Starting phenix.real_space_refine on Sat Feb 17 18:38:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oet_20037/02_2024/6oet_20037.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oet_20037/02_2024/6oet_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_20037/02_2024/6oet_20037.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oet_20037/02_2024/6oet_20037.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oet_20037/02_2024/6oet_20037.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oet_20037/02_2024/6oet_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-dev-5238/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: 14.12, per 1000 atoms: 0.72 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: 8.26 Conformation dependent library (CDL) restraints added in 4.3 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: 7.18 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: 9.88 Time building geometry restraints manager: 8.81 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.570 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 67.490 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.570 ------------------------------------------------------------------------------- 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 : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 MET cc_start: 0.7425 (mmm) cc_final: 0.7204 (mmp) REVERT: A 847 MET cc_start: 0.7935 (ptt) cc_final: 0.7577 (ptm) REVERT: B 52 GLN cc_start: 0.8172 (mp10) cc_final: 0.7903 (mm110) REVERT: B 110 MET cc_start: 0.8742 (mmt) cc_final: 0.8417 (mmt) REVERT: C 456 GLN cc_start: 0.7652 (mt0) cc_final: 0.7165 (mt0) REVERT: C 458 ARG cc_start: 0.6880 (ttp80) cc_final: 0.6471 (mmt180) REVERT: C 857 LEU cc_start: 0.9292 (tp) cc_final: 0.9058 (tp) REVERT: C 1003 MET cc_start: 0.8971 (mmt) cc_final: 0.8375 (mmt) REVERT: D 120 VAL cc_start: 0.7752 (OUTLIER) cc_final: 0.7297 (t) REVERT: D 152 MET cc_start: 0.7463 (tpp) cc_final: 0.7240 (tpp) REVERT: D 162 MET cc_start: 0.8699 (mmt) cc_final: 0.8449 (mmp) REVERT: D 209 SER cc_start: 0.8097 (OUTLIER) cc_final: 0.7896 (p) REVERT: D 259 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8337 (p) REVERT: D 326 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8466 (p) outliers start: 57 outliers final: 9 residues processed: 219 average time/residue: 0.3229 time to fit residues: 107.8399 Evaluate side-chains 121 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 326 THR 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: 2.9990 chunk 63 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 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 337 GLN C 443 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20461 Z= 0.178 Angle : 0.576 9.244 28545 Z= 0.320 Chirality : 0.039 0.191 3128 Planarity : 0.005 0.061 2955 Dihedral : 23.537 120.329 4376 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.60 % Allowed : 12.41 % Favored : 85.99 % 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: -1.86 (0.18), residues: 1922 helix: -0.47 (0.19), residues: 660 sheet: -0.72 (0.29), residues: 333 loop : -1.99 (0.18), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 317 HIS 0.006 0.001 HIS A 990 PHE 0.016 0.001 PHE B 48 TYR 0.013 0.001 TYR A 757 ARG 0.003 0.000 ARG C 927 *********************** 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 173 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 GLU cc_start: 0.8671 (pt0) cc_final: 0.8454 (pp20) REVERT: A 807 ILE cc_start: 0.9006 (mm) cc_final: 0.8520 (mt) REVERT: A 847 MET cc_start: 0.7919 (ptt) cc_final: 0.7617 (ptm) REVERT: A 858 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8129 (mmp) REVERT: B 25 ASP cc_start: 0.7436 (p0) cc_final: 0.7027 (p0) REVERT: B 52 GLN cc_start: 0.8051 (mp10) cc_final: 0.7847 (tp40) REVERT: C 456 GLN cc_start: 0.7506 (mt0) cc_final: 0.7023 (mt0) REVERT: C 458 ARG cc_start: 0.6768 (ttp80) cc_final: 