Starting phenix.real_space_refine on Sat Mar 16 16:07:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nn6_0458/03_2024/6nn6_0458.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nn6_0458/03_2024/6nn6_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_0458/03_2024/6nn6_0458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nn6_0458/03_2024/6nn6_0458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nn6_0458/03_2024/6nn6_0458.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nn6_0458/03_2024/6nn6_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.63, per 1000 atoms: 0.50 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: 7.86 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: 6.57 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: 5.65 Time building geometry restraints manager: 8.25 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: 1.730 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: 8.020 Check model and map are aligned: 0.200 Set scattering table: 0.150 Process input model: 45.680 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.280 ------------------------------------------------------------------------------- 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 : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9345 (m) cc_final: 0.8720 (p) REVERT: B 53 GLU cc_start: 0.8396 (tp30) cc_final: 0.8048 (tp30) REVERT: C 91 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8035 (tp30) REVERT: C 94 ASN cc_start: 0.8724 (t0) cc_final: 0.8483 (t0) REVERT: C 95 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8673 (mttm) REVERT: D 42 TYR cc_start: 0.7942 (t80) cc_final: 0.7541 (t80) REVERT: D 87 SER cc_start: 0.8668 (m) cc_final: 0.8441 (t) REVERT: E 122 LYS cc_start: 0.9370 (ptpt) cc_final: 0.9085 (ptpp) REVERT: F 59 LYS cc_start: 0.8846 (tttp) cc_final: 0.8639 (tttm) REVERT: G 61 GLU cc_start: 0.8581 (tp30) cc_final: 0.8157 (tp30) REVERT: G 74 LYS cc_start: 0.8904 (mppt) cc_final: 0.8395 (mmtp) REVERT: G 112 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8429 (mm-40) REVERT: H 32 THR cc_start: 0.7817 (p) cc_final: 0.7519 (p) REVERT: H 43 LYS cc_start: 0.9214 (mttt) cc_final: 0.8842 (mttp) REVERT: H 76 GLU cc_start: 0.8449 (tp30) cc_final: 0.8116 (tp30) REVERT: H 87 SER cc_start: 0.8994 (m) cc_final: 0.8635 (p) REVERT: K 71 MET cc_start: 0.5125 (mmm) cc_final: 0.4323 (mmm) REVERT: K 149 ASP cc_start: 0.6601 (m-30) cc_final: 0.6289 (m-30) REVERT: K 189 ASP cc_start: 0.7951 (m-30) cc_final: 0.7277 (p0) REVERT: K 198 MET cc_start: 0.2109 (mmm) cc_final: 0.1409 (mmm) REVERT: K 205 TRP cc_start: 0.5089 (m100) cc_final: 0.4829 (m100) REVERT: K 206 MET cc_start: 0.6165 (mmm) cc_final: 0.5609 (ppp) REVERT: K 252 GLN cc_start: 0.7306 (mt0) cc_final: 0.6991 (mp10) REVERT: K 291 MET cc_start: 0.8538 (ptp) cc_final: 0.8209 (ptp) REVERT: L 51 GLU cc_start: 0.7849 (tt0) cc_final: 0.7308 (mp0) outliers start: 8 outliers final: 3 residues processed: 368 average time/residue: 0.4033 time to fit residues: 193.0727 Evaluate side-chains 249 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 246 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain K residue 282 ARG 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: 0.9990 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: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 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 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: 0.7883 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16003 Z= 0.233 Angle : 0.672 7.181 22877 Z= 0.392 Chirality : 0.039 0.192 2589 Planarity : 0.005 0.038 1901 Dihedral : 30.540 178.380 4451 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.86 % Allowed : 10.37 % Favored : 85.77 % 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: -2.87 (0.21), residues: 1129 helix: -2.21 (0.16), residues: 634 sheet: -0.82 (0.60), residues: 78 loop : -1.26 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 205 HIS 0.010 0.001 HIS G 31 PHE 0.019 0.001 PHE L 45 TYR 0.016 0.001 TYR F 51 ARG 0.005 0.001 ARG B 95 *********************** 