Starting phenix.real_space_refine on Thu Nov 16 23:19:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxb_14197/11_2023/7qxb_14197.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxb_14197/11_2023/7qxb_14197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxb_14197/11_2023/7qxb_14197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxb_14197/11_2023/7qxb_14197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxb_14197/11_2023/7qxb_14197.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxb_14197/11_2023/7qxb_14197.pdb" } resolution = 3.9 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= 0.002 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: 5 Type Number sf(0) Gaussians P 277 5.49 5 S 42 5.16 5 C 9714 2.51 5 N 3124 2.21 5 O 3896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 11": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A ARG 486": "NH1" <-> "NH2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 515": "NH1" <-> "NH2" Residue "A ARG 521": "NH1" <-> "NH2" Residue "A ARG 522": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 613": "NH1" <-> "NH2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A ARG 643": "NH1" <-> "NH2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A ARG 647": "NH1" <-> "NH2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A ARG 653": "NH1" <-> "NH2" Residue "A ARG 657": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 688": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A ARG 743": "NH1" <-> "NH2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ARG 774": "NH1" <-> "NH2" Residue "A ARG 787": "NH1" <-> "NH2" Residue "A ARG 811": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 821": "NH1" <-> "NH2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A ARG 865": "NH1" <-> "NH2" Residue "A ARG 885": "NH1" <-> "NH2" Residue "A ARG 889": "NH1" <-> "NH2" Residue "A ARG 901": "NH1" <-> "NH2" Residue "A ARG 938": "NH1" <-> "NH2" Residue "A ARG 951": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 962": "NH1" <-> "NH2" Residue "A ARG 968": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 972": "NH1" <-> "NH2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "A ARG 1011": "NH1" <-> "NH2" Residue "A PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1034": "NH1" <-> "NH2" Residue "A ARG 1084": "NH1" <-> "NH2" Residue "A ARG 1086": "NH1" <-> "NH2" Residue "A ARG 1097": "NH1" <-> "NH2" Residue "A ARG 1105": "NH1" <-> "NH2" Residue "L GLU 42": "OE1" <-> "OE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "M GLU 36": "OE1" <-> "OE2" Residue "M GLU 77": "OE1" <-> "OE2" Residue "O ARG 92": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O GLU 119": "OE1" <-> "OE2" Residue "O ARG 159": "NH1" <-> "NH2" Residue "O GLU 160": "OE1" <-> "OE2" Residue "O GLU 169": "OE1" <-> "OE2" Residue "O GLU 171": "OE1" <-> "OE2" Residue "O ARG 175": "NH1" <-> "NH2" Residue "O GLU 178": "OE1" <-> "OE2" Residue "O ARG 180": "NH1" <-> "NH2" Residue "O ARG 208": "NH1" <-> "NH2" Residue "O ARG 220": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 17053 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 951, 7626 Classifications: {'peptide': 951} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 54, 'TRANS': 893} Chain breaks: 3 Chain: "B" Number of atoms: 5431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 5431 Classifications: {'RNA': 256} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 16, 'rna3p_pur': 99, 'rna3p_pyr': 124} Link IDs: {'rna2p': 33, 'rna3p': 222} Chain breaks: 3 Chain: "L" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 643 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "M" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "N" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 461 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "O" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 955 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 3 Chain: "P" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1238 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PTRANS': 9, 'TRANS': 241} Chain breaks: 3 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 814 Unresolved non-hydrogen angles: 1054 Unresolved non-hydrogen dihedrals: 678 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 13, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 13, 'GLU:plan': 7, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 420 Time building chain proxies: 10.74, per 1000 atoms: 0.63 Number of scatterers: 17053 At special positions: 0 Unit cell: (166.77, 128.62, 143.