0.6323 (mmt180) REVERT: C 841 MET cc_start: 0.8676 (mmm) cc_final: 0.8389 (mtp) REVERT: D 162 MET cc_start: 0.8701 (mmt) cc_final: 0.8400 (mmp) REVERT: D 218 ILE cc_start: 0.8115 (pt) cc_final: 0.7885 (mt) REVERT: D 285 MET cc_start: 0.8225 (mmm) cc_final: 0.7656 (mmm) outliers start: 25 outliers final: 19 residues processed: 165 average time/residue: 0.3064 time to fit residues: 79.9685 Evaluate side-chains 142 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 105 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 157 optimal weight: 0.0870 chunk 129 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 205 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- 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 54 HIS B 181 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20461 Z= 0.249 Angle : 0.591 9.582 28545 Z= 0.325 Chirality : 0.040 0.218 3128 Planarity : 0.004 0.077 2955 Dihedral : 23.515 110.721 4367 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.84 % Allowed : 13.90 % Favored : 84.26 % 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: -1.14 (0.19), residues: 1922 helix: 0.43 (0.20), residues: 660 sheet: -0.49 (0.29), residues: 332 loop : -1.76 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 317 HIS 0.004 0.001 HIS C 990 PHE 0.015 0.001 PHE A 916 TYR 0.015 0.001 TYR C 707 ARG 0.004 0.000 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 164 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 ASN cc_start: 0.8848 (t0) cc_final: 0.8612 (t0) REVERT: A 847 MET cc_start: 0.7944 (ptt) cc_final: 0.7695 (ptm) REVERT: C 455 MET cc_start: 0.6428 (mmt) cc_final: 0.5876 (tpp) REVERT: C 456 GLN cc_start: 0.7395 (mt0) cc_final: 0.6805 (mt0) REVERT: C 458 ARG cc_start: 0.6663 (ttp80) cc_final: 0.6186 (mmt180) REVERT: C 578 MET cc_start: 0.7208 (ptp) cc_final: 0.6924 (ptm) REVERT: C 841 MET cc_start: 0.8718 (mmm) cc_final: 0.8427 (mtp) REVERT: C 1003 MET cc_start: 0.8717 (mmt) cc_final: 0.8406 (mmt) REVERT: D 162 MET cc_start: 0.8726 (mmt) cc_final: 0.8444 (mmp) REVERT: D 218 ILE cc_start: 0.8168 (pt) cc_final: 0.7910 (mt) REVERT: D 285 MET cc_start: 0.8342 (mmm) cc_final: 0.7876 (mmm) outliers start: 29 outliers final: 23 residues processed: 153 average time/residue: 0.3049 time to fit residues: 74.0523 Evaluate side-chains 144 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 187 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 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** B 10 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN C 991 HIS ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20461 Z= 0.333 Angle : 0.632 10.516 28545 Z= 0.344 Chirality : 0.042 0.218 3128 Planarity : 0.005 0.078 2955 Dihedral : 23.634 101.935 4367 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.61 % Allowed : 15.68 % 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: -0.88 (0.19), residues: 1922 helix: 0.61 (0.21), residues: 654 sheet: -0.36 (0.29), residues: 335 loop : -1.56 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 893 HIS 0.006 0.001 HIS A 991 PHE 0.020 0.002 PHE A 916 TYR 0.018 0.002 TYR C 805 ARG 0.004 0.001 ARG A 621 *********************** 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 164 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 122 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 847 MET cc_start: 0.7974 (ptt) cc_final: 0.7715 (ptm) REVERT: A 936 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8457 (m-10) REVERT: B 322 MET cc_start: 0.6379 (mtm) cc_final: 0.5555 (mtm) REVERT: C 455 MET cc_start: 0.6455 (mmt) cc_final: 0.5959 (tpp) REVERT: C 456 GLN cc_start: 0.7422 (mt0) cc_final: 0.7213 (mt0) REVERT: C 529 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7606 (mmm-85) REVERT: C 708 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8197 (p0) REVERT: C 1003 MET cc_start: 0.8793 (mmt) cc_final: 0.8421 (mmt) REVERT: D 91 