Starting phenix.real_space_refine on Fri Mar 15 22:25:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3t_41011/03_2024/8t3t_41011.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3t_41011/03_2024/8t3t_41011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3t_41011/03_2024/8t3t_41011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3t_41011/03_2024/8t3t_41011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3t_41011/03_2024/8t3t_41011.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3t_41011/03_2024/8t3t_41011.pdb" } resolution = 3.21 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= 0.015 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 292 5.49 5 S 32 5.16 5 C 7243 2.51 5 N 2423 2.21 5 O 2997 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 97": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "K ARG 681": "NH1" <-> "NH2" Residue "L GLU 669": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12991 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "L" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12156 SG CYS K 663 99.375 75.126 80.380 1.00227.89 S ATOM 12315 SG CYS K 683 101.649 76.294 83.194 1.00249.62 S ATOM 12335 SG CYS K 686 98.552 74.224 84.036 1.00253.88 S ATOM 12039 SG CYS K 648 105.375 86.157 77.237 1.00280.67 S ATOM 12059 SG CYS K 651 107.516 88.976 76.374 1.00289.30 S ATOM 12194 SG CYS K 668 108.042 85.897 74.379 1.00267.32 S ATOM 12217 SG CYS K 671 109.223 85.686 77.834 1.00266.56 S ATOM 12699 SG CYS L 663 95.659 76.176 60.519 1.00160.31 S ATOM 12858 SG CYS L 683 92.975 77.494 58.092 1.00136.58 S ATOM 12878 SG CYS L 686 96.246 76.198 56.724 1.00148.23 S ATOM 12582 SG CYS L 648 85.727 83.231 65.188 1.00193.20 S ATOM 12602 SG CYS L 651 82.289 84.005 66.644 1.00193.10 S ATOM 12737 SG CYS L 668 83.899 80.805 67.477 1.00167.52 S ATOM 12760 SG CYS L 671 82.719 80.984 64.086 1.00156.96 S Time building chain proxies: 7.43, per 1000 atoms: 0.57 Number of scatterers: 12991 At special positions: 0 Unit cell: (129.96, 119.7, 117.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 32 16.00 P 292 15.00 O 2997 8.00 N 2423 7.00 C 7243 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: 6.31 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 801 " pdb="ZN ZN K 801 " - pdb=" ND1 HIS K 665 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 683 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 686 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 663 " pdb=" ZN K 802 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 668 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 651 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 648 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 671 " pdb=" ZN L 801 " pdb="ZN ZN L 801 " - pdb=" ND1 HIS L 665 " pdb="ZN ZN L 801 " - pdb=" SG CYS L 683 " pdb="ZN ZN L 801 " - pdb=" SG CYS L 686 " pdb="ZN ZN L 801 " - pdb=" SG CYS L 663 " pdb=" ZN L 802 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 668 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 651 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 648 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 671 " Number of angles added : 18 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1670 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 66.7% alpha, 3.6% beta 133 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 5.98 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.684A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.574A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.786A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.940A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.816A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.887A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.581A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.607A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.509A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.834A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.781A pdb=" N SER D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.758A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.594A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.750A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.598A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.927A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.530A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.514A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.856A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.703A pdb=" N GLU H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA H 77 " --> pdb=" O ILE H 73 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.608A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.756A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 633 through 647 Processing helix chain 'K' and resid 668 through 678 removed outlier: 3.893A pdb=" N CYS K 672 " --> pdb=" O CYS K 668 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS K 673 " --> pdb=" O GLU K 669 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU K 674 " --> pdb=" O ASN K 670 " (cutoff:3.500A) Processing helix chain 'L' and resid 633 through 647 removed outlier: 3.592A pdb=" N TYR L 647 " --> pdb=" O ARG L 643 " (cutoff:3.500A) Processing helix chain 'L' and resid 668 through 677 removed outlier: 3.654A pdb=" N GLU L 674 " --> pdb=" O ASN L 670 " (cutoff:3.500A) Processing helix chain 'L' and resid 691 through 693 No H-bonds generated for 'chain 'L' and resid 691 through 693' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.970A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.523A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.673A pdb=" N THR G 101 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.250A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.891A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.021A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.580A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.136A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 666 through 667 Processing sheet with id=AB3, first strand: chain 'L' and resid 666 through 667 364 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 342 hydrogen bonds 684 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 6.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3057 1.34 - 1.46: 4223 1.46 - 1.58: 5903 1.58 - 1.70: 582 1.70 - 1.82: 46 Bond restraints: 13811 Sorted by residual: bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.92e+00 bond pdb=" N GLY D 53 " pdb=" CA GLY D 53 " ideal model delta sigma weight residual 1.442 1.451 -0.009 7.70e-03 1.69e+04 1.46e+00 bond pdb=" N ASN K 687 " pdb=" CA ASN K 687 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.25e+00 bond pdb=" CA ASP E 81 " pdb=" CB ASP E 81 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.21e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.18e+00 ... (remaining 13806 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.65: 1463 105.65 - 112.72: 7639 112.72 - 119.79: 4719 119.79 - 126.86: 5295 126.86 - 133.93: 789 Bond angle restraints: 19905 Sorted by residual: angle pdb=" CA GLU L 669 " pdb=" CB GLU L 669 " pdb=" CG GLU L 669 " ideal model delta sigma weight residual 114.10 121.86 -7.76 2.00e+00 2.50e-01 1.51e+01 angle pdb=" CA GLY D 53 " pdb=" C GLY D 53 " pdb=" N ILE D 54 " ideal model delta sigma weight residual 114.65 117.96 -3.31 9.20e-01 1.18e+00 1.30e+01 angle pdb=" O3' DG J 137 " pdb=" C3' DG J 137 " pdb=" C2' DG J 137 " ideal model delta sigma weight residual 111.50 106.47 5.03 1.50e+00 4.44e-01 1.12e+01 angle pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 121.54 127.86 -6.32 1.91e+00 2.74e-01 1.10e+01 angle pdb=" CA LYS K 661 " pdb=" CB LYS K 661 " pdb=" CG LYS K 661 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 ... (remaining 19900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.18: 5811 30.18 - 60.35: 1716 60.35 - 90.53: 35 90.53 - 120.70: 0 120.70 - 150.88: 3 Dihedral angle restraints: 7565 sinusoidal: 4988 harmonic: 2577 Sorted by residual: dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 69.12 150.88 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" CA CYS L 686 " pdb=" C CYS L 686 " pdb=" N ASN L 687 " pdb=" CA ASN L 687 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual -140.00 2.57 -142.57 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 7562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1718 0.037 - 0.074: 450 0.074 - 0.111: 86 0.111 - 0.148: 18 0.148 - 0.185: 1 Chirality restraints: 2273 Sorted by residual: chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA ASP E 77 " pdb=" N ASP E 77 " pdb=" C ASP E 77 " pdb=" CB ASP E 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ASN K 687 " pdb=" N ASN K 687 " pdb=" C ASN K 687 " pdb=" CB ASN K 687 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 2270 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP K 694 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ASP K 694 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP K 694 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU K 695 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 117 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C ALA D 117 " 0.034 2.00e-02 2.50e+03 pdb=" O ALA D 117 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL D 118 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU L 669 " 0.009 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" CD GLU L 669 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU L 669 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU L 669 " 0.012 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1146 2.74 - 3.28: 11111 3.28 - 3.82: 22524 3.82 - 4.36: 27629 4.36 - 4.90: 40823 Nonbonded interactions: 103233 Sorted by model distance: nonbonded pdb=" N4 DC I 11 " pdb=" N2 DG J 137 " model vdw 2.202 3.200 nonbonded pdb=" OG1 THR A 80 " pdb=" OD1 ASP A 81 " model vdw 2.229 2.440 nonbonded pdb=" O TYR K 647 " pdb=" NZ LYS K 656 " model vdw 2.254 2.520 nonbonded pdb=" N LYS K 661 " pdb=" OD1 ASP K 694 " model vdw 2.264 2.520 nonbonded pdb=" O TYR L 647 " pdb=" NZ LYS L 656 " model vdw 2.265 2.520 ... (remaining 103228 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 10.120 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 44.510 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 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 : 0.004 0.042 13811 Z= 0.197 Angle : 0.597 9.090 19905 Z= 0.365 Chirality : 0.035 0.185 2273 Planarity : 0.004 0.033 1505 Dihedral : 27.438 150.879 5895 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.27 % Allowed : 27.52 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 865 helix: 1.24 (0.23), residues: 541 sheet: None (None), residues: 0 loop : -1.83 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 655 HIS 0.006 0.001 HIS C 82 PHE 0.012 0.001 PHE H 65 TYR 0.007 0.001 TYR F 51 ARG 0.004 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 170 average time/residue: 0.3768 time to fit residues: 82.3625 Evaluate side-chains 171 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13811 Z= 0.263 Angle : 0.555 6.129 19905 Z= 0.336 Chirality : 0.036 0.162 2273 Planarity : 0.004 0.033 1505 Dihedral : 29.348 150.702 4170 