues: 340 loop : -1.70 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 760 HIS 0.007 0.001 HIS A 991 PHE 0.022 0.002 PHE A 916 TYR 0.018 0.002 TYR C 805 ARG 0.004 0.001 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 139 average time/residue: 0.3254 time to fit residues: 71.7047 Evaluate side-chains 122 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 2.045 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1912 time to fit residues: 7.0243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 187 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 127 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN A 495 GLN ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20461 Z= 0.300 Angle : 0.613 9.971 28545 Z= 0.335 Chirality : 0.041 0.187 3128 Planarity : 0.004 0.053 2955 Dihedral : 23.593 102.766 4362 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.25 % Allowed : 16.69 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.19), residues: 1922 helix: 0.60 (0.21), residues: 651 sheet: -0.44 (0.29), residues: 339 loop : -1.53 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 317 HIS 0.006 0.001 HIS A 991 PHE 0.017 0.001 PHE A 916 TYR 0.015 0.001 TYR C 805 ARG 0.006 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 137 average time/residue: 0.3192 time to fit residues: 69.3771 Evaluate side-chains 128 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 2.018 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1878 time to fit residues: 6.5326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 168 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20461 Z= 0.190 Angle : 0.551 9.541 28545 Z= 0.303 Chirality : 0.039 0.186 3128 Planarity : 0.004 0.048 2955 Dihedral : 23.398 96.145 4362 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.71 % Allowed : 17.58 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 1922 helix: 0.98 (0.21), residues: 659 sheet: -0.38 (0.29), residues: 339 loop : -1.37 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 317 HIS 0.003 0.001 HIS C 501 PHE 0.014 0.001 PHE B 48 TYR 0.016 0.001 TYR B 234 ARG 0.003 0.000 ARG C 855 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 135 average time/residue: 0.3304 time to fit residues: 70.6180 Evaluate side-chains 118 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.644 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1787 time to fit residues: 3.0924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 67 optimal weight: 4.9990 chunk 181 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 202 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 93 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20461 Z= 0.180 Angle : 0.544 10.825 28545 Z= 0.298 Chirality : 0.038 0.184 3128 Planarity : 0.004 0.047 2955 Dihedral : 23.312 90.127 4362 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.65 % Allowed : 18.41 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1922 helix: 1.14 (0.21), residues: 659 sheet: -0.28 (0.29), residues: 340 loop : -1.20 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 317 HIS 0.003 0.001 HIS A 937 PHE 0.013 0.001 PHE B 48 TYR 0.014 0.001 TYR B 234 ARG 0.006 0.000 ARG C 927 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 125 average time/residue: 0.3351 time to fit residues: 67.2113 Evaluate side-chains 120 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 2.195 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1993 time to fit residues: 4.6987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 194 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 114 optimal weight: 0.1980 chunk 170 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 93 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20461 Z= 0.150 Angle : 0.522 10.216 28545 Z= 0.286 Chirality : 0.038 0.185 3128 Planarity : 0.003 0.046 2955 Dihedral : 23.146 83.989 4362 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.48 % Allowed : 18.53 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1922 helix: 1.33 (0.21), residues: 658 sheet: -0.09 (0.29), residues: 344 loop : -1.10 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 317 HIS 0.003 0.001 HIS B 222 PHE 0.014 0.001 PHE B 48 TYR 0.013 0.001 TYR A 757 ARG 0.004 0.000 ARG C 927 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 137 average time/residue: 0.3258 time to fit residues: 71.2374 Evaluate side-chains 120 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 2.074 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1822 time to fit residues: 3.6242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 124 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 99 optimal weight: 0.0570 chunk 18 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20461 Z= 0.164 Angle : 0.526 9.635 28545 Z= 0.288 Chirality : 0.038 0.173 3128 Planarity : 0.003 0.046 2955 Dihedral : 23.124 78.675 4362 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.30 % Allowed : 19.24 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1922 helix: 1.40 (0.21), residues: 658 sheet: 0.05 (0.29), residues: 337 loop : -1.05 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 317 HIS 0.003 0.001 HIS B 222 PHE 0.013 0.001 PHE B 48 TYR 0.013 0.001 TYR B 234 ARG 0.010 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 124 average time/residue: 0.3253 time to fit residues: 64.0392 Evaluate side-chains 115 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 2.008 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2058 time to fit residues: 3.3706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 192 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 187 optimal weight: 0.3980 chunk 112 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 169 optimal weight: 0.4980 chunk 177 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 198 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20461 Z= 0.172 Angle : 0.535 9.440 28545 Z= 0.290 Chirality : 0.038 0.174 3128 Planarity : 0.003 0.045 2955 Dihedral : 23.099 76.836 4362 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.30 % Allowed : 19.54 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.20), residues: 1922 helix: 1.42 (0.21), residues: 659 sheet: 0.18 (0.29), residues: 337 loop : -1.00 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 317 HIS 0.003 0.001 HIS A 937 PHE 0.013 0.001 PHE B 48 TYR 0.014 0.001 TYR B 234 ARG 0.006 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 119 average time/residue: 0.3308 time to fit residues: 63.3259 Evaluate side-chains 117 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.976 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1804 time to fit residues: 2.9743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 121 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 128 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 ASN ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 20461 Z= 0.385 Angle : 0.650 9.561 28545 Z= 0.350 Chirality : 0.043 0.167 3128 Planarity : 0.004 0.049 2955 Dihedral : 23.478 76.293 4362 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.30 % Allowed : 19.60 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 1922 helix: 1.03 (0.21), residues: 660 sheet: 0.06 (0.29), residues: 331 loop : -1.15 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 317 HIS 0.008 0.001 HIS A 991 PHE 0.021 0.002 PHE A 916 TYR 0.019 0.002 TYR C 805 ARG 0.007 0.001 ARG A 440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 111 average time/residue: 0.3314 time to fit residues: 59.1913 Evaluate side-chains 109 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 2.006 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1849 time to fit residues: 3.3523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 50 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 166 optimal weight: 0.5980 chunk 69 optimal weight: 0.0980 chunk 170 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 ASN ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.120344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.084915 restraints weight = 99974.178| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.23 r_work: 0.3073 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20461 Z= 0.160 Angle : 0.540 9.319 28545 Z= 0.295 Chirality : 0.038 0.172 3128 Planarity : 0.004 0.046 2955 Dihedral : 23.087 77.032 4362 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.36 % Allowed : 19.54 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1922 helix: 1.36 (0.21), residues: 660 sheet: 0.11 (0.29), residues: 337 loop : -1.00 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 317 HIS 0.004 0.001 HIS A 937 PHE 0.014 0.001 PHE B 48 TYR 0.014 0.001 TYR B 234 ARG 0.005 0.000 ARG A 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3571.55 seconds wall clock time: 69 minutes 16.86 seconds (4156.86 seconds total)