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.6711 (t80) REVERT: D 162 MET cc_start: 0.8727 (mmt) cc_final: 0.8461 (mmp) REVERT: D 285 MET cc_start: 0.8243 (mmm) cc_final: 0.7767 (mmm) outliers start: 42 outliers final: 33 residues processed: 152 average time/residue: 0.2983 time to fit residues: 72.5311 Evaluate side-chains 155 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 CYS Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 168 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2313 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= 0.197 Angle : 0.552 9.194 28545 Z= 0.304 Chirality : 0.039 0.207 3128 Planarity : 0.004 0.065 2955 Dihedral : 23.420 97.521 4367 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.96 % Allowed : 17.04 % 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: -0.56 (0.19), residues: 1922 helix: 0.96 (0.21), residues: 658 sheet: -0.33 (0.29), residues: 336 loop : -1.38 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 317 HIS 0.004 0.001 HIS C 990 PHE 0.013 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 158 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 GLN cc_start: 0.8045 (tp40) cc_final: 0.7776 (mm110) REVERT: A 847 MET cc_start: 0.7970 (ptt) cc_final: 0.7710 (ptm) REVERT: A 936 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8423 (m-10) REVERT: B 322 MET cc_start: 0.6286 (mtm) cc_final: 0.5553 (mtm) REVERT: C 455 MET cc_start: 0.6440 (mmt) cc_final: 0.6024 (tpp) REVERT: C 456 GLN cc_start: 0.7314 (mt0) cc_final: 0.7082 (mt0) REVERT: C 578 MET cc_start: 0.7195 (ptp) cc_final: 0.6819 (ptm) REVERT: C 708 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8227 (p0) REVERT: C 841 MET cc_start: 0.8674 (mmm) cc_final: 0.8419 (mtp) REVERT: C 1003 MET cc_start: 0.8703 (mmt) cc_final: 0.8319 (mmt) REVERT: D 162 MET cc_start: 0.8705 (mmt) cc_final: 0.8441 (mmp) REVERT: D 285 MET cc_start: 0.8315 (mmm) cc_final: 0.7820 (mmm) outliers start: 31 outliers final: 26 residues processed: 152 average time/residue: 0.3006 time to fit residues: 72.8967 Evaluate side-chains 148 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 67 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 39 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 202 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.0770 overall best weight: 0.8740 ------------------------------------------------------------------------------- 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: 0.8172 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20461 Z= 0.176 Angle : 0.537 8.852 28545 Z= 0.295 Chirality : 0.038 0.203 3128 Planarity : 0.004 0.058 2955 Dihedral : 23.305 92.247 4366 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.43 % Allowed : 17.04 % Favored : 80.52 % 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 (0.19), residues: 1922 helix: 1.14 (0.21), residues: 659 sheet: -0.15 (0.30), residues: 329 loop : -1.25 (0.20), residues: 934 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 A 757 ARG 0.003 0.000 ARG B 123 *********************** 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 173 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 134 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 520 GLN cc_start: 0.7998 (tp40) cc_final: 0.7777 (mm110) REVERT: A 847 MET cc_start: 0.7953 (ptt) cc_final: 0.7696 (ptm) REVERT: A 936 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8425 (m-10) REVERT: A 1003 MET cc_start: 0.8949 (mmm) cc_final: 0.8681 (mmp) REVERT: B 322 MET cc_start: 0.6262 (mtm) cc_final: 0.5665 (mtm) REVERT: B 349 ARG cc_start: 0.6324 (ppt170) cc_final: 0.5763 (ptm-80) REVERT: C 455 MET cc_start: 0.6546 (mmt) cc_final: 0.6160 (tpp) REVERT: C 456 GLN cc_start: 0.7371 (mt0) cc_final: 0.7154 (mt0) REVERT: C 578 MET cc_start: 0.7162 (ptp) cc_final: 0.6798 (ptm) REVERT: C 708 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8202 (p0) REVERT: C 1003 MET