Starting phenix.real_space_refine on Mon Sep 14 17:52:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ypu_10869/09_2026/6ypu_10869.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ypu_10869/09_2026/6ypu_10869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ypu_10869/09_2026/6ypu_10869.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ypu_10869/09_2026/6ypu_10869.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ypu_10869/09_2026/6ypu_10869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ypu_10869/09_2026/6ypu_10869.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ypu_10869/09_2026/6ypu_10869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ypu_10869/09_2026/6ypu_10869.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1040 5.49 5 Mg 59 5.21 5 S 28 5.16 5 C 16728 2.51 5 N 6241 2.21 5 O 9226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33322 Number of models: 1 Model: "" Number of chains: 17 Chain: "2" Number of atoms: 19228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 19228 Classifications: {'RNAv2': 894} Modifications used: {'rna2p_pur': 72, 'rna2p_pyr': 41, 'rna3p_pur': 457, 'rna3p_pyr': 324} Link IDs: {'rna2p': 113, 'rna3p': 780} Chain breaks: 3 Chain: "4" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3129 Classifications: {'RNAv2': 146} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 73, 'rna3p_pyr': 59} Link IDs: {'rna2p': 14, 'rna3p': 131} Chain: "c" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1079 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PTRANS': 7, 'TRANS': 211} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 669 Unresolved non-hydrogen angles: 854 Unresolved non-hydrogen dihedrals: 550 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'ARG:plan': 15, 'ASP:plan': 14, 'GLN:plan1': 11, 'HIS:plan': 6, 'PHE:plan': 7, 'TRP:plan': 3, 'ASN:plan1': 16, 'TYR:plan': 4, 'GLU:plan': 9} Unresolved non-hydrogen planarities: 372 Chain: "e" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1592 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 200} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "f" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "g" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 858 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "i" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 984 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "l" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 836 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "p" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 704 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "q" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "r" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "s" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 434 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "u" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "v" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 389 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "2" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Unusual residues: {' MG': 53} Classifications: {'undetermined': 53} Link IDs: {None: 52} Chain: "4" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 46 Unusual residues: {' MG': 6, 'AKN': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 6.87, per 1000 atoms: 0.21 Number of scatterers: 33322 At special positions: 0 Unit cell: (206.51, 159.43, 153.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 1040 15.00 Mg 59 11.99 O 9226 8.00 N 6241 7.00 C 16728 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 - 3.00 Amino acid : True - 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: 2.84 Conformation dependent library (CDL) restraints added in 681.5 milliseconds 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 14 sheets defined 40.4% alpha, 20.1% beta 331 base pairs and 588 stacking pairs defined. Time for finding SS restraints: 5.02 Creating SS restraints... Processing helix chain 'c' and resid 26 through 30 removed outlier: 3.647A pdb=" N ARG c 30 " --> pdb=" O PRO c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 64 Proline residue: c 50 - end of helix removed outlier: 3.752A pdb=" N ASN c 53 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP c 54 " --> pdb=" O PRO c 50 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE c 58 " --> pdb=" O ASP c 54 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA c 59 " --> pdb=" O ALA c 55 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN c 60 " --> pdb=" O LEU c 56 " (cutoff:3.500A) Processing helix chain 'c' and resid 78 through 88 removed outlier: 4.392A pdb=" N GLU c 84 " --> pdb=" O ASN c 80 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA c 86 " --> pdb=" O ILE c 82 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN c 87 " --> pdb=" O ARG c 83 " (cutoff:3.500A) Processing helix chain 'c' and resid 105 through 122 removed outlier: 4.704A pdb=" N GLN c 111 " --> pdb=" O LYS c 107 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER c 112 " --> pdb=" O THR c 108 " (cutoff:3.500A) Processing helix chain 'c' and resid 132 through 149 removed outlier: 4.222A pdb=" N SER c 149 " --> pdb=" O LYS c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 150 through 154 removed outlier: 3.504A pdb=" N LYS c 154 " --> pdb=" O GLY c 151 " (cutoff:3.500A) Processing helix chain 'c' and resid 171 through 182 removed outlier: 3.688A pdb=" N GLU c 177 " --> pdb=" O ILE c 173 " (cutoff:3.500A) Processing helix chain 'c' and resid 208 through 225 Processing helix chain 'e' and resid 9 through 16 removed outlier: 3.615A pdb=" N ARG e 14 " --> pdb=" O LYS e 10 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU e 15 " --> pdb=" O LEU e 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 53 through 68 Processing helix chain 'e' and resid 70 through 82 Processing helix chain 'e' and resid 87 through 98 removed outlier: 3.576A pdb=" N ASN e 91 " --> pdb=" O ALA e 87 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU e 92 " --> pdb=" O THR e 88 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU e 93 " --> pdb=" O GLY e 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 99 through 107 removed outlier: 3.509A pdb=" N VAL e 103 " --> pdb=" O ARG e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 112 through 122 removed outlier: 4.267A pdb=" N GLN e 118 " --> pdb=" O ALA e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 152 removed outlier: 4.088A pdb=" N LYS e 152 " --> pdb=" O GLU e 149 " (cutoff:3.500A) Processing helix chain 'e' and resid 155 through 165 removed outlier: 4.367A pdb=" N ASN e 159 " --> pdb=" O LEU e 155 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA e 160 " --> pdb=" O ARG e 156 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU e 162 " --> pdb=" O LYS e 158 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA e 165 " --> pdb=" O ILE e 161 " (cutoff:3.500A) Processing helix chain 'e' and resid 199 through 206 removed outlier: 3.796A pdb=" N VAL e 203 " --> pdb=" O GLU e 199 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU e 204 " --> pdb=" O SER e 200 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 67 Processing helix chain 'f' and resid 108 through 116 removed outlier: 3.648A pdb=" N ALA f 112 " --> pdb=" O GLY f 108 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL f 113 " --> pdb=" O ALA f 109 " (cutoff:3.500A) Processing helix chain 'f' and resid 131 through 145 Processing helix chain 'f' and resid 148 through 156 removed outlier: 3.576A pdb=" N VAL f 152 " --> pdb=" O SER f 148 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA f 153 " --> pdb=" O PRO f 149 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 15 Processing helix chain 'g' and resid 18 through 32 removed outlier: 4.155A pdb=" N ARG g 24 " --> pdb=" O GLY g 20 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA g 32 " --> pdb=" O GLN g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 67 through 80 removed outlier: 3.587A pdb=" N LEU g 71 " --> pdb=" O GLY g 67 " (cutoff:3.500A) Processing helix chain 'i' and resid 6 through 20 Processing helix chain 'i' and resid 30 through 43 Processing helix chain 'i' and resid 95 through 100 removed outlier: 4.219A pdb=" N GLN i 98 " --> pdb=" O SER i 95 " (cutoff:3.500A) Processing helix chain 'i' and resid 114 through 121 removed outlier: 3.646A pdb=" N ALA i 119 " --> pdb=" O ARG i 115 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA i 120 " --> pdb=" O ALA i 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 52 through 57 removed outlier: 3.755A pdb=" N ARG l 55 " --> pdb=" O ARG l 52 " (cutoff:3.500A) Processing helix chain 'l' and resid 58 through 75 removed outlier: 4.145A pdb=" N ASP l 75 " --> pdb=" O LYS l 71 " (cutoff:3.500A) Processing helix chain 'l' and resid 89 through 91 No H-bonds generated for 'chain 'l' and resid 89 through 91' Processing helix chain 'l' and resid 92 through 101 removed outlier: 4.166A pdb=" N VAL l 96 " --> pdb=" O ARG l 92 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 10 Processing helix chain 'm' and resid 21 through 25 removed outlier: 3.537A pdb=" N LEU m 24 " --> pdb=" O VAL m 21 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS m 25 " --> pdb=" O PRO m 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 21 through 25' Processing helix chain 'm' and resid 113 through 117 Processing helix chain 'p' and resid 4 through 16 removed outlier: 3.505A pdb=" N ILE p 12 " --> pdb=" O ARG p 8 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS p 14 " --> pdb=" O GLU p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 24 through 39 Processing helix chain 'p' and resid 39 through 44 Processing helix chain 'p' and resid 52 through 74 removed outlier: 3.712A pdb=" N LYS p 65 " --> pdb=" O ASN p 61 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY p 72 " --> pdb=" O ASP p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 74 through 86 removed outlier: 3.698A pdb=" N TYR p 78 " --> pdb=" O ASP p 74 " (cutoff:3.500A) Processing helix chain 'q' and resid 53 through 64 Processing helix chain 'q' and resid 70 through 78 removed outlier: 3.557A pdb=" N ALA q 76 " --> pdb=" O ALA q 72 " (cutoff:3.500A) Processing helix chain 's' and resid 25 through 30 removed outlier: 3.680A pdb=" N LEU s 29 " --> pdb=" O ASP s 25 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS s 30 " --> pdb=" O ILE s 26 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 25 through 30' Processing helix chain 's' and resid 31 through 33 No H-bonds generated for 'chain 's' and resid 31 through 33' Processing helix chain 's' and resid 41 through 46 removed outlier: 3.635A pdb=" N THR s 45 " --> pdb=" O PRO s 41 " (cutoff:3.500A) Processing helix chain 's' and resid 48 through 66 removed outlier: 3.583A pdb=" N ARG s 53 " --> pdb=" O ALA s 49 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN s 54 " --> pdb=" O ARG s 50 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR s 64 " --> pdb=" O LYS s 60 " (cutoff:3.500A) Processing helix chain 'u' and resid 4 through 42 removed outlier: 3.671A pdb=" N LYS u 8 " --> pdb=" O SER u 4 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS u 16 " --> pdb=" O ARG u 12 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER u 23 " --> pdb=" O LYS u 19 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU u 24 " --> pdb=" O HIS u 20 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY u 41 " --> pdb=" O SER u 37 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY u 42 " --> pdb=" O ALA u 38 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 52 removed outlier: 3.576A pdb=" N LYS u 52 " --> pdb=" O THR u 48 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 64 Processing helix chain 'u' and resid 68 through 81 Processing helix chain 'v' and resid 15 through 23 removed outlier: 3.844A pdb=" N ARG v 21 " --> pdb=" O ARG v 17 " (cutoff:3.500A) Processing helix chain 'v' and resid 40 through 56 removed outlier: 3.526A pdb=" N ALA v 50 " --> pdb=" O LYS v 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 18 through 21 removed outlier: 5.141A pdb=" N HIS c 41 " --> pdb=" O GLY c 19 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE c 40 " --> pdb=" O ALA c 36 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA c 36 " --> pdb=" O ILE c 40 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE c 42 " --> pdb=" O PHE c 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 70 through 72 removed outlier: 3.755A pdb=" N ILE c 188 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL c 185 " --> pdb=" O TYR c 200 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE c 202 " --> pdb=" O VAL c 185 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLY c 187 " --> pdb=" O ILE c 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'f' and resid 11 through 23 removed outlier: 6.577A pdb=" N LEU f 35 " --> pdb=" O VAL f 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL f 17 " --> pdb=" O THR f 33 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR f 33 " --> pdb=" O VAL f 17 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG f 19 " --> pdb=" O SER f 31 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER f 31 " --> pdb=" O ARG f 19 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA f 21 " --> pdb=" O ILE f 29 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE f 29 " --> pdb=" O ALA f 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 84 through 88 removed outlier: 6.336A pdb=" N ILE f 105 " --> pdb=" O ALA f 124 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N CYS f 126 " --> pdb=" O ILE f 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'g' and resid 35 through 39 removed outlier: 6.694A pdb=" N ASN g 63 " --> pdb=" O HIS g 37 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU g 39 " --> pdb=" O LEU g 61 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU g 61 " --> pdb=" O LEU g 39 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N HIS g 55 " --> pdb=" O LEU g 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'g' and resid 35 through 39 removed outlier: 6.694A pdb=" N ASN g 63 " --> pdb=" O HIS g 37 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU g 39 " --> pdb=" O LEU g 61 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU g 61 " --> pdb=" O LEU g 39 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE g 6 " --> pdb=" O MET g 62 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N HIS g 3 " --> pdb=" O ARG g 91 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG g 91 " --> pdb=" O HIS g 3 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU g 5 " --> pdb=" O ILE g 89 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE g 89 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL g 7 " --> pdb=" O ASN g 87 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN g 87 " --> pdb=" O VAL g 7 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU g 9 " --> pdb=" O ILE g 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'i' and resid 24 through 28 removed outlier: 3.772A pdb=" N ASN i 48 " --> pdb=" O THR i 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'i' and resid 66 through 67 Processing sheet with id=AB1, first strand: chain 'i' and resid 76 through 78 removed outlier: 6.787A pdb=" N ILE i 104 " --> pdb=" O ILE i 127 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE i 129 " --> pdb=" O ILE i 102 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE i 102 " --> pdb=" O PHE i 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'l' and resid 40 through 45 removed outlier: 6.966A pdb=" N ILE l 33 " --> pdb=" O LEU l 41 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TRP l 43 " --> pdb=" O VAL l 31 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL l 31 " --> pdb=" O TRP l 43 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR l 45 " --> pdb=" O THR l 29 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR l 29 " --> pdb=" O THR l 45 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLY l 18 " --> pdb=" O ASP l 82 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N LEU l 84 " --> pdb=" O GLY l 18 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA l 20 " --> pdb=" O LEU l 84 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LYS l 86 " --> pdb=" O ALA l 20 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE l 22 " --> pdb=" O LYS l 86 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU l 81 " --> pdb=" O ILE l 106 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER l 108 " --> pdb=" O LEU l 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 30 through 40 removed outlier: 6.379A pdb=" N ARG m 54 " --> pdb=" O THR m 35 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL m 37 " --> pdb=" O VAL m 52 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL m 52 " --> pdb=" O VAL m 37 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR m 39 " --> pdb=" O ARG m 50 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG m 50 " --> pdb=" O THR m 39 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR m 95 " --> pdb=" O SER m 64 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'q' and resid 50 through 52 removed outlier: 6.085A pdb=" N ILE q 19 " --> pdb=" O ILE q 36 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE q 38 " --> pdb=" O TYR q 17 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR q 17 " --> pdb=" O PHE q 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'r' and resid 8 through 18 removed outlier: 16.880A pdb=" N THR r 8 " --> pdb=" O ARG r 29 " (cutoff:3.500A) removed outlier: 13.372A pdb=" N ARG r 29 " --> pdb=" O THR r 8 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR r 10 " --> pdb=" O GLU r 27 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLU r 27 " --> pdb=" O THR r 10 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL r 23 " --> pdb=" O VAL r 14 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP r 16 " --> pdb=" O SER r 21 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER r 21 " --> pdb=" O ASP r 16 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N LYS r 72 " --> pdb=" O LYS r 44 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N HIS r 46 " --> pdb=" O LYS r 72 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TRP