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.09 % Allowed : 24.70 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.28), residues: 865 helix: 1.68 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -1.84 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 655 HIS 0.005 0.001 HIS C 82 PHE 0.011 0.001 PHE H 65 TYR 0.008 0.001 TYR F 51 ARG 0.004 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8128 (ptp90) outliers start: 23 outliers final: 15 residues processed: 178 average time/residue: 0.3713 time to fit residues: 85.5496 Evaluate side-chains 182 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 688 LYS Chi-restraints excluded: chain L residue 697 THR Chi-restraints excluded: chain L residue 699 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13811 Z= 0.195 Angle : 0.541 5.980 19905 Z= 0.329 Chirality : 0.035 0.184 2273 Planarity : 0.003 0.034 1505 Dihedral : 29.354 151.006 4168 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.68 % Allowed : 26.17 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.29), residues: 865 helix: 1.92 (0.22), residues: 549 sheet: -1.86 (1.11), residues: 20 loop : -1.96 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP L 655 HIS 0.003 0.001 HIS C 82 PHE 0.009 0.001 PHE H 65 TYR 0.009 0.001 TYR C 50 ARG 0.002 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 669 GLU cc_start: 0.8690 (tp30) cc_final: 0.8134 (tp30) REVERT: L 673 LYS cc_start: 0.8862 (ptpp) cc_final: 0.8590 (ptpp) outliers start: 20 outliers final: 19 residues processed: 175 average time/residue: 0.3459 time to fit residues: 78.4466 Evaluate side-chains 184 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 688 LYS Chi-restraints excluded: chain L residue 697 THR Chi-restraints excluded: chain L residue 699 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 0.0030 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13811 Z= 0.249 Angle : 0.541 6.461 19905 Z= 0.328 Chirality : 0.035 0.179 2273 Planarity : 0.004 0.032 1505 Dihedral : 29.379 150.463 4168 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.30 % Allowed : 24.43 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.29), residues: 865 helix: 1.97 (0.22), residues: 556 sheet: -2.01 (1.07), residues: 20 loop : -1.94 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 655 HIS 0.004 0.001 HIS C 82 PHE 0.009 0.001 PHE H 65 TYR 0.007 0.001 TYR F 51 ARG 0.004 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8783 (pm20) cc_final: 0.8575 (pm20) REVERT: G 42 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.7912 (ptm160) REVERT: G 73 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8555 (t0) outliers start: 32 outliers final: 22 residues processed: 188 average time/residue: 0.3695 time to fit residues: 89.9148 Evaluate side-chains 191 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 672 CYS Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 688 LYS Chi-restraints excluded: chain L residue 697 THR Chi-restraints excluded: chain L residue 699 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.0770 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN L 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13811 Z= 0.324 Angle : 0.568 6.361 19905 Z= 0.343 Chirality : 0.037 0.186 2273 Planarity : 0.004 0.033 1505 Dihedral : 29.466 150.329 4168 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.56 % Allowed : 24.56 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.29), residues: 865 helix: 1.98 (0.22), residues: 554 sheet: -1.85 (1.11), residues: 20 loop : -1.98 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 655 HIS 0.004 0.001 HIS C 31 PHE 0.011 0.001 PHE D 70 TYR 0.008 0.001 TYR F 51 ARG 0.005 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8892 (pm20) cc_final: 0.8663 (pm20) REVERT: G 42 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.7986 (ptm160) REVERT: G 73 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8626 (t0) REVERT: K 658 MET cc_start: 0.6877 (tpp) cc_final: 0.6660 (tpp) REVERT: L 658 MET cc_start: 0.8537 (tpp) cc_final: 0.8235 (tpp) outliers start: 34 outliers final: 23 residues processed: 188 average time/residue: 0.3577 time to fit residues: 86.6487 Evaluate side-chains 194 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 688 LYS Chi-restraints excluded: chain L residue 697 THR Chi-restraints excluded: chain L residue 699 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13811 Z= 0.219 Angle : 0.556 8.407 19905 Z= 0.336 Chirality : 0.035 0.190 2273 Planarity : 0.004 0.032 1505 Dihedral : 29.465 150.890 4168 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.30 % Allowed : 25.50 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.29), residues: 865 helix: 2.07 (0.22), residues: 554 sheet: -1.88 (1.09), residues: 20 loop : -1.93 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 655 HIS 0.003 0.001 HIS A 113 PHE 0.009 0.001 PHE H 65 TYR 0.009 0.001 TYR C 50 ARG 0.003 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 171 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 42 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.7956 (ptm160) REVERT: G 73 ASN cc_start: 0.9164 (OUTLIER) cc_final: 0.8627 (t0) outliers start: 32 outliers final: 25 residues processed: 188 average time/residue: 0.3654 time to fit residues: 88.7912 Evaluate side-chains 198 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 688 LYS Chi-restraints excluded: chain L residue 697 THR Chi-restraints excluded: chain L residue 699 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13811 Z= 0.195 Angle : 0.553 9.468 19905 Z= 0.334 Chirality : 0.035 0.189 2273 Planarity : 0.003 0.032 1505 Dihedral : 29.447 151.109 4168 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.43 % Allowed : 25.37 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.13 (0.29), residues: 865 helix: 2.12 (0.22), residues: 555 sheet: -1.92 (1.12), residues: 20 loop : -1.92 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 655 HIS 0.002 0.001 HIS C 82 PHE 0.008 0.001 PHE H 65 TYR 0.008 0.001 TYR C 50 ARG 0.003 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8755 (pm20) cc_final: 0.8528 (pm20) REVERT: G 73 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8623 (t0) outliers start: 33 outliers final: 27 residues processed: 185 average time/residue: 0.3576 time to fit residues: 85.7337 Evaluate side-chains 198 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain K residue 673 LYS Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 688 LYS Chi-restraints excluded: chain L residue 697 THR Chi-restraints excluded: chain L residue 699 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.0070 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13811 Z= 0.209 Angle : 0.547 8.503 19905 Z= 0.331 Chirality : 0.035 0.185 2273 Planarity : 0.003 0.032 1505 Dihedral : 29.422 151.141 4168 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.43 % Allowed : 25.10 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.29), residues: 865 helix: 2.16 (0.22), residues: 556 sheet: -1.99 (1.14), residues: 20 loop : -1.90 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 655 HIS 0.003 0.001 HIS C 82 PHE 0.007 0.001 PHE H 65 TYR 0.007 0.001 TYR F 51 ARG 0.004 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8764 (pm20) cc_final: 0.8522 (pm20) REVERT: G 42 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.7942 (ptm160) REVERT: G 73 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8624 (t0) outliers start: 33 outliers final: 28 residues processed: 186 average time/residue: 0.3599 time to fit residues: 86.7344 Evaluate side-chains 200 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 688 LYS Chi-restraints excluded: chain L residue 697 THR Chi-restraints excluded: chain L residue 699 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 0.0030 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13811 Z= 0.204 Angle : 0.537 8.190 19905 Z= 0.326 Chirality : 0.035 0.178 2273 Planarity : 0.003 0.032 1505 Dihedral : 29.386 151.030 4168 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.30 % Allowed : 24.83 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.29), residues: 865 helix: 2.22 (0.22), residues: 556 sheet: -1.92 (1.14), residues: 20 loop : -1.86 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 655 HIS 0.003 0.001 HIS C 82 PHE 0.007 0.001 PHE H 65 TYR 0.008 0.001 TYR C 50 ARG 0.007 0.000 ARG L 675 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8791 (pm20) cc_final: 0.8545 (pm20) REVERT: G 42 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7929 (ptm160) REVERT: G 73 ASN cc_start: 0.9159 (OUTLIER) cc_final: 0.8620 (t0) REVERT: L 669 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8512 (tm-30) outliers start: 32 outliers final: 27 residues processed: 190 average time/residue: 0.3709 time to fit residues: 91.4734 Evaluate side-chains 202 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 688 LYS Chi-restraints excluded: chain L residue 697 THR Chi-restraints excluded: chain L residue 699 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13811 Z= 0.209 Angle : 0.539 7.683 19905 Z= 0.325 Chirality : 0.035 0.182 2273 Planarity : 0.003 0.032 1505 Dihedral : 29.347 150.465 4168 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.76 % Allowed : 25.77 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.29), residues: 865 helix: 2.30 (0.22), residues: 556 sheet: -1.43 (1.23), residues: 20 loop : -1.83 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 655 HIS 0.002 0.001 HIS C 82 PHE 0.008 0.001 PHE H 65 TYR 0.008 0.001 TYR C 50 ARG 0.004 0.000 ARG F 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8821 (pm20) cc_final: 0.8558 (pm20) REVERT: G 42 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.7918 (ptm160) REVERT: G 73 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8647 (t0) REVERT: L 673 LYS cc_start: 0.8456 (mtmm) cc_final: 0.8130 (mtmm) outliers start: 28 outliers final: 24 residues processed: 187 average time/residue: 0.3607 time to fit residues: 87.1735 Evaluate side-chains 199 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 688 LYS Chi-restraints excluded: chain L residue 697 THR Chi-restraints excluded: chain L residue 699 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.0050 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** L 654 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 = 0.3541 r_free = 0.3541 target = 0.098486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.063626 restraints weight = 27170.387| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.74 r_work: 0.2677 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13811 Z= 0.195 Angle : 0.541 7.953 19905 Z= 0.326 Chirality : 0.034 0.180 2273 Planarity : 0.003 0.032 1505 Dihedral : 29.348 150.505 4168 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.62 % Allowed : 26.17 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.29), residues: 865 helix: 2.30 (0.22), residues: 556 sheet: -1.43 (1.21), residues: 20 loop : -1.82 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 655 HIS 0.003 0.001 HIS C 82 PHE 0.007 0.001 PHE H 65 TYR 0.008 0.001 TYR C 50 ARG 0.004 0.000 ARG F 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2784.53 seconds wall clock time: 50 minutes 12.83 seconds (3012.83 seconds total)