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 277 15.00 O 3896 8.00 N 3124 7.00 C 9714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 982 " - pdb=" SG CYS A1043 " distance=2.57 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: 8.84 Conformation dependent library (CDL) restraints added in 2.4 seconds 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2806 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 12 sheets defined 50.9% alpha, 19.5% beta 70 base pairs and 135 stacking pairs defined. Time for finding SS restraints: 6.86 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.742A pdb=" N ARG A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.559A pdb=" N LEU A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.904A pdb=" N TRP A 387 " --> pdb=" O PRO A 383 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 390 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 404 through 413 Processing helix chain 'A' and resid 445 through 454 removed outlier: 3.554A pdb=" N GLN A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.666A pdb=" N VAL A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.852A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 497 removed outlier: 3.882A pdb=" N GLU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 Processing helix chain 'A' and resid 530 through 551 Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'A' and resid 578 through 596 removed outlier: 3.786A pdb=" N LYS A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 Processing helix chain 'A' and resid 653 through 672 removed outlier: 3.792A pdb=" N ARG A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 677 Processing helix chain 'A' and resid 682 through 688 removed outlier: 3.742A pdb=" N ILE A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 721 through 734 removed outlier: 3.529A pdb=" N LEU A 725 " --> pdb=" O PRO A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 772 through 784 Processing helix chain 'A' and resid 802 through 815 Processing helix chain 'A' and resid 835 through 854 removed outlier: 3.719A pdb=" N THR A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU A 840 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 853 " --> pdb=" O MET A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 861 removed outlier: 4.271A pdb=" N ASP A 860 " --> pdb=" O GLY A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 890 Processing helix chain 'A' and resid 899 through 902 removed outlier: 3.699A pdb=" N LYS A 902 " --> pdb=" O ASN A 899 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 899 through 902' Processing helix chain 'A' and resid 965 through 982 removed outlier: 3.521A pdb=" N ASN A 969 " --> pdb=" O LYS A 965 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 980 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 removed outlier: 3.704A pdb=" N LEU A 987 " --> pdb=" O HIS A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1018 removed outlier: 3.516A pdb=" N TYR A1010 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1028 removed outlier: 3.504A pdb=" N LYS A1027 " --> pdb=" O GLN A1024 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN A1028 " --> pdb=" O VAL A1025 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1024 through 1028' Processing helix chain 'A' and resid 1029 through 1051 removed outlier: 4.271A pdb=" N CYS A1043 " --> pdb=" O THR A1039 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1085 removed outlier: 3.758A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.618A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Proline residue: A1091 - end of helix removed outlier: 4.150A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1119 Processing helix chain 'A' and resid 1124 through 1129 removed outlier: 3.899A pdb=" N LYS A1128 " --> pdb=" O PRO A1124 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR A1129 " --> pdb=" O SER A1125 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1124 through 1129' Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 27 through 38 removed outlier: 3.826A pdb=" N ARG L 32 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG L 33 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU L 35 " --> pdb=" O VAL L 31 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG L 36 " --> pdb=" O ARG L 32 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS L 37 " --> pdb=" O ARG L 33 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 73 removed outlier: 4.571A pdb=" N VAL L 50 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR L 51 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL L 55 " --> pdb=" O TYR L 51 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR L 58 " --> pdb=" O ALA L 54 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU L 64 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA L 67 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP L 73 " --> pdb=" O ASN L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 90 removed outlier: 3.816A pdb=" N LEU L 84 " --> pdb=" O ILE L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 removed outlier: 3.590A pdb=" N LEU L 97 " --> pdb=" O GLU L 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 50 removed outlier: 3.843A pdb=" N TYR M 43 " --> pdb=" O SER M 39 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL M 45 " --> pdb=" O TYR M 41 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL M 49 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 86 removed outlier: 4.111A pdb=" N SER M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL M 67 " --> pdb=" O MET M 63 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN M 68 " --> pdb=" O ASN M 64 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE M 74 " --> pdb=" O ILE M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 103 removed outlier: 4.149A pdb=" N ILE M 95 " --> pdb=" O THR M 91 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN M 96 " --> pdb=" O SER M 92 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR M 97 " --> pdb=" O ARG M 93 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU M 101 " --> pdb=" O THR M 97 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 124 removed outlier: 3.593A pdb=" N LYS M 109 " --> pdb=" O GLY M 105 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS M 121 " --> pdb=" O LYS M 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 104 Processing helix chain 'O' and resid 158 through 165 Processing helix chain 'O' and resid 169 through 173 Processing helix chain 'O' and resid 223 through 226 Processing helix chain 'O' and resid 227 through 238 Processing helix chain 'P' and resid 65 through 69 removed outlier: 3.525A pdb=" N LEU P 69 " --> pdb=" O TYR P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 156 Processing helix chain 'P' and resid 206 through 214 removed outlier: 3.529A pdb=" N GLN P 214 " --> pdb=" O ILE P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 217 No H-bonds generated for 'chain 'P' and resid 215 through 217' Processing helix chain 'P' and resid 225 through 232 removed outlier: 4.198A pdb=" N VAL P 229 " --> pdb=" O ASN P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 273 Processing helix chain 'P' and resid 282 through 299 removed outlier: 3.697A pdb=" N THR P 298 " --> pdb=" O SER P 294 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 4.110A pdb=" N ALA A 167 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU A 793 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 790 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU A 798 " --> pdb=" O TYR A 739 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TYR A 739 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA4, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA5, first strand: chain 'A' and resid 599 through 600 removed outlier: 7.101A pdb=" N LEU A 617 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ARG A 819 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 633 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 624 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 629 " --> pdb=" O LYS A 626 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 863 through 865 Processing sheet with id=AA7, first strand: chain 'A' and resid 927 through 930 Processing sheet with id=AA8, first strand: chain 'L' and resid 43 through 44 removed outlier: 7.850A pdb=" N ARG L 43 " --> pdb=" O ILE M 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'O' and resid 113 through 122 removed outlier: 6.832A pdb=" N LEU O 145 " --> pdb=" O LEU O 118 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL O 120 " --> pdb=" O THR O 143 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR O 143 " --> pdb=" O VAL O 120 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL O 206 " --> pdb=" O CYS O 187 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS O 187 " --> pdb=" O VAL O 206 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ARG O 208 " --> pdb=" O GLN O 185 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU O 181 " --> pdb=" O LEU O 212 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG O 180 " --> pdb=" O LEU O 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 21 through 37 removed outlier: 6.728A pdb=" N THR P 48 " --> pdb=" O LYS P 30 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE P 32 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL P 46 " --> pdb=" O PHE P 32 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N CYS P 44 " --> pdb=" O PRO P 34 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N THR P 93 " --> pdb=" O LYS P 56 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N