r 74 " --> pdb=" O HIS r 46 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA r 73 " --> pdb=" O SER r 65 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR r 61 " --> pdb=" O VAL r 77 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL r 79 " --> pdb=" O VAL r 59 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL r 59 " --> pdb=" O VAL r 79 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 832 hydrogen bonds 1280 hydrogen bond angles 0 basepair planarities 331 basepair parallelities 588 stacking parallelities Total time for adding SS restraints: 13.74 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3407 1.30 - 1.43: 15692 1.43 - 1.56: 14854 1.56 - 1.68: 2075 1.68 - 1.81: 48 Bond restraints: 36076 Sorted by residual: bond pdb=" C35 AKN 41607 " pdb=" N12 AKN 41607 " ideal model delta sigma weight residual 1.339 1.471 -0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C24 AKN 41607 " pdb=" C26 AKN 41607 " ideal model delta sigma weight residual 1.532 1.450 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C7 AKN 41607 " pdb=" O8 AKN 41607 " ideal model delta sigma weight residual 1.420 1.496 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C28 AKN 41607 " pdb=" O29 AKN 41607 " ideal model delta sigma weight residual 1.421 1.491 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C4 AKN 41607 " pdb=" C5 AKN 41607 " ideal model delta sigma weight residual 1.525 1.457 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 36071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 49726 2.12 - 4.24: 3443 4.24 - 6.35: 710 6.35 - 8.47: 70 8.47 - 10.59: 4 Bond angle restraints: 53953 Sorted by residual: angle pdb=" N TYR e 53 " pdb=" CA TYR e 53 " pdb=" C TYR e 53 " ideal model delta sigma weight residual 114.56 106.68 7.88 1.27e+00 6.20e-01 3.85e+01 angle pdb=" C3' G 41526 " pdb=" O3' G 41526 " pdb=" P G 41527 " ideal model delta sigma weight residual 119.70 125.35 -5.65 1.20e+00 6.94e-01 2.22e+01 angle pdb=" N VAL r 14 " pdb=" CA VAL r 14 " pdb=" C VAL r 14 " ideal model delta sigma weight residual 113.71 109.26 4.45 9.50e-01 1.11e+00 2.20e+01 angle pdb=" O3' A 2 496 " pdb=" C3' A 2 496 " pdb=" C2' A 2 496 " ideal model delta sigma weight residual 113.80 105.84 7.96 2.00e+00 2.50e-01 1.59e+01 angle pdb=" C3' G 2 186 " pdb=" O3' G 2 186 " pdb=" P G 2 187 " ideal model delta sigma weight residual 119.70 124.02 -4.32 1.20e+00 6.94e-01 1.29e+01 ... (remaining 53948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.98: 17028 33.98 - 67.96: 2036 67.96 - 101.94: 155 101.94 - 135.93: 2 135.93 - 169.91: 2 Dihedral angle restraints: 19223 sinusoidal: 14937 harmonic: 4286 Sorted by residual: dihedral pdb=" C4' A 2 125 " pdb=" C3' A 2 125 " pdb=" C2' A 2 125 " pdb=" C1' A 2 125 " ideal model delta sinusoidal sigma weight residual 36.35 -42.43 78.78 1 3.10e+00 1.04e-01 8.05e+02 dihedral pdb=" C4' G 2 424 " pdb=" C3' G 2 424 " pdb=" C2' G 2 424 " pdb=" C1' G 2 424 " ideal model delta sinusoidal sigma weight residual 36.34 -40.92 77.26 1 3.10e+00 1.04e-01 7.79e+02 dihedral pdb=" C4' U 2 425 " pdb=" C3' U 2 425 " pdb=" C2' U 2 425 " pdb=" C1' U 2 425 " ideal model delta sinusoidal sigma weight residual 36.35 -40.87 77.21 1 3.10e+00 1.04e-01 7.78e+02 ... (remaining 19220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4518 0.071 - 0.142: 1112 0.142 - 0.212: 671 0.212 - 0.283: 510 0.283 - 0.354: 124 Chirality restraints: 6935 Sorted by residual: chirality pdb=" C2' G 2 815 " pdb=" C3' G 2 815 " pdb=" O2' G 2 815 " pdb=" C1' G 2 815 " both_signs ideal model delta sigma weight residual False -2.79 -2.44 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C2' G 2 612 " pdb=" C3' G 2 612 " pdb=" O2' G 2 612 " pdb=" C1' G 2 612 " both_signs ideal model delta sigma weight residual False -2.79 -2.44 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C1' U 2 361 " pdb=" O4' U 2 361 " pdb=" C2' U 2 361 " pdb=" N1 U 2 361 " both_signs ideal model delta sigma weight residual False 2.46 2.10 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 6932 not shown) Planarity restraints: 2985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 2 612 " 0.066 2.00e-02 2.50e+03 2.81e-02 2.38e+01 pdb=" N9 G 2 612 " -0.066 2.00e-02 2.50e+03 pdb=" C8 G 2 612 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G 2 612 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G 2 612 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 2 612 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G 2 612 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G 2 612 " 0.008 2.00e-02 2.50e+03 pdb=" C2 G 2 612 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G 2 612 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 2 612 " -0.015 2.00e-02 2.50e+03 pdb=" C4 G 2 612 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 360 " -0.060 2.00e-02 2.50e+03 2.82e-02 2.19e+01 pdb=" N9 A 2 360 " 0.059 2.00e-02 2.50e+03 pdb=" C8 A 2 360 " 0.013 2.00e-02 2.50e+03 pdb=" N7 A 2 360 " -0.017 2.00e-02 2.50e+03 pdb=" C5 A 2 360 " 0.019 2.00e-02 2.50e+03 pdb=" C6 A 2 360 " -0.020 2.00e-02 2.50e+03 pdb=" N6 A 2 360 " -0.015 2.00e-02 2.50e+03 pdb=" N1 A 2 360 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A 2 360 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A 2 360 " -0.000 2.00e-02 2.50e+03 pdb=" C4 A 2 360 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 2 331 " 0.055 2.00e-02 2.50e+03 2.97e-02 1.99e+01 pdb=" N1 C 2 331 " -0.068 2.00e-02 2.50e+03 pdb=" C2 C 2 331 " -0.004 2.00e-02 2.50e+03 pdb=" O2 C 2 331 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C 2 331 " 0.008 2.00e-02 2.50e+03 pdb=" C4 C 2 331 " 0.006 2.00e-02 2.50e+03 pdb=" N4 C 2 331 " 0.014 2.00e-02 2.50e+03 pdb=" C5 C 2 331 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C 2 331 " -0.008 2.00e-02 2.50e+03 ... (remaining 2982 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 123 2.46 - 3.07: 19297 3.07 - 3.68: 57171 3.68 - 4.29: 94218 4.29 - 4.90: 125210 Nonbonded interactions: 296019 Sorted by model distance: nonbonded pdb=" OP1 G 41502 " pdb="MG MG 41602 " model vdw 1.849 2.170 nonbonded pdb=" OP1 A 2 530 " pdb="MG