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 339 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 301 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9294 (m) cc_final: 0.8623 (p) REVERT: A 120 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7884 (mtt) REVERT: B 24 ASP cc_start: 0.6308 (t0) cc_final: 0.6024 (t0) REVERT: B 64 ASN cc_start: 0.9199 (m-40) cc_final: 0.8892 (m-40) REVERT: C 91 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7854 (tp30) REVERT: D 42 TYR cc_start: 0.7745 (t80) cc_final: 0.7508 (t80) REVERT: D 86 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7429 (mtm-85) REVERT: D 87 SER cc_start: 0.8767 (m) cc_final: 0.8366 (t) REVERT: F 80 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.8956 (p) REVERT: G 59 THR cc_start: 0.9413 (p) cc_final: 0.9020 (m) REVERT: G 74 LYS cc_start: 0.8837 (mppt) cc_final: 0.8584 (mtmm) REVERT: G 75 LYS cc_start: 0.8260 (mttm) cc_final: 0.8013 (mtpp) REVERT: K 71 MET cc_start: 0.5888 (mmm) cc_final: 0.4904 (mmm) REVERT: K 108 ARG cc_start: 0.7223 (ttm110) cc_final: 0.6830 (tpt170) REVERT: K 147 MET cc_start: 0.7116 (tmm) cc_final: 0.5772 (mtt) REVERT: K 198 MET cc_start: 0.2261 (mmm) cc_final: 0.1177 (mmm) REVERT: K 206 MET cc_start: 0.6147 (mmm) cc_final: 0.5621 (ppp) REVERT: K 212 LYS cc_start: 0.2482 (tptt) cc_final: 0.1768 (tptm) REVERT: K 282 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7638 (ttm-80) REVERT: K 286 ASP cc_start: 0.8478 (t70) cc_final: 0.8201 (t70) outliers start: 38 outliers final: 19 residues processed: 315 average time/residue: 0.3149 time to fit residues: 136.0826 Evaluate side-chains 274 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 251 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 282 ARG Chi-restraints excluded: chain K residue 318 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 85 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 C 38 ASN C 94 ASN D 67 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN G 38 ASN H 67 ASN ** K 168 GLN ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16003 Z= 0.246 Angle : 0.622 6.511 22877 Z= 0.360 Chirality : 0.038 0.145 2589 Planarity : 0.004 0.043 1901 Dihedral : 30.177 176.189 4443 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.27 % Allowed : 14.13 % Favored : 81.61 % 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: -1.62 (0.23), residues: 1129 helix: -1.02 (0.19), residues: 634 sheet: -0.89 (0.60), residues: 78 loop : -0.91 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 205 HIS 0.009 0.001 HIS K 251 PHE 0.010 0.001 PHE B 100 TYR 0.014 0.002 TYR H 40 ARG 0.005 0.001 ARG K 203 *********************** 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 302 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 260 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9302 (m) cc_final: 0.8563 (p) REVERT: A 120 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7722 (mtt) REVERT: B 24 ASP cc_start: 0.6089 (t0) cc_final: 0.5202 (t0) REVERT: D 86 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7586 (mtm-85) REVERT: D 87 SER cc_start: 0.8791 (m) cc_final: 0.8337 (t) REVERT: G 75 LYS cc_start: 0.8238 (mttm) cc_final: 0.7906 (mtpp) REVERT: K 55 MET cc_start: -0.1560 (mmp) cc_final: -0.1776 (mmt) REVERT: K 71 MET cc_start: 0.6013 (mmm) cc_final: 0.5219 (mmm) REVERT: K 108 ARG cc_start: 0.7285 (ttm110) cc_final: 0.6836 (tpt170) REVERT: K 147 MET cc_start: 0.6869 (tmm) cc_final: 0.5679 (mtt) REVERT: K 286 ASP cc_start: 0.8604 (t70) cc_final: 0.8327 (t70) outliers start: 42 outliers final: 26 residues processed: 279 average time/residue: 0.3155 time to fit residues: 121.2481 Evaluate side-chains 264 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 236 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain L residue 39 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 111 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 93 GLN A 108 ASN B 25 ASN E 68 GLN G 31 HIS G 38 ASN K 168 GLN ** K 251 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16003 Z= 0.215 Angle : 0.587 6.008 22877 Z= 0.340 Chirality : 0.037 0.145 2589 Planarity : 0.004 0.044 1901 Dihedral : 29.967 174.197 4439 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.37 % Allowed : 15.24 % Favored : 80.39 % 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: -0.94 (0.24), residues: 1129 helix: -0.37 (0.20), residues: 633 sheet: -0.86 (0.60), residues: 78 loop : -0.73 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 228 HIS 0.021 0.001 HIS K 251 PHE 0.019 0.001 PHE K 159 TYR 0.026 0.002 TYR H 83 ARG 0.004 0.000 ARG K 256 *********************** 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 296 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 253 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8885 (mm) cc_final: 0.8678 (mp) REVERT: A 108 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8649 (t0) REVERT: A 120 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7613 (mtt) REVERT: D 86 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7669 (mtm-85) REVERT: D 87 SER cc_start: 0.8811 (m) cc_final: 0.8359 (t) REVERT: E 90 MET cc_start: 0.8081 (mmp) cc_final: 0.7880 (mmt) REVERT: F 88 TYR cc_start: 0.8560 (m-10) cc_final: 0.8194 (m-10) REVERT: G 75 LYS cc_start: 0.8224 (mttm) cc_final: 0.7922 (mtpp) REVERT: H 113 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: K 71 MET cc_start: 0.6232 (mmm) cc_final: 0.5489 (mmm) REVERT: K 108 ARG cc_start: 0.7332 (ttm110) cc_final: 0.6661 (tpt170) REVERT: K 147 MET cc_start: 0.6785 (tmm) cc_final: 0.5764 (mtt) REVERT: K 198 MET cc_start: 0.3469 (mmm) cc_final: 0.2292 (mmm) REVERT: K 286 ASP cc_start: 0.8624 (t70) cc_final: 0.8285 (t70) outliers start: 43 outliers final: 32 residues processed: 272 average time/residue: 0.3208 time to fit residues: 120.6959 Evaluate side-chains 272 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 236 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 39 ASP 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: 5.9990 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4402 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= 0.258 Angle : 0.605 6.317 22877 Z= 0.347 Chirality : 0.037 0.141 2589 Planarity : 0.004 0.043 1901 Dihedral : 29.958 173.986 4439 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.78 % Allowed : 16.67 % Favored : 78.56 % 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: -0.09 (0.20), residues: 637 sheet: -1.06 (0.59), residues: 80 loop : -0.66 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 228 HIS 0.008 0.001 HIS K 251 PHE 0.013 0.001 PHE K 159 TYR 0.021 0.002 TYR H 83 ARG 0.006 0.001 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 280 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 233 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9319 (m) cc_final: 0.8594 (p) REVERT: A 120 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7688 (mtt) REVERT: D 86 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7686 (mtm-85) REVERT: D 87 SER cc_start: 0.8806 (m) cc_final: 0.8376 (t) REVERT: G 75 LYS cc_start: 0.8301 (mttm) cc_final: 0.7891 (mtpp) REVERT: K 71 MET cc_start: 0.6347 (mmm) cc_final: 0.5561 (mmm) REVERT: K 108 ARG cc_start: 0.7426 (ttm110) cc_final: 0.6748 (tpt170) REVERT: K 147 MET cc_start: 0.6690 (tmm) cc_final: 0.5797 (mtt) REVERT: K 198 MET cc_start: 0.3413 (mmm) cc_final: 0.2302 (mmm) REVERT: K 203 ARG cc_start: 0.7296 (ttp80) cc_final: 0.6900 (ptp-170) REVERT: K 212 LYS cc_start: 0.2597 (tptt) cc_final: 0.1405 (tptm) REVERT: K 270 LYS cc_start: 0.5496 (tmtt) cc_final: 0.5272 (tmmt) REVERT: K 286 ASP cc_start: 0.8642 (t70) cc_final: 0.8260 (t70) outliers start: 47 outliers final: 34 residues processed: 255 average time/residue: 0.3067 time to fit residues: 108.8107 Evaluate side-chains 264 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 228 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain L residue 39 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 128 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN G 38 ASN H 63 ASN K 113 GLN ** 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: 0.7895 moved from start: 0.4663 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= 0.231 Angle : 0.585 