cc_start: 0.8715 (mmt) cc_final: 0.8361 (mmt) REVERT: D 91 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.6524 (t80) REVERT: D 162 MET cc_start: 0.8667 (mmt) cc_final: 0.8416 (mmp) REVERT: D 285 MET cc_start: 0.8324 (mmm) cc_final: 0.7843 (mmm) outliers start: 39 outliers final: 29 residues processed: 165 average time/residue: 0.3075 time to fit residues: 80.7606 Evaluate side-chains 153 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 327 ILE 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: 0.0870 chunk 115 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 201 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 93 optimal weight: 0.3980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN ** A 740 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: 0.8140 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20461 Z= 0.154 Angle : 0.525 10.692 28545 Z= 0.287 Chirality : 0.038 0.198 3128 Planarity : 0.004 0.053 2955 Dihedral : 23.143 86.215 4365 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.20 % Allowed : 17.87 % Favored : 79.93 % 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: 1.35 (0.21), residues: 659 sheet: -0.03 (0.30), residues: 336 loop : -1.15 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 317 HIS 0.003 0.001 HIS B 222 PHE 0.012 0.001 PHE B 48 TYR 0.014 0.001 TYR B 234 ARG 0.003 0.000 ARG A 621 *********************** 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 171 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 2.174 Fit side-chains revert: symmetry clash REVERT: A 520 GLN cc_start: 0.7962 (tp40) cc_final: 0.7693 (mm110) REVERT: A 716 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7844 (mm-30) REVERT: A 797 ASP cc_start: 0.7827 (m-30) cc_final: 0.7276 (m-30) REVERT: A 847 MET cc_start: 0.7869 (ptt) cc_final: 0.7665 (ptm) REVERT: A 936 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8524 (m-10) REVERT: A 1003 MET cc_start: 0.8926 (mmm) cc_final: 0.8686 (mmp) REVERT: B 25 ASP cc_start: 0.7592 (p0) cc_final: 0.7298 (p0) REVERT: B 322 MET cc_start: 0.6341 (mtm) cc_final: 0.5844 (mtm) REVERT: B 349 ARG cc_start: 0.6304 (ppt170) cc_final: 0.5777 (ptm-80) REVERT: C 455 MET cc_start: 0.6547 (mmt) cc_final: 0.6252 (tpp) REVERT: C 456 GLN cc_start: 0.7411 (mt0) cc_final: 0.7181 (mt0) REVERT: C 578 MET cc_start: 0.7190 (ptp) cc_final: 0.6820 (ptm) REVERT: C 708 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8142 (p0) REVERT: C 984 MET cc_start: 0.8049 (mmm) cc_final: 0.7831 (mmm) REVERT: C 1003 MET cc_start: 0.8726 (mmt) cc_final: 0.8358 (mmt) REVERT: D 91 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.6515 (t80) REVERT: D 162 MET cc_start: 0.8640 (mmt) cc_final: 0.8398 (mmp) REVERT: D 285 MET cc_start: 0.8345 (mmm) cc_final: 0.7850 (mmm) REVERT: D 348 LEU cc_start: 0.8947 (tp) cc_final: 0.8677 (tt) outliers start: 35 outliers final: 26 residues processed: 163 average time/residue: 0.3021 time to fit residues: 78.7467 Evaluate side-chains 153 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 124 optimal weight: 0.7980 chunk 80 optimal weight: 0.2980 chunk 120 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 183 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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** D 281 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20461 Z= 0.149 Angle : 0.518 10.091 28545 Z= 0.283 Chirality : 0.037 0.193 3128 Planarity : 0.003 0.050 2955 Dihedral : 23.090 87.048 4365 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.96 % Allowed : 18.35 % Favored : 79.69 % 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: 0.04 (0.20), residues: 1922 helix: 1.46 (0.21), residues: 659 sheet: 0.12 (0.29), residues: 341 loop : -1.08 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 317 HIS 0.003 0.001 HIS A 937 PHE 0.011 0.001 PHE B 48 TYR 0.014 0.001 TYR B 234 ARG 0.007 0.000 ARG C 761 *********************** 