MG 21636 " model vdw 1.897 2.170 nonbonded pdb=" O2 C 2 152 " pdb=" N2 G 2 161 " model vdw 1.931 2.496 nonbonded pdb=" OP2 G 2 285 " pdb="MG MG 21602 " model vdw 2.051 2.170 nonbonded pdb=" OP2 A 2 191 " pdb="MG MG 21629 " model vdw 2.056 2.170 ... (remaining 296014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 39.360 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.012 0.132 36076 Z= 0.581 Angle : 1.232 10.588 53953 Z= 0.520 Chirality : 0.108 0.354 6935 Planarity : 0.007 0.065 2985 Dihedral : 21.510 169.908 16457 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.25 % Favored : 90.54 % Rotamer: Outliers : 11.02 % Allowed : 20.24 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.18), residues: 1470 helix: -2.40 (0.17), residues: 558 sheet: -1.23 (0.32), residues: 234 loop : -3.35 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG l 127 TYR 0.026 0.003 TYR m 117 PHE 0.021 0.003 PHE p 43 TRP 0.021 0.003 TRP q 60 HIS 0.006 0.002 HIS f 120 Details of bonding type rmsd/Z covalent geometry : bond 0.01184 / 0.58 (36076) covalent geometry : angle 1.23194 / 0.52 (53953) hydrogen bonds : bond 0.13889 / 7.18 ( 1304) hydrogen bonds : angle 5.08144 / 2.03 ( 2630) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 199 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: e 41 GLN cc_start: 0.7417 (tt0) cc_final: 0.7170 (tt0) REVERT: e 72 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7921 (ttt180) REVERT: f 14 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8469 (tt) REVERT: g 92 ARG cc_start: 0.8270 (mmt180) cc_final: 0.7930 (mmt180) REVERT: l 33 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8331 (mm) REVERT: p 58 ARG cc_start: 0.8467 (ttm170) cc_final: 0.8212 (ttp-170) REVERT: p 71 ASN cc_start: 0.8955 (t0) cc_final: 0.8733 (t0) REVERT: r 29 ARG cc_start: 0.7922 (ttm-80) cc_final: 0.7586 (ttm110) REVERT: s 28 THR cc_start: 0.8494 (t) cc_final: 0.8231 (t) REVERT: v 54 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7863 (tttt) outliers start: 110 outliers final: 81 residues processed: 295 average time/residue: 0.6974 time to fit residues: 245.4328 Evaluate side-chains 269 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 185 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 13 ARG Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 72 ARG Chi-restraints excluded: chain e residue 75 SER Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 121 SER Chi-restraints excluded: chain e residue 130 ARG Chi-restraints excluded: chain e residue 136 SER Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 193 LEU Chi-restraints excluded: chain e residue 197 ILE Chi-restraints excluded: chain e residue 200 SER Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 31 SER Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 79 THR Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 159 SER Chi-restraints excluded: chain f residue 162 GLU Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 65 GLU Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain i residue 80 SER Chi-restraints excluded: chain i residue 95 SER Chi-restraints excluded: chain i residue 107 THR Chi-restraints excluded: chain i residue 108 SER Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 17 GLU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 32 THR Chi-restraints excluded: chain l residue 33 ILE Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 84 LEU Chi-restraints excluded: chain l residue 102 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 113 THR Chi-restraints excluded: chain l residue 118 ASN Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 12 ARG Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 59 SER Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 52 SER Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 61 VAL Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 77 SER Chi-restraints excluded: chain v residue 55 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 56 GLN e 122 HIS e 177 HIS f 88 HIS f 120 HIS f 137 ASN g 3 HIS g 58 HIS g 63 ASN i 16 ASN i 42 GLN l 49 GLN l 63 GLN m 96 HIS m 111 ASN p 42 HIS p 62 GLN q 26 ASN q 44 GLN r 32 HIS s 52 GLN u 13 GLN u 20 HIS u 68 HIS u 70 ASN u 75 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.143003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.127353 restraints weight = 37788.656| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 0.22 r_work: 0.3143 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 36076 Z= 0.238 Angle : 1.323 20.099 53953 Z= 0.531 Chirality : 0.117 1.269 6935 Planarity : 0.005 0.055 2985 Dihedral : 18.680 172.057 14225 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.10 % Favored : 94.83 % Rotamer: Outliers : 7.41 % Allowed : 24.55 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.20), residues: 1470 helix: -0.76 (0.21), residues: 569 sheet: -0.79 (0.31), residues: 245 loop : -2.84 (0.20), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG p 8 TYR 0.019 0.002 TYR m 117 PHE 0.013 0.001 PHE f 140 TRP 0.014 0.001 TRP q 60 HIS 0.004 0.001 HIS r 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.24 (36076) covalent geometry : angle 1.32259 / 0.53 (53953) hydrogen bonds : bond 0.06775 / 3.56 ( 1304) hydrogen bonds : angle 3.48483 / 1.36 ( 2630) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 186 time to evaluate : 0.711 Fit side-chains REVERT: e 204 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7208 (mt-10) REVERT: l 17 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.5928 (mp0) REVERT: p 64 ARG cc_start: 0.8988 (tpp-160) cc_final: 0.8623 (tpm170) REVERT: r 29 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7414 (ttm110) REVERT: s 25 ASP cc_start: 0.8506 (t0) cc_final: 0.8229 (t0) REVERT: s 31 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: v 54 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7871 (tttm) REVERT: v 56 TYR cc_start: 0.8606 (t80) cc_final: 0.8384 (t80) outliers start: 74 outliers final: 39 residues processed: 241 average time/residue: 0.7074 time to fit residues: 202.2493 Evaluate side-chains 210 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 130 ARG Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain l residue 17 GLU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 102 VAL Chi-restraints excluded: chain l residue 113 THR Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 52 SER Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 68 ILE Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain u residue 77 SER Chi-restraints excluded: chain v residue 55 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 94 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 126 optimal weight: 0.0050 chunk 161 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 205 optimal weight: 0.0070 chunk 56 optimal weight: 3.9990 overall best weight: 2.