THR P 58 " --> pdb=" O THR P 93 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE P 62 " --> pdb=" O THR P 97 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N SER P 99 " --> pdb=" O PHE P 62 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG P 83 " --> pdb=" O SER P 98 " (cutoff:3.500A) removed outlier: 11.364A pdb=" N GLY P 100 " --> pdb=" O PHE P 81 " (cutoff:3.500A) removed outlier: 9.816A pdb=" N PHE P 81 " --> pdb=" O GLY P 100 " (cutoff:3.500A) removed outlier: 11.031A pdb=" N ALA P 102 " --> pdb=" O VAL P 79 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N VAL P 79 " --> pdb=" O ALA P 102 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE P 78 " --> pdb=" O VAL P 29 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL P 29 " --> pdb=" O ILE P 78 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ARG P 80 " --> pdb=" O GLY P 27 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLY P 27 " --> pdb=" O ARG P 80 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N HIS P 82 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL P 25 " --> pdb=" O HIS P 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 204 through 205 removed outlier: 6.580A pdb=" N LYS P 182 " --> pdb=" O LEU P 169 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS P 171 " --> pdb=" O LEU P 180 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU P 180 " --> pdb=" O LYS P 171 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU P 173 " --> pdb=" O SER P 178 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N SER P 178 " --> pdb=" O GLU P 173 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE P 263 " --> pdb=" O ASP P 219 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE P 238 " --> pdb=" O LEU P 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 204 through 205 removed outlier: 5.081A pdb=" N PHE P 162 " --> pdb=" O SER P 243 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE P 238 " --> pdb=" O LEU P 278 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 186 hydrogen bonds 352 hydrogen bond angles 0 basepair planarities 70 basepair parallelities 135 stacking parallelities Total time for adding SS restraints: 9.53 Time building geometry restraints manager: 9.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3290 1.33 - 1.46: 5953 1.46 - 1.59: 8201 1.59 - 1.73: 445 1.73 - 1.86: 55 Bond restraints: 17944 Sorted by residual: bond pdb=" N SER A 586 " pdb=" CA SER A 586 " ideal model delta sigma weight residual 1.459 1.529 -0.070 1.20e-02 6.94e+03 3.38e+01 bond pdb=" CE1 TYR A 638 " pdb=" CZ TYR A 638 " ideal model delta sigma weight residual 1.378 1.501 -0.123 2.40e-02 1.74e+03 2.64e+01 bond pdb=" N PHE A 544 " pdb=" CA PHE A 544 " ideal model delta sigma weight residual 1.459 1.402 0.057 1.17e-02 7.31e+03 2.40e+01 bond pdb=" CA VAL A1087 " pdb=" CB VAL A1087 " ideal model delta sigma weight residual 1.540 1.606 -0.066 1.36e-02 5.41e+03 2.38e+01 bond pdb=" N LEU A1082 " pdb=" CA LEU A1082 " ideal model delta sigma weight residual 1.458 1.518 -0.060 1.30e-02 5.92e+03 2.13e+01 ... (remaining 17939 not shown) Histogram of bond angle deviations from ideal: 92.51 - 100.90: 137 100.90 - 109.28: 4399 109.28 - 117.67: 10618 117.67 - 126.06: 9582 126.06 - 134.45: 923 Bond angle restraints: 25659 Sorted by residual: angle pdb=" O3' C B 142 " pdb=" C3' C B 142 " pdb=" C2' C B 142 " ideal model delta sigma weight residual 113.70 128.61 -14.91 1.50e+00 4.44e-01 9.88e+01 angle pdb=" C4' G B 300 " pdb=" C3' G B 300 " pdb=" O3' G B 300 " ideal model delta sigma weight residual 109.40 122.48 -13.08 1.50e+00 4.44e-01 7.60e+01 angle pdb=" N ARG A1084 " pdb=" CA ARG A1084 " pdb=" C ARG A1084 " ideal model delta sigma weight residual 111.14 119.63 -8.49 1.08e+00 8.57e-01 6.17e+01 angle pdb=" C4' C B 321 " pdb=" C3' C B 321 " pdb=" O3' C B 321 " ideal model delta sigma weight residual 113.00 124.45 -11.45 1.50e+00 4.44e-01 5.83e+01 angle pdb=" N ASP A 516 " pdb=" CA ASP A 516 " pdb=" C ASP A 516 " ideal model delta sigma weight residual 111.82 120.52 -8.70 1.16e+00 7.43e-01 5.62e+01 ... (remaining 25654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.39: 9741 34.39 - 68.78: 338 68.78 - 103.17: 37 103.17 - 137.56: 9 137.56 - 171.95: 14 Dihedral angle restraints: 10139 sinusoidal: 5815 harmonic: 4324 Sorted by residual: dihedral pdb=" C5' A B 176 " pdb=" C4' A B 176 " pdb=" C3' A B 176 " pdb=" O3' A B 176 " ideal model delta sinusoidal sigma weight residual 147.00 71.59 75.41 1 8.00e+00 1.56e-02 1.12e+02 dihedral pdb=" O4' U B 194 " pdb=" C1' U B 194 " pdb=" N1 U B 194 " pdb=" C2 U B 194 " ideal model delta sinusoidal sigma weight residual 200.00 28.05 171.95 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U