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 167 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 2.103 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.7013 (tt) REVERT: A 520 GLN cc_start: 0.8072 (tp40) cc_final: 0.7818 (mm110) REVERT: A 547 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7629 (mm-30) REVERT: A 716 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7845 (mm-30) REVERT: A 797 ASP cc_start: 0.7699 (m-30) cc_final: 0.7204 (m-30) REVERT: A 841 MET cc_start: 0.8516 (mmm) cc_final: 0.8314 (mtp) REVERT: A 847 MET cc_start: 0.7967 (ptt) cc_final: 0.7716 (ptm) REVERT: A 936 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8514 (m-10) REVERT: A 1003 MET cc_start: 0.8968 (mmm) cc_final: 0.8726 (mmp) REVERT: B 322 MET cc_start: 0.6344 (mtm) cc_final: 0.5883 (mtm) REVERT: B 349 ARG cc_start: 0.6302 (ppt170) cc_final: 0.5803 (ptm-80) REVERT: C 434 LEU cc_start: 0.5226 (tt) cc_final: 0.4636 (mp) REVERT: C 455 MET cc_start: 0.6354 (mmt) cc_final: 0.5716 (mmm) REVERT: C 456 GLN cc_start: 0.7473 (mt0) cc_final: 0.7271 (mt0) REVERT: C 578 MET cc_start: 0.7109 (ptp) cc_final: 0.6767 (ptm) REVERT: C 708 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8152 (p0) REVERT: C 1003 MET cc_start: 0.8724 (mmt) cc_final: 0.8352 (mmt) REVERT: D 91 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.6426 (t80) REVERT: D 162 MET cc_start: 0.8662 (mmt) cc_final: 0.8378 (mmp) REVERT: D 285 MET cc_start: 0.8342 (mmm) cc_final: 0.7891 (mmm) outliers start: 31 outliers final: 25 residues processed: 161 average time/residue: 0.3107 time to fit residues: 79.7225 Evaluate side-chains 157 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 327 ILE 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: 0.9990 chunk 187 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** ** 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: 0.8178 moved from start: 0.2800 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= 0.207 Angle : 0.549 9.955 28545 Z= 0.298 Chirality : 0.039 0.189 3128 Planarity : 0.004 0.052 2955 Dihedral : 23.184 87.380 4365 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.14 % Allowed : 18.17 % Favored : 79.69 % 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: 1.37 (0.21), residues: 660 sheet: 0.14 (0.29), residues: 336 loop : -1.06 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 893 HIS 0.004 0.001 HIS A 937 PHE 0.013 0.001 PHE A 916 TYR 0.013 0.001 TYR A 757 ARG 0.010 0.000 ARG A 529 *********************** 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 162 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 1.932 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7112 (tt) REVERT: A 520 GLN cc_start: 0.7957 (tp40) cc_final: 0.7727 (mm110) REVERT: A 797 ASP cc_start: 0.7783 (m-30) cc_final: 0.7259 (m-30) REVERT: A 841 MET cc_start: 0.8557 (mmm) cc_final: 0.8335 (mtp) REVERT: A 847 MET cc_start: 0.8060 (ptt) cc_final: 0.7833 (ptm) REVERT: A 936 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8555 (m-10) REVERT: A 1003 MET cc_start: 0.8969 (mmm) cc_final: 0.8714 (mmp) REVERT: B 322 MET cc_start: 0.6389 (mtm) cc_final: 0.5935 (mtm) REVERT: B 349 ARG cc_start: 0.6360 (ppt170) cc_final: 0.5830 (ptm-80) REVERT: C 434 LEU cc_start: 0.5205 (tt) cc_final: 0.4632 (mp) REVERT: C 455 MET cc_start: 0.6480 (mmt) cc_final: 0.5825 (mmm) REVERT: C 456 GLN cc_start: 0.7508 (mt0) cc_final: 0.7292 (mt0) REVERT: C 578 MET cc_start: 0.7175 (ptp) cc_final: 0.6796 (ptm) REVERT: C 708 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8210 (p0) REVERT: C 1003 MET cc_start: 0.8782 (mmt) cc_final: 0.8386 (mmt) REVERT: D 91 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.6580 (t80) REVERT: D 162 MET cc_start: 0.8642 (mmt) cc_final: 0.8377 (mmp) REVERT: D 285 MET cc_start: 0.8359 (mmm) cc_final: 0.7872 (mmm) outliers start: 34 outliers final: 29 residues processed: 153 average