6.266 22877 Z= 0.336 Chirality : 0.037 0.139 2589 Planarity : 0.004 0.043 1901 Dihedral : 29.809 173.971 4439 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.27 % Allowed : 17.28 % Favored : 78.46 % 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: -0.33 (0.25), residues: 1129 helix: 0.26 (0.21), residues: 633 sheet: -1.06 (0.59), residues: 80 loop : -0.58 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 228 HIS 0.007 0.001 HIS K 251 PHE 0.019 0.001 PHE L 45 TYR 0.018 0.002 TYR H 40 ARG 0.006 0.000 ARG G 42 *********************** 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 282 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 240 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7593 (mtt) REVERT: D 86 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7670 (mtm-85) REVERT: D 87 SER cc_start: 0.8802 (m) cc_final: 0.8394 (t) REVERT: E 90 MET cc_start: 0.8001 (mmp) cc_final: 0.7787 (mmt) REVERT: G 75 LYS cc_start: 0.8353 (mttm) cc_final: 0.7977 (mtpp) REVERT: G 99 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.8019 (mmm160) REVERT: G 112 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8352 (mm-40) REVERT: K 71 MET cc_start: 0.6383 (mmm) cc_final: 0.5622 (mmm) REVERT: K 108 ARG cc_start: 0.7475 (ttm110) cc_final: 0.6794 (tpt170) REVERT: K 147 MET cc_start: 0.6576 (tmm) cc_final: 0.5820 (mtt) REVERT: K 197 THR cc_start: 0.4177 (OUTLIER) cc_final: 0.3770 (p) REVERT: K 198 MET cc_start: 0.3379 (mmm) cc_final: 0.2451 (mmm) REVERT: K 270 LYS cc_start: 0.5666 (tmtt) cc_final: 0.5382 (ttpt) REVERT: K 286 ASP cc_start: 0.8641 (t70) cc_final: 0.8241 (t70) outliers start: 42 outliers final: 36 residues processed: 261 average time/residue: 0.3130 time to fit residues: 113.1702 Evaluate side-chains 266 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 227 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 39 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 61 optimal weight: 0.0970 chunk 82 optimal weight: 4.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- 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 D 67 ASN G 38 ASN H 63 ASN ** 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: 0.7918 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16003 Z= 0.286 Angle : 0.621 7.620 22877 Z= 0.353 Chirality : 0.038 0.141 2589 Planarity : 0.004 0.035 1901 Dihedral : 29.850 173.532 4439 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.57 % Allowed : 18.60 % Favored : 76.83 % 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: -0.26 (0.25), residues: 1129 helix: 0.35 (0.21), residues: 631 sheet: -1.09 (0.59), residues: 80 loop : -0.61 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 228 HIS 0.006 0.001 HIS H 82 PHE 0.015 0.001 PHE B 100 TYR 0.020 0.002 TYR F 88 ARG 0.011 0.000 ARG K 203 *********************** 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 273 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7694 (mtt) REVERT: D 86 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7696 (mtm-85) REVERT: D 87 SER cc_start: 0.8854 (m) cc_final: 0.8425 (t) REVERT: D 106 LEU cc_start: 0.9211 (tp) cc_final: 0.8996 (tt) REVERT: G 75 LYS cc_start: 0.8428 (mttm) cc_final: 0.7976 (mtpp) REVERT: K 71 MET cc_start: 0.6381 (mmm) cc_final: 0.5615 (mmm) REVERT: K 108 ARG cc_start: 0.7522 (ttm110) cc_final: 0.7002 (tpt170) REVERT: K 147 MET cc_start: 0.6447 (tmm) cc_final: 0.5739 (mtt) REVERT: K 203 ARG cc_start: 0.6999 (ttp-110) cc_final: 0.6441 (ptp-170) REVERT: K 270 LYS cc_start: 0.5467 (tmtt) cc_final: 0.5214 (ttpt) REVERT: K 286 ASP cc_start: 0.8680 (t70) cc_final: 0.8295 (t70) outliers start: 45 outliers final: 40 residues processed: 251 average time/residue: 0.3149 time to fit residues: 110.5375 Evaluate side-chains 264 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 222 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 291 MET Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain L residue 39 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 40 optimal weight: 0.0070 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- 