Starting phenix.real_space_refine on Sun Dec 10 17:02:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nn6_0458/12_2023/6nn6_0458.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nn6_0458/12_2023/6nn6_0458.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/6nn6_0458/12_2023/6nn6_0458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nn6_0458/12_2023/6nn6_0458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nn6_0458/12_2023/6nn6_0458.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nn6_0458/12_2023/6nn6_0458.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= 0.004 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 288 5.49 5 S 27 5.16 5 C 8631 2.51 5 N 2781 2.21 5 O 3398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 282": "NH1" <-> "NH2" Residue "K TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15125 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" 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: "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: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2671 Classifications: {'peptide': 328} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 309} Chain: "L" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 593 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 Time building chain proxies: 8.14, per 1000 atoms: 0.54 Number of scatterers: 15125 At special positions: 0 Unit cell: (124.2, 117.72, 116.64, 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 27 16.00 P 288 15.00 O 3398 8.00 N 2781 7.00 C 8631 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: 7.87 Conformation dependent library (CDL) restraints added in 1.6 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 10 sheets defined 56.5% alpha, 5.4% beta 115 base pairs and 212 stacking pairs defined. Time for finding SS restraints: 6.14 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.599A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 4.035A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 87 through 114 removed outlier: 3.625A pdb=" N LEU A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.809A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.775A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.579A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 4.084A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 removed outlier: 4.024A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.506A pdb=" N GLU C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.551A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 49 removed outlier: 3.583A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 84 removed outlier: 3.715A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N MET D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.360A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.603A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 4.125A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 75 removed outlier: 3.808A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 86 through 114 removed outlier: 3.684A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 131 removed outlier: 4.002A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 removed outlier: 3.568A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 76 removed outlier: 3.902A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.094A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.659A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 34 removed outlier: 3.573A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 71 removed outlier: 3.841A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.773A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.688A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 47 removed outlier: 3.765A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS H 43 " --> pdb=" O ILE H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 74 removed outlier: 3.874A pdb=" N MET H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER H 64 " --> pdb=" O SER H 60 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL H 66 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 removed outlier: 3.810A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 102 removed outlier: 4.040A pdb=" N LEU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.564A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 124 " --> pdb=" O CYS H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 45 removed outlier: 3.628A pdb=" N ILE K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 57 removed outlier: 3.641A pdb=" N LEU K 53 " --> pdb=" O PRO K 49 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA K 54 " --> pdb=" O ASP K 50 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN K 57 " --> pdb=" O LEU K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 90 removed outlier: 3.576A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA K 81 " --> pdb=" O LYS K 77 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP K 83 " --> pdb=" O ASN K 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 118 removed outlier: 3.680A pdb=" N HIS K 109 " --> pdb=" O GLY K 105 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU K 111 " --> pdb=" O LEU K 107 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN K 112 " --> pdb=" O ARG K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 127 removed outlier: 3.637A pdb=" N ASN K 127 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 151 removed outlier: 3.890A pdb=" N VAL K 144 " --> pdb=" O SER K 140 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA K 145 " --> pdb=" O PHE K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 175 Processing helix chain 'K' and resid 189 through 209 removed outlier: 4.300A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE K 202 " --> pdb=" O MET K 198 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS K 207 " --> pdb=" O ARG K 203 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR K 209 " --> pdb=" O TRP K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 233 removed outlier: 3.880A pdb=" N ARG K 231 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 257 Processing helix chain 'K' and resid 286 through 289 removed outlier: 3.686A pdb=" N THR K 289 " --> pdb=" O ASP K 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 286 through 289' Processing helix chain 'K' and resid 319 through 331 removed outlier: 4.259A pdb=" N GLU K 323 " --> pdb=" O ARG K 319 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN K 324 " --> pdb=" O THR K 320 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS K 330 " --> pdb=" O PHE K 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 34 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.943A 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 'B' and resid 96 through 98 removed outlier: 6.498A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.173A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.116A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.837A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'K' and resid 6 through 9 removed outlier: 3.603A pdb=" N LEU K 9 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA K 18 " --> pdb=" O LEU K 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 218 through 220 removed outlier: 5.792A pdb=" N GLY K 184 " --> pdb=" O GLU K 219 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N VAL K 185 " --> pdb=" O PHE K 159 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP K 161 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE K 266 " --> pdb=" O HIS K 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.642A pdb=" N VAL L 5 " --> pdb=" O ILE L 13 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU L 15 " --> pdb=" O ILE L 3 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N LEU L 67 " --> pdb=" O GLN L 2 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE L 4 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU L 69 " --> pdb=" O PHE L 4 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LYS L 6 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N LEU L 71 " --> pdb=" O LYS L 6 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 271 hydrogen bonds 486 hydrogen bond angles 0 basepair planarities 115 basepair parallelities 212 stacking parallelities Total time for adding SS restraints: 5.51 Time building geometry restraints manager: 8.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2821 1.33 - 1.45: 5116 1.45 - 1.57: 7443 1.57 - 1.69: 576 1.69 - 1.82: 47 Bond restraints: 16003 Sorted by residual: bond pdb=" C LEU A 65 " pdb=" N PRO A 66 " ideal model delta sigma weight residual 1.336 1.381 -0.046 1.23e-02 6.61e+03 1.37e+01 bond pdb=" C LEU H 101 " pdb=" N LEU H 102 " ideal model delta sigma weight residual 1.331 1.231 0.100 2.83e-02 1.25e+03 1.26e+01 bond pdb=" C LEU G 108 " pdb=" N PRO G 109 " ideal model delta sigma weight residual 1.333 1.304 0.030 1.01e-02 9.80e+03 8.75e+00 bond pdb=" C GLN C 24 " pdb=" N PHE C 25 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.47e-02 4.63e+03 6.67e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.89e+00 ... (remaining 15998 not shown) Histogram of bond angle deviations from ideal: 97.50 - 104.83: 1311 104.83 - 112.16: 8678 112.16 - 119.49: 5258 119.49 - 126.83: 6789 126.83 - 134.16: 841 Bond angle restraints: 22877 Sorted by residual: angle pdb=" N VAL C 27 " pdb=" CA VAL C 27 " pdb=" C VAL C 27 " ideal model delta sigma weight residual 113.43 108.54 4.89 1.09e+00 8.42e-01 2.01e+01 angle pdb=" C THR D 115 " pdb=" N LYS D 116 " pdb=" CA LYS D 116 " ideal model delta sigma weight residual 120.28 126.19 -5.91 1.34e+00 5.57e-01 1.94e+01 angle pdb=" N ARG K 282 " pdb=" CA ARG K 282 " pdb=" C ARG K 282 " ideal model delta sigma weight residual 114.04 109.04 5.00 1.24e+00 6.50e-01 1.63e+01 angle pdb=" N ILE L 36 " pdb=" CA ILE L 36 " pdb=" C ILE L 36 " ideal model delta sigma weight residual 109.02 105.28 3.74 9.30e-01 1.16e+00 1.62e+01 angle pdb=" C ALA G 103 " pdb=" N GLN G 104 " pdb=" CA GLN G 104 " ideal model delta sigma weight residual 122.40 127.97 -5.57 1.45e+00 4.76e-01 1.47e+01 ... (remaining 22872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 7467 35.46 - 70.91: 1377 70.91 - 106.37: 42 106.37 - 141.82: 5 141.82 - 177.28: 1 Dihedral angle restraints: 8892 sinusoidal: 5543 harmonic: 3349 Sorted by residual: dihedral pdb=" CA LEU D 100 " pdb=" C LEU D 100 " pdb=" N LEU D 101 " pdb=" CA LEU D 101 " ideal model delta harmonic sigma weight residual -180.00 -150.22 -29.78 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual 180.00 -156.34 -23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA SER H 60 " pdb=" C SER H 60 " pdb=" N ILE H 61 " pdb=" CA ILE H 61 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 8889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1825 0.052 - 0.103: 639 0.103 - 0.155: 112 0.155 - 0.207: 12 0.207 - 0.259: 1 Chirality restraints: 2589 Sorted by residual: chirality pdb=" CB ILE K 279 " pdb=" CA ILE K 279 " pdb=" CG1 ILE K 279 " pdb=" CG2 ILE K 279 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2586 not shown) Planarity restraints: 1901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 40 " -0.022 2.00e-02 2.50e+03 2.12e-02 8.96e+00 pdb=" CG TYR H 40 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR H 40 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR H 40 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR H 40 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR H 40 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR H 40 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 40 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER K 132 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO K 133 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO K 133 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 133 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO G 80 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.033 5.00e-02 4.00e+02 ... (remaining 1898 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 978 2.70 - 3.25: 13268 3.25 - 3.80: 27575 3.80 - 4.35: 34217 4.35 - 4.90: 49936 Nonbonded interactions: 125974 Sorted by model distance: nonbonded pdb=" O ILE E 62 " pdb=" O ARG E 63 " model vdw 2.144 3.040 nonbonded pdb=" OE2 GLU C 56 " pdb=" NH2 ARG K 282 " model vdw 2.267 2.520 nonbonded pdb=" OH TYR K 136 " pdb=" OE2 GLU K 138 " model vdw 2.273 2.440 nonbonded pdb=" O LYS C 15 " pdb=" O THR C 16 " model vdw 2.274 3.040 nonbonded pdb=" O2 DC I 56 " pdb=" N2 DG J -56 " model vdw 2.284 2.520 ... (remaining 125969 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.850 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 45.980 Find NCS groups from input model: 0.520 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 0.100 16003 Z= 0.577 Angle : 1.016 8.280 22877 Z= 0.597 Chirality : 0.051 0.259 2589 Planarity : 0.007 0.061 1901 Dihedral : 25.945 177.280 6728 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.81 % Favored : 96.01 % Rotamer: Outliers : 0.81 % Allowed : 1.73 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -5.04 (0.18), residues: 1129 helix: -4.32 (0.09), residues: 622 sheet: -1.07 (0.58), residues: 74 loop : -1.83 (0.25), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K 228 HIS 0.020 0.003 HIS B 75 PHE 0.022 0.003 PHE B 100 TYR 0.049 0.004 TYR H 40 ARG 0.010 0.001 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 364 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 368 average time/residue: 0.4027 time to fit residues: 193.3833 Evaluate side-chains 240 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 237 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6453 time to fit residues: 3.9077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 108 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN A 125 GLN B 75 HIS C 94 ASN C 110 ASN D 67 ASN E 68 GLN E 76 GLN G 84 GLN G 104 GLN H 67 ASN H 95 GLN K 109 HIS K 113 GLN K 259 ASN ** K 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16003 Z= 0.223 Angle : 0.674 7.521 22877 Z= 0.392 Chirality : 0.039 0.211 2589 Planarity : 0.005 0.039 1901 Dihedral : 30.537 177.976 4439 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.17 % Allowed : 10.57 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -2.76 (0.22), residues: 1129 helix: -2.11 (0.17), residues: 633 sheet: -0.72 (0.62), residues: 77 loop : -1.25 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 205 HIS 0.010 0.001 HIS G 31 PHE 0.018 0.001 PHE L 45 TYR 0.019 0.002 TYR K 209 ARG 0.007 0.001 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 291 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 21 residues processed: 308 average time/residue: 0.3257 time to fit residues: 138.0084 Evaluate side-chains 274 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 253 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1477 time to fit residues: 7.2406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 85 GLN A 108 ASN B 25 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN E 68 GLN E 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** K 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16003 Z= 0.348 Angle : 0.693 7.605 22877 Z= 0.394 Chirality : 0.040 0.158 2589 Planarity : 0.005 0.043 1901 Dihedral : 30.437 176.014 4439 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.54 % Allowed : 14.94 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -1.80 (0.23), residues: 1129 helix: -1.19 (0.19), residues: 638 sheet: -1.03 (0.59), residues: 78 loop : -0.93 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 228 HIS 0.007 0.002 HIS K 251 PHE 0.016 0.002 PHE B 100 TYR 0.018 0.002 TYR E 99 ARG 0.004 0.001 ARG K 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 254 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 268 average time/residue: 0.3442 time to fit residues: 126.2680 Evaluate side-chains 243 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 229 time to evaluate : 1.330 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1319 time to fit residues: 5.0897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 111 optimal weight: 30.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 85 GLN C 38 ASN E 68 GLN G 31 HIS G 38 ASN K 168 GLN ** K 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16003 Z= 0.213 Angle : 0.600 6.667 22877 Z= 0.348 Chirality : 0.037 0.185 2589 Planarity : 0.004 0.049 1901 Dihedral : 30.073 174.337 4439 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.54 % Allowed : 16.26 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -1.05 (0.24), residues: 1129 helix: -0.44 (0.20), residues: 635 sheet: -1.01 (0.59), residues: 78 loop : -0.78 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 228 HIS 0.006 0.001 HIS K 251 PHE 0.017 0.001 PHE K 159 TYR 0.021 0.001 TYR H 83 ARG 0.005 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 255 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 268 average time/residue: 0.3317 time to fit residues: 123.2223 Evaluate side-chains 251 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 235 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1308 time to fit residues: 5.5132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.0030 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN B 25 ASN E 68 GLN G 38 ASN H 63 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16003 Z= 0.240 Angle : 0.605 7.805 22877 Z= 0.349 Chirality : 0.038 0.206 2589 Planarity : 0.004 0.039 1901 Dihedral : 30.017 174.067 4439 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.93 % Allowed : 17.99 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.68 (0.25), residues: 1129 helix: -0.08 (0.20), residues: 636 sheet: -1.18 (0.59), residues: 80 loop : -0.65 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 228 HIS 0.005 0.001 HIS F 75 PHE 0.015 0.001 PHE K 159 TYR 0.026 0.002 TYR H 83 ARG 0.005 0.000 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 233 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 242 average time/residue: 0.3222 time to fit residues: 108.5091 Evaluate side-chains 229 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 217 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1635 time to fit residues: 4.9782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 0.0270 chunk 133 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 108 ASN G 38 ASN H 63 ASN ** K 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16003 Z= 0.178 Angle : 0.568 8.824 22877 Z= 0.329 Chirality : 0.036 0.164 2589 Planarity : 0.003 0.045 1901 Dihedral : 29.689 174.680 4439 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.32 % Allowed : 18.60 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1129 helix: 0.50 (0.21), residues: 635 sheet: -1.08 (0.60), residues: 80 loop : -0.45 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 228 HIS 0.005 0.001 HIS K 251 PHE 0.019 0.001 PHE L 45 TYR 0.032 0.002 TYR H 83 ARG 0.014 0.000 ARG K 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 249 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 252 average time/residue: 0.3278 time to fit residues: 114.1428 Evaluate side-chains 233 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 225 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1349 time to fit residues: 3.6418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN H 47 GLN H 63 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16003 Z= 0.394 Angle : 0.694 7.646 22877 Z= 0.388 Chirality : 0.041 0.178 2589 Planarity : 0.005 0.037 1901 Dihedral : 30.128 172.253 4439 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.13 % Allowed : 18.90 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.45 (0.25), residues: 1129 helix: 0.11 (0.21), residues: 629 sheet: -1.26 (0.59), residues: 80 loop : -0.51 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 205 HIS 0.010 0.002 HIS K 251 PHE 0.018 0.002 PHE A 104 TYR 0.020 0.002 TYR H 40 ARG 0.005 0.001 ARG K 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 221 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 230 average time/residue: 0.3324 time to fit residues: 106.8974 Evaluate side-chains 222 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 208 time to evaluate : 1.240 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1558 time to fit residues: 5.8686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16003 Z= 0.207 Angle : 0.596 8.411 22877 Z= 0.341 Chirality : 0.037 0.178 2589 Planarity : 0.003 0.042 1901 Dihedral : 29.690 174.161 4439 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.71 % Allowed : 20.43 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1129 helix: 0.49 (0.21), residues: 634 sheet: -1.10 (0.60), residues: 80 loop : -0.43 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 228 HIS 0.007 0.001 HIS K 251 PHE 0.025 0.001 PHE L 45 TYR 0.019 0.002 TYR H 40 ARG 0.006 0.000 ARG K 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 235 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 239 average time/residue: 0.3267 time to fit residues: 108.3852 Evaluate side-chains 225 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 219 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1361 time to fit residues: 3.0913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 112 optimal weight: 0.1980 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN D 67 ASN H 63 ASN K 113 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16003 Z= 0.230 Angle : 0.612 11.756 22877 Z= 0.346 Chirality : 0.037 0.186 2589 Planarity : 0.003 0.036 1901 Dihedral : 29.632 173.934 4439 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.91 % Allowed : 21.65 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1129 helix: 0.51 (0.21), residues: 634 sheet: -1.02 (0.59), residues: 80 loop : -0.41 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP K 228 HIS 0.007 0.001 HIS K 251 PHE 0.019 0.001 PHE L 45 TYR 0.020 0.002 TYR H 40 ARG 0.005 0.000 ARG K 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 224 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 228 average time/residue: 0.3284 time to fit residues: 105.0256 Evaluate side-chains 217 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 210 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1315 time to fit residues: 3.2998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 85 GLN A 108 ASN D 67 ASN E 113 HIS ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 16003 Z= 0.463 Angle : 0.752 9.933 22877 Z= 0.417 Chirality : 0.044 0.212 2589 Planarity : 0.005 0.036 1901 Dihedral : 30.207 171.765 4439 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.91 % Allowed : 21.85 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.72 (0.25), residues: 1129 helix: -0.12 (0.20), residues: 625 sheet: -1.32 (0.58), residues: 80 loop : -0.62 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 228 HIS 0.009 0.002 HIS K 251 PHE 0.019 0.002 PHE A 104 TYR 0.023 0.003 TYR F 88 ARG 0.008 0.001 ARG K 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 195 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 199 average time/residue: 0.3389 time to fit residues: 93.6855 Evaluate side-chains 199 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 190 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1990 time to fit residues: 4.4130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 112 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 85 GLN A 108 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.130589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.095817 restraints weight = 42853.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.094389 restraints weight = 34526.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.094586 restraints weight = 30362.231| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16003 Z= 0.193 Angle : 0.612 10.557 22877 Z= 0.345 Chirality : 0.037 0.216 2589 Planarity : 0.003 0.034 1901 Dihedral : 29.516 175.096 4439 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.71 % Allowed : 22.36 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1129 helix: 0.50 (0.21), residues: 629 sheet: -1.06 (0.60), residues: 80 loop : -0.38 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 228 HIS 0.007 0.001 HIS K 251 PHE 0.023 0.001 PHE L 45 TYR 0.018 0.002 TYR H 40 ARG 0.007 0.000 ARG K 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3004.59 seconds wall clock time: 55 minutes 11.34 seconds (3311.34 seconds total)