time/residue: 0.2837 time to fit residues: 70.1355 Evaluate side-chains 159 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 121 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 176 optimal weight: 0.0370 overall best weight: 1.3862 ------------------------------------------------------------------------------- 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 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20461 Z= 0.219 Angle : 0.556 9.902 28545 Z= 0.301 Chirality : 0.039 0.189 3128 Planarity : 0.004 0.052 2955 Dihedral : 23.172 87.063 4365 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.38 % Allowed : 18.05 % Favored : 79.57 % 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: -0.02 (0.20), residues: 1922 helix: 1.33 (0.21), residues: 660 sheet: 0.12 (0.29), residues: 336 loop : -1.05 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 893 HIS 0.004 0.001 HIS A 937 PHE 0.013 0.001 PHE A 916 TYR 0.013 0.001 TYR A 757 ARG 0.010 0.000 ARG A 529 ********************** 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 165 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 127 time to evaluate : 2.102 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6976 (tt) REVERT: A 797 ASP cc_start: 0.7879 (m-30) cc_final: 0.7361 (m-30) REVERT: A 841 MET cc_start: 0.8588 (mmm) cc_final: 0.8299 (mtp) REVERT: A 847 MET cc_start: 0.8048 (ptt) cc_final: 0.7805 (ptm) REVERT: A 936 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8531 (m-10) REVERT: A 1003 MET cc_start: 0.8965 (mmm) cc_final: 0.8708 (mmp) REVERT: B 322 MET cc_start: 0.6346 (mtm) cc_final: 0.5839 (mtm) REVERT: B 349 ARG cc_start: 0.6374 (ppt170) cc_final: 0.5825 (ptm-80) REVERT: C 434 LEU cc_start: 0.4964 (tt) cc_final: 0.4415 (mp) REVERT: C 455 MET cc_start: 0.6534 (mmt) cc_final: 0.5830 (mmm) REVERT: C 456 GLN cc_start: 0.7530 (mt0) cc_final: 0.7309 (mt0) REVERT: C 578 MET cc_start: 0.7177 (ptp) cc_final: 0.6794 (ptm) REVERT: C 708 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8217 (p0) REVERT: C 841 MET cc_start: 0.8587 (mtp) cc_final: 0.8237 (mtp) REVERT: C 984 MET cc_start: 0.8182 (mmm) cc_final: 0.7875 (mmm) REVERT: C 1003 MET cc_start: 0.8830 (mmt) cc_final: 0.8446 (mmt) REVERT: D 91 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.6579 (t80) REVERT: D 162 MET cc_start: 0.8660 (mmt) cc_final: 0.8390 (mmp) REVERT: D 285 MET cc_start: 0.8343 (mmm) cc_final: 0.7878 (mmm) outliers start: 38 outliers final: 33 residues processed: 155 average time/residue: 0.2776 time to fit residues: 69.7041 Evaluate side-chains 162 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 965 ASN Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 50 optimal weight: 0.4980 chunk 152 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 145 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.120999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.085051 restraints weight = 100220.380| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.26 r_work: 0.3080 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 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 = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2930 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= 0.157 Angle : 0.531 9.717 28545 Z= 0.289 Chirality : 0.038 0.189 3128 Planarity : 0.004 0.048 2955 Dihedral : 23.064 87.424 4365 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.32 % Allowed : 18.29 % Favored : 79.39 % 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: 0.10 (0.20), residues: 1922 helix: 1.44 (0.21), residues: 659 sheet: 0.20 (0.29), residues: 336 loop : -1.00 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 317 HIS 0.003 0.001 HIS A 937 PHE 0.012 0.001 PHE B 48 TYR 0.014 0.001 TYR B 234 ARG 0.010 0.000 ARG A 529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3631.50 seconds wall clock time: 67 minutes 31.73 seconds (4051.73 seconds total)