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 ** 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: 0.7879 moved from start: 0.4963 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= 0.208 Angle : 0.581 8.348 22877 Z= 0.332 Chirality : 0.036 0.144 2589 Planarity : 0.004 0.036 1901 Dihedral : 29.607 174.142 4439 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.86 % Allowed : 19.21 % 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: 0.58 (0.21), residues: 632 sheet: -1.02 (0.59), residues: 80 loop : -0.50 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP K 228 HIS 0.007 0.001 HIS K 251 PHE 0.028 0.001 PHE L 45 TYR 0.019 0.001 TYR H 40 ARG 0.009 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 280 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 242 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7531 (mtt) REVERT: C 110 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7844 (p0) REVERT: D 86 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7697 (mtm-85) REVERT: D 87 SER cc_start: 0.8767 (m) cc_final: 0.8404 (t) REVERT: E 90 MET cc_start: 0.7985 (mmp) cc_final: 0.7767 (mmt) REVERT: G 75 LYS cc_start: 0.8454 (mttm) cc_final: 0.8019 (mtpp) REVERT: H 83 TYR cc_start: 0.7325 (m-80) cc_final: 0.6939 (m-80) REVERT: K 71 MET cc_start: 0.6483 (mmm) cc_final: 0.5664 (mmm) REVERT: K 108 ARG cc_start: 0.7524 (ttm110) cc_final: 0.6825 (tpt170) REVERT: K 147 MET cc_start: 0.6590 (tmm) cc_final: 0.5938 (mtt) REVERT: K 203 ARG cc_start: 0.6908 (ttp-110) cc_final: 0.6467 (ptp-170) REVERT: K 270 LYS cc_start: 0.5577 (tmtt) cc_final: 0.5321 (ttpt) REVERT: K 286 ASP cc_start: 0.8573 (t70) cc_final: 0.8200 (t70) REVERT: K 322 LEU cc_start: 0.8300 (mp) cc_final: 0.8083 (mp) outliers start: 38 outliers final: 28 residues processed: 260 average time/residue: 0.3178 time to fit residues: 114.7219 Evaluate side-chains 257 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 226 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 291 MET Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 39 ASP 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: 2.9990 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 47 GLN ** 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: 0.7941 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16003 Z= 0.353 Angle : 0.665 10.869 22877 Z= 0.371 Chirality : 0.039 0.157 2589 Planarity : 0.004 0.037 1901 Dihedral : 29.887 172.966 4439 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.17 % Allowed : 19.72 % Favored : 76.12 % 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: -0.24 (0.25), residues: 1129 helix: 0.32 (0.21), residues: 635 sheet: -1.12 (0.57), residues: 80 loop : -0.51 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 228 HIS 0.008 0.001 HIS K 251 PHE 0.015 0.002 PHE A 104 TYR 0.035 0.002 TYR F 88 ARG 0.008 0.001 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 260 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 219 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 110 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7700 (p0) REVERT: D 86 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7596 (mtm-85) REVERT: D 87 SER cc_start: 0.8880 (m) cc_final: 0.8483 (t) REVERT: D 106 LEU cc_start: 0.9245 (tp) cc_final: 0.9015 (tt) REVERT: E 90 MET cc_start: 0.8150 (mmp) cc_final: 0.7925 (mmt) REVERT: E 94 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7585 (mm-30) REVERT: G 74 LYS cc_start: 0.9095 (mtmm) cc_final: 0.8858 (mtmm) REVERT: G 75 LYS cc_start: 0.8510 (mttm) cc_final: 0.8026 (mtpp) REVERT: G 112 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8309 (mm-40) REVERT: H 62 MET cc_start: 0.9207 (mmm) cc_final: 0.8853 (mmp) REVERT: K 71 MET cc_start: 0.6416 (mmm) cc_final: 0.5608 (mmm) REVERT: K 108 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7125 (tpt170) REVERT: K 147 MET cc_start: 0.6654 (tmm) cc_final: 0.5888 (mtp) REVERT: K 203 ARG cc_start: 0.6629 (ttp-110) cc_final: 0.6180 (ptp-170) REVERT: K 270 LYS cc_start: 0.5527 (tmtt) cc_final: 0.5275 (ttpt) REVERT: K 286 ASP cc_start: 0.8605 (t70) cc_final: 0.8207 (t70) outliers start: 