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 41 GLN ** f 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 GLN i 42 GLN p 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.139969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.124165 restraints weight = 37695.797| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 0.23 r_work: 0.3080 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 36076 Z= 0.333 Angle : 1.282 19.427 53953 Z= 0.519 Chirality : 0.112 1.285 6935 Planarity : 0.005 0.057 2985 Dihedral : 18.979 176.605 14142 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.07 % Favored : 92.86 % Rotamer: Outliers : 8.82 % Allowed : 24.15 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.21), residues: 1470 helix: -0.22 (0.22), residues: 568 sheet: -0.52 (0.33), residues: 231 loop : -2.63 (0.21), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG g 79 TYR 0.021 0.002 TYR m 117 PHE 0.015 0.002 PHE f 140 TRP 0.015 0.002 TRP q 60 HIS 0.005 0.001 HIS p 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.33 (36076) covalent geometry : angle 1.28220 / 0.52 (53953) hydrogen bonds : bond 0.07183 / 3.72 ( 1304) hydrogen bonds : angle 3.34638 / 1.31 ( 2630) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 180 time to evaluate : 0.707 Fit side-chains REVERT: e 20 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7402 (mt0) REVERT: e 193 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5484 (mt) REVERT: e 204 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: f 14 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8385 (tp) REVERT: f 100 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7447 (tp30) REVERT: g 14 GLN cc_start: 0.6855 (OUTLIER) cc_final: 0.6635 (mt0) REVERT: l 17 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6006 (mp0) REVERT: q 14 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7843 (mtp180) REVERT: q 55 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7003 (p0) REVERT: r 29 ARG cc_start: 0.7648 (ttm-80) cc_final: 0.7338 (ttm110) REVERT: v 54 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7879 (tttm) REVERT: v 56 TYR cc_start: 0.8624 (t80) cc_final: 0.8386 (t80) outliers start: 88 outliers final: 50 residues processed: 245 average time/residue: 0.6728 time to fit residues: 198.0585 Evaluate side-chains 234 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 20 GLN Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 130 ARG Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 193 LEU Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 79 THR Chi-restraints excluded: chain f residue 100 GLU Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 14 GLN Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 56 LYS Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain l residue 17 GLU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 32 THR Chi-restraints excluded: chain l residue 102 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain l residue 118 ASN Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 52 SER Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 68 ILE Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain u residue 77 SER Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 55 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 92 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 41 GLN f 96 GLN f 121 ASN i 42 GLN l 27 ASN l 63 GLN p 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.135157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.118806 restraints weight = 37893.179| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 0.30 r_work: 0.3004 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.104 36076 Z= 0.538 Angle : 1.523 21.963 53953 Z= 0.615 Chirality : 0.132 1.584 6935 Planarity : 0.007 0.063 2985 Dihedral : 19.201 179.348 14139 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.03 % Favored : 91.90 % Rotamer: Outliers : 10.32 % Allowed : 23.75 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.21), residues: 1470 helix: -0.41 (0.22), residues: 567 sheet: -0.68 (0.33), residues: 234 loop : -2.63 (0.21), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG g 91 TYR 0.024 0.003 TYR m 117 PHE 0.020 0.002 PHE p 43 TRP 0.020 0.003 TRP q 60 HIS 0.006 0.002 HIS p 48 Details of bonding type rmsd/Z covalent geometry : bond 0.01104 / 0.54 (36076) covalent geometry : angle 1.52296 / 0.61 (53953) hydrogen bonds : bond 0.08712 / 4.53 ( 1304) hydrogen bonds : angle 3.58320 / 1.41 ( 2630) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 178 time to evaluate : 0.684 Fit side-chains REVERT: e 20 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7386 (mt0) REVERT: e 22 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6775 (mtpp) REVERT: e 193 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.5405 (mt) REVERT: e 204 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7315 (mt-10) REVERT: f 14 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8366 (tp) REVERT: f 100 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: g 14 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6697 (mt0) REVERT: g 44 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7698 (ptt180) REVERT: g 46 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7198 (tt0) REVERT: l 17 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.5998 (mp0) REVERT: m 75 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: p 64 ARG cc_start: 0.9046 (tpm170) cc_final: 0.8680 (tpm170) REVERT: q 14 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7935 (mtp180) REVERT: q 55 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7048 (p0) REVERT: r 29 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7477 (ttm110) REVERT: r 40 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7142 (mtm-85) REVERT: s 31 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8212 (mt0) REVERT: v 54 LYS cc_start: 0.8244 (ttmm) cc_final: 0.7934 (tttt) REVERT: v 56 TYR cc_start: 0.8637 (t80) cc_final: 0.8388 (t80) outliers start: 103 outliers final: 64 residues processed: 253 average time/residue: 0.7116 time to fit residues: 214.4205 Evaluate side-chains 252 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 173 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 20 GLN Chi-restraints excluded: chain e residue 22 LYS Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 130 ARG Chi-restraints excluded: chain e residue 166 GLN Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 193 LEU Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 100 GLU Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 162 GLU Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 14 GLN Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 44 ARG Chi-restraints excluded: chain g residue 46 GLN Chi-restraints excluded: chain g residue 56 LYS Chi-restraints excluded: chain g residue 65 GLU Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 77 LEU Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain i residue 112 MET Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 17 GLU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 32 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 84 LEU Chi-restraints excluded: chain l residue 102 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain l residue 113 THR Chi-restraints excluded: chain l residue 118 ASN Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 75 GLN Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 52 SER Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 40 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain u residue 46 VAL Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain u residue 77 SER Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 55 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 68 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 140 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 41 GLN e 61 GLN i 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.142273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.126662 restraints weight = 37792.628| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 0.23 r_work: 0.3117 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 36076 Z= 0.255 Angle : 1.167 16.985 53953 Z= 0.474 Chirality : 0.102 1.141 6935 Planarity : 0.005 0.058 2985 Dihedral : 19.047 179.794 14138 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.78 % Favored : 94.15 % Rotamer: Outliers : 8.42 % Allowed : 26.25 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.21), residues: 1470 helix: 0.13 (0.22), residues: 574 sheet: -0.45 (0.32), residues: 239 loop : -2.49 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG g 79 TYR 0.019 0.002 TYR m 117 PHE 0.014 0.001 PHE f 140 TRP 0.016 0.002 TRP q 60 HIS 0.003 0.001 HIS g 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.26 (36076) covalent geometry : angle 1.16696 / 0.47 (53953) hydrogen bonds : bond 0.06479 / 3.35 ( 1304) hydrogen bonds : angle 3.22668 / 1.26 ( 2630) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 181 time to evaluate : 0.731 Fit side-chains REVERT: e 158 LYS cc_start: 0.4962 (OUTLIER) cc_final: 0.4757 (tmtt) REVERT: e 193 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.5194 (mp) REVERT: e 204 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: f 14 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8370 (tp) REVERT: g 14 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.6634 (mt0) REVERT: g 44 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7513 (ptt180) REVERT: g 91 ARG cc_start: 0.8401 (ttt-90) cc_final: 0.8157 (mtp180) REVERT: l 17 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5926 (mp0) REVERT: l 125 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8452 (ttmt) REVERT: p 10 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.7006 (mt-10) REVERT: q 14 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7828 (mtp180) REVERT: q 55 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.6984 (p0) REVERT: r 29 ARG cc_start: 0.7572 (ttm-80) cc_final: 0.7280 (ttm110) REVERT: v 54 LYS cc_start: 0.8188 (ttmm) cc_final: 0.7885 (tttm) REVERT: v 56 TYR cc_start: 0.8644 (t80) cc_final: 0.8417 (t80) outliers start: 84 outliers final: 55 residues processed: 245 average time/residue: 0.6858 time to fit residues: 200.9626 Evaluate side-chains 238 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 130 ARG Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain e residue 166 GLN Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 193 LEU Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 14 GLN Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 44 ARG Chi-restraints excluded: chain g residue 56 LYS Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 77 LEU Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain l residue 17 GLU Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 102 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain l residue 118 ASN Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 31 ARG Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 49 LYS Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain u residue 77 SER Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 55 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 207 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 209 optimal weight: 0.0040 chunk 245 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 41 GLN i 42 GLN i 53 GLN l 63 