B 316 " pdb=" C1' U B 316 " pdb=" N1 U B 316 " pdb=" C2 U B 316 " ideal model delta sinusoidal sigma weight residual 200.00 40.96 159.04 1 1.50e+01 4.44e-03 8.25e+01 ... (remaining 10136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2533 0.118 - 0.236: 552 0.236 - 0.354: 53 0.354 - 0.472: 10 0.472 - 0.590: 5 Chirality restraints: 3153 Sorted by residual: chirality pdb=" C3' A B 176 " pdb=" C4' A B 176 " pdb=" O3' A B 176 " pdb=" C2' A B 176 " both_signs ideal model delta sigma weight residual False -2.74 -2.15 -0.59 2.00e-01 2.50e+01 8.71e+00 chirality pdb=" C3' C B 142 " pdb=" C4' C B 142 " pdb=" O3' C B 142 " pdb=" C2' C B 142 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" C3' G B 292 " pdb=" C4' G B 292 " pdb=" O3' G B 292 " pdb=" C2' G B 292 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.50 2.00e-01 2.50e+01 6.34e+00 ... (remaining 3150 not shown) Planarity restraints: 2272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 75 " -0.220 2.00e-02 2.50e+03 1.00e-01 2.25e+02 pdb=" N1 C B 75 " 0.114 2.00e-02 2.50e+03 pdb=" C2 C B 75 " 0.058 2.00e-02 2.50e+03 pdb=" O2 C B 75 " 0.055 2.00e-02 2.50e+03 pdb=" N3 C B 75 " -0.012 2.00e-02 2.50e+03 pdb=" C4 C B 75 " -0.057 2.00e-02 2.50e+03 pdb=" N4 C B 75 " -0.081 2.00e-02 2.50e+03 pdb=" C5 C B 75 " 0.037 2.00e-02 2.50e+03 pdb=" C6 C B 75 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 292 " 0.196 2.00e-02 2.50e+03 8.08e-02 1.96e+02 pdb=" N9 G B 292 " -0.012 2.00e-02 2.50e+03 pdb=" C8 G B 292 " -0.079 2.00e-02 2.50e+03 pdb=" N7 G B 292 " -0.076 2.00e-02 2.50e+03 pdb=" C5 G B 292 " -0.035 2.00e-02 2.50e+03 pdb=" C6 G B 292 " 0.046 2.00e-02 2.50e+03 pdb=" O6 G B 292 " 0.112 2.00e-02 2.50e+03 pdb=" N1 G B 292 " 0.036 2.00e-02 2.50e+03 pdb=" C2 G B 292 " -0.033 2.00e-02 2.50e+03 pdb=" N2 G B 292 " -0.020 2.00e-02 2.50e+03 pdb=" N3 G B 292 " -0.069 2.00e-02 2.50e+03 pdb=" C4 G B 292 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 27 " 0.193 2.00e-02 2.50e+03 7.96e-02 1.74e+02 pdb=" N9 DA N 27 " -0.041 2.00e-02 2.50e+03 pdb=" C8 DA N 27 " -0.067 2.00e-02 2.50e+03 pdb=" N7 DA N 27 " -0.051 2.00e-02 2.50e+03 pdb=" C5 DA N 27 " -0.023 2.00e-02 2.50e+03 pdb=" C6 DA N 27 " 0.044 2.00e-02 2.50e+03 pdb=" N6 DA N 27 " 0.095 2.00e-02 2.50e+03 pdb=" N1 DA N 27 " 0.028 2.00e-02 2.50e+03 pdb=" C2 DA N 27 " -0.037 2.00e-02 2.50e+03 pdb=" N3 DA N 27 " -0.080 2.00e-02 2.50e+03 pdb=" C4 DA N 27 " -0.061 2.00e-02 2.50e+03 ... (remaining 2269 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1283 2.74 - 3.28: 16577 3.28 - 3.82: 28842 3.82 - 4.36: 35195 4.36 - 4.90: 52349 Nonbonded interactions: 134246 Sorted by model distance: nonbonded pdb=" OE1 GLN A 943 " pdb=" NZ LYS A1003 " model vdw 2.203 2.520 nonbonded pdb=" NZ LYS A1027 " pdb=" OP1 U B 312 " model vdw 2.209 2.520 nonbonded pdb=" OP2 C B 244 " pdb=" NH2 ARG L 43 " model vdw 2.266 2.520 nonbonded pdb=" NH1 ARG A 481 " pdb=" OP2 C B 183 " model vdw 2.269 2.520 nonbonded pdb=" O TRP A 510 " pdb=" O2' C B 313 " model vdw 2.314 2.440 ... (remaining 134241 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.650 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 57.640 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 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 0.123 17944 Z= 0.636 Angle : 1.461 14.913 25659 Z= 0.987 Chirality : 0.096 0.590 3153 Planarity : 0.011 0.118 2272 Dihedral : 17.665 171.949 7330 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.64 % Favored : 95.02 % Rotamer: Outliers : 0.47 % Allowed : 4.01 % Favored : 95.52 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.19), residues: 1466 helix: -0.97 (0.18), residues: 591 sheet: -1.19 (0.34), residues: 188 loop : -1.71 (0.21), residues: 687 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 224 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 227 average time/residue: 0.3887 time to fit residues: 121.8651 Evaluate side-chains 120 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.519 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1522 time to fit residues: 2.1102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 74 optimal weight: 0.0050 chunk 45 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 137 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 HIS A 571 ASN A 700 GLN A 969 ASN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 50 HIS M 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17944 Z= 0.209 Angle : 0.733 9.683 25659 Z= 0.380 Chirality : 0.042 0.315 3153 Planarity : 0.005 0.050 2272 Dihedral : 18.021 178.135 4918 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.15 % Allowed : 10.83 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: -0.22 (0.21), residues: 1466 helix: 0.98 (0.20), residues: 617 sheet: -0.58 (0.35), residues: 204 loop : -1.08 (0.22), residues: 645 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 151 average time/residue: 0.3053 time to fit residues: 70.1418 Evaluate side-chains 112 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.536 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2173 time to fit residues: 5.4444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 133 optimal weight: 30.0000 chunk 108 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 160 optimal weight: 50.0000 chunk 172 optimal weight: 40.0000 chunk 142 optimal weight: 10.0000 chunk 158 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN M 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17944 Z= 0.288 Angle : 0.747 9.133 25659 Z= 0.388 Chirality : 0.042 0.229 3153 Planarity : 0.005 0.050 2272 Dihedral : 18.033 170.196 4918 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.50 % Favored : 95.43 % Rotamer: Outliers : 3.08 % Allowed : 14.10 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: -0.19 (0.21), residues: 1466 helix: 0.98 (0.20), residues: 619 sheet: -0.56 (0.36), residues: 199 loop : -1.03 (0.23), residues: 648 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 130 average time/residue: 0.3148 time to fit residues: 61.8629 Evaluate side-chains 106 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.449 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1872 time to fit residues: 8.0133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 8.9990 chunk 120 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 107 optimal weight: 30.0000 chunk 160 optimal weight: 40.0000 chunk 170 optimal weight: 5.9990 chunk 152 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 330 HIS ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 ASN M 83 HIS M 96 GLN O 216 GLN O 225 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17944 Z= 0.241 Angle : 0.674 9.262 25659 Z= 0.347 Chirality : 0.040 0.230 3153 Planarity : 0.005 0.048 2272 Dihedral : 18.061 165.639 4918 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.02 % Favored : 95.91 % Rotamer: Outliers : 2.61 % Allowed : 16.25 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: -0.00 (0.21), residues: 1466 helix: 1.17 (0.21), residues: 618 sheet: -0.35 (0.35), residues: 204 loop : -1.01 (0.23), residues: 644 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 126 average time/residue: 0.3065 time to fit residues: 58.9797 Evaluate side-chains 107 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.523 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2075 time to fit residues: 6.0589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 30.0000 chunk 2 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 0.0970 chunk 117 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 152 optimal weight: 50.0000 chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 HIS ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17944 Z= 0.224 Angle : 0.655 9.460 25659 Z= 0.335 Chirality : 0.039 0.204 3153 Planarity : 0.005 0.048 2272 Dihedral : 18.070 165.181 4918 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.16 % Favored : 95.77 % Rotamer: Outliers : 1.31 % Allowed : 17.93 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1466 helix: 1.29 (0.21), residues: 625 sheet: -0.50 (0.34), residues: 220 loop : -0.98 (0.24), residues: 621 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 121 average time/residue: 0.2860 time to fit residues: 54.3020 Evaluate side-chains 103 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 1.572 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2383 time to fit residues: 5.5718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 170 optimal weight: 30.0000 chunk 141 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17944 Z= 0.287 Angle : 0.706 10.172 25659 Z= 0.362 Chirality : 0.040 0.203 3153 Planarity : 0.005 0.051 2272 Dihedral : 18.340 167.047 4918 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.84 % Favored : 95.09 % Rotamer: Outliers : 2.61 % Allowed : 18.58 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.21), residues: 1466 helix: 1.00 (0.20), residues: 621 sheet: -0.49 (0.35), residues: 210 loop : -1.12 (0.24), residues: 635 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 113 average time/residue: 0.2827 time to fit residues: 50.9102 Evaluate side-chains 106 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.679 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1752 time to fit residues: 7.1771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 96 optimal weight: 30.0000 chunk 143 optimal weight: 2.9990 chunk 95 optimal weight: 30.0000 chunk 169 optimal weight: 40.0000 chunk 106 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 HIS ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 17944 Z= 0.364 Angle : 0.782 9.492 25659 Z= 0.403 Chirality : 0.043 0.227 3153 Planarity : 0.006 0.060 2272 Dihedral : 18.779 166.290 4918 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.27 % Rotamer: Outliers : 1.87 % Allowed : 19.89 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: -0.82 (0.21), residues: 1466 helix: 0.32 (0.20), residues: 621 sheet: -0.67 (0.35), residues: 207 loop : -1.32 (0.24), residues: 638 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 108 average time/residue: 0.2783 time to fit residues: 47.8445 Evaluate side-chains 97 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 1.459 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2069 time to fit residues: 5.3657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 154 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.6701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17944 Z= 0.346 Angle : 0.770 10.324 25659 Z= 0.394 Chirality : 0.043 0.242 3153 Planarity : 0.005 0.056 2272 Dihedral : 18.909 161.412 4918 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.59 % Favored : 94.34 % Rotamer: Outliers : 1.03 % Allowed : 21.76 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: -0.92 (0.21), residues: 1466 helix: 0.27 (0.20), residues: 620 sheet: -0.78 (0.35), residues: 208 loop : -1.38 (0.24), residues: 638 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 96 average time/residue: 0.2796 time to fit residues: 43.1411 Evaluate side-chains 86 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 1.614 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2388 time to fit residues: 3.8384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17944 Z= 0.168 Angle : 0.634 9.814 25659 Z= 0.320 Chirality : 0.037 0.194 3153 Planarity : 0.004 0.054 2272 Dihedral : 18.363 163.976 4918 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.82 % Favored : 96.11 % Rotamer: Outliers : 0.37 % Allowed : 22.50 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: -0.09 (0.22), residues: 1466 helix: 1.14 (0.21), residues: 617 sheet: -0.57 (0.35), residues: 224 loop : -1.04 (0.25), residues: 625 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 101 average time/residue: 0.2972 time to fit residues: 47.1339 Evaluate side-chains 88 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.574 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1739 time to fit residues: 2.5267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 50.0000 chunk 102 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 175 optimal weight: 30.0000 chunk 161 optimal weight: 50.0000 chunk 139 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 30.0000 overall best weight: 6.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.7026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17944 Z= 0.398 Angle : 0.813 10.411 25659 Z= 0.415 Chirality : 0.044 0.237 3153 Planarity : 0.006 0.050 2272 Dihedral : 18.903 158.087 4918 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 24.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.34 % Favored : 93.59 % Rotamer: Outliers : 0.19 % Allowed : 22.60 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: -0.89 (0.21), residues: 1466 helix: 0.39 (0.20), residues: 623 sheet: -0.94 (0.34), residues: 220 loop : -1.42 (0.25), residues: 623 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.716 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 80 average time/residue: 0.2948 time to fit residues: 38.0434 Evaluate side-chains 80 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.498 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2078 time to fit residues: 2.3015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 17 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.097291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.071121 restraints weight = 93326.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.072548 restraints weight = 54581.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.072664 restraints weight = 40032.220| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17944 Z= 0.259 Angle : 0.702 13.496 25659 Z= 0.356 Chirality : 0.040 0.227 3153 Planarity : 0.005 0.049 2272 Dihedral : 18.712 160.325 4918 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 0.65 % Allowed : 22.04 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: -0.54 (0.22), residues: 1466 helix: 0.75 (0.20), residues: 622 sheet: -0.82 (0.35), residues: 213 loop : -1.26 (0.25), residues: 631 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2700.74 seconds wall clock time: 50 minutes 25.65 seconds (3025.65 seconds total)