41 outliers final: 37 residues processed: 243 average time/residue: 0.3213 time to fit residues: 108.0985 Evaluate side-chains 253 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 214 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 291 MET Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain L residue 39 ASP 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: 2.9990 chunk 91 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 126 optimal weight: 0.0970 chunk 109 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.1580 ------------------------------------------------------------------------------- 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 ** 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: 0.7904 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16003 Z= 0.242 Angle : 0.614 11.766 22877 Z= 0.347 Chirality : 0.037 0.264 2589 Planarity : 0.004 0.035 1901 Dihedral : 29.672 173.766 4439 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.66 % Allowed : 20.53 % Favored : 75.81 % 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: -0.02 (0.25), residues: 1129 helix: 0.55 (0.21), residues: 633 sheet: -1.05 (0.57), residues: 80 loop : -0.49 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 228 HIS 0.008 0.001 HIS K 251 PHE 0.019 0.001 PHE L 45 TYR 0.028 0.002 TYR F 88 ARG 0.007 0.000 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 261 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 225 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7636 (mtt) REVERT: C 110 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7704 (p0) REVERT: D 86 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7717 (mtm-85) REVERT: D 87 SER cc_start: 0.8848 (m) cc_final: 0.8491 (t) REVERT: D 106 LEU cc_start: 0.9192 (tp) cc_final: 0.8942 (tt) REVERT: E 90 MET cc_start: 0.8034 (mmp) cc_final: 0.7812 (mmt) REVERT: E 94 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7493 (mm-30) REVERT: G 74 LYS cc_start: 0.9095 (mtmm) cc_final: 0.8880 (mtmm) REVERT: G 75 LYS cc_start: 0.8520 (mttm) cc_final: 0.8063 (mtpp) REVERT: K 71 MET cc_start: 0.6427 (mmm) cc_final: 0.5599 (mmm) REVERT: K 108 ARG cc_start: 0.7627 (ttm110) cc_final: 0.7065 (tpt170) REVERT: K 147 MET cc_start: 0.6626 (tmm) cc_final: 0.5895 (mtp) REVERT: K 198 MET cc_start: 0.3795 (tpt) cc_final: 0.3407 (tpt) REVERT: K 203 ARG cc_start: 0.6659 (ttp-110) cc_final: 0.6338 (ptp-170) REVERT: K 270 LYS cc_start: 0.5474 (tmtt) cc_final: 0.5212 (ttpt) REVERT: K 286 ASP cc_start: 0.8602 (t70) cc_final: 0.8228 (t70) REVERT: K 322 LEU cc_start: 0.8271 (mp) cc_final: 0.8046 (mp) outliers start: 36 outliers final: 29 residues processed: 245 average time/residue: 0.3230 time to fit residues: 108.8966 Evaluate side-chains 251 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 219 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 291 MET Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 39 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 112 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 G 38 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.131605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097040 restraints weight = 43781.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.096386 restraints weight = 34150.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.096612 restraints weight = 32732.188| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16003 Z= 0.177 Angle : 0.583 11.492 22877 Z= 0.329 Chirality : 0.035 0.161 2589 Planarity : 0.003 0.035 1901 Dihedral : 29.231 175.053 4439 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.13 % Allowed : 21.65 % Favored : 76.22 % 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: 0.41 (0.26), residues: 1129 helix: 0.94 (0.21), residues: 625 sheet: -0.90 (0.58), residues: 80 loop : -0.35 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 228 HIS 0.006 0.001 HIS K 251 PHE 0.019 0.001 PHE L 45 TYR 0.020 0.001 TYR H 40 ARG 0.010 0.000 ARG K 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3054.07 seconds wall clock time: 55 minutes 42.68 seconds (3342.68 seconds total)