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.143625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.127754 restraints weight = 37577.807| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 0.23 r_work: 0.3138 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 36076 Z= 0.236 Angle : 1.126 16.601 53953 Z= 0.456 Chirality : 0.097 1.058 6935 Planarity : 0.005 0.055 2985 Dihedral : 18.972 178.616 14136 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 8.22 % Allowed : 26.45 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.21), residues: 1470 helix: 0.50 (0.23), residues: 571 sheet: -0.37 (0.33), residues: 237 loop : -2.26 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG r 41 TYR 0.017 0.001 TYR m 117 PHE 0.014 0.001 PHE f 140 TRP 0.014 0.002 TRP q 60 HIS 0.003 0.001 HIS m 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.24 (36076) covalent geometry : angle 1.12576 / 0.46 (53953) hydrogen bonds : bond 0.06341 / 3.29 ( 1304) hydrogen bonds : angle 3.10592 / 1.21 ( 2630) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 179 time to evaluate : 0.662 Fit side-chains REVERT: e 158 LYS cc_start: 0.5051 (OUTLIER) cc_final: 0.4783 (tmtt) REVERT: e 204 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: g 14 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6612 (mt0) REVERT: g 44 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7548 (ptt180) REVERT: g 91 ARG cc_start: 0.8408 (ttt-90) cc_final: 0.8164 (mtp180) REVERT: i 125 GLU cc_start: 0.8403 (tt0) cc_final: 0.8198 (tt0) REVERT: l 41 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7649 (mt) REVERT: p 10 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7147 (mt-10) REVERT: p 64 ARG cc_start: 0.8928 (tpm170) cc_final: 0.8699 (tpm170) REVERT: q 14 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7797 (mtp180) REVERT: q 55 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.6947 (p0) REVERT: r 66 ARG cc_start: 0.8396 (ptm160) cc_final: 0.7576 (ptp-170) REVERT: r 78 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: u 34 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7586 (mtt90) REVERT: v 54 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7885 (tttm) outliers start: 82 outliers final: 50 residues processed: 241 average time/residue: 0.6928 time to fit residues: 198.5621 Evaluate side-chains 232 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 172 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain e residue 166 GLN Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 14 GLN Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 44 ARG Chi-restraints excluded: chain g residue 56 LYS Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 77 LEU Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain i residue 104 ILE Chi-restraints excluded: chain i residue 112 MET Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain l residue 113 THR Chi-restraints excluded: chain l residue 118 ASN Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 78 GLU Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 68 ILE Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain u residue 77 SER Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 55 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 24 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 42 GLN l 27 ASN l 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.143624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.128480 restraints weight = 37720.410| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 0.22 r_work: 0.3139 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 36076 Z= 0.238 Angle : 1.122 16.538 53953 Z= 0.455 Chirality : 0.096 1.052 6935 Planarity : 0.005 0.053 2985 Dihedral : 18.930 178.429 14126 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 6.81 % Allowed : 28.36 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.22), residues: 1470 helix: 0.58 (0.23), residues: 575 sheet: -0.23 (0.33), residues: 236 loop : -2.18 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG g 79 TYR 0.017 0.002 TYR m 117 PHE 0.014 0.001 PHE f 140 TRP 0.014 0.002 TRP q 60 HIS 0.004 0.001 HIS m 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.24 (36076) covalent geometry : angle 1.12219 / 0.45 (53953) hydrogen bonds : bond 0.06332 / 3.28 ( 1304) hydrogen bonds : angle 3.07946 / 1.20 ( 2630) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 171 time to evaluate : 0.461 Fit side-chains REVERT: e 193 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5365 (mt) REVERT: e 204 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: g 44 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7572 (ptt180) REVERT: g 91 ARG cc_start: 0.8423 (ttt-90) cc_final: 0.8161 (mtp180) REVERT: l 41 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7669 (mt) REVERT: p 10 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7163 (mt-10) REVERT: q 14 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7807 (mtp180) REVERT: q 55 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6920 (p0) REVERT: r 40 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7049 (mtm-85) REVERT: r 66 ARG cc_start: 0.8377 (ptm160) cc_final: 0.7537 (ptp-170) REVERT: r 78 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.8003 (pt0) REVERT: u 34 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7618 (mtt90) REVERT: v 54 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7859 (tttm) REVERT: v 55 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7644 (ttm170) outliers start: 68 outliers final: 49 residues processed: 223 average time/residue: 0.7220 time to fit residues: 190.2755 Evaluate side-chains 228 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 130 ARG Chi-restraints excluded: chain e residue 166 GLN Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 193 LEU Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 44 ARG Chi-restraints excluded: chain g residue 56 LYS Chi-restraints excluded: chain g residue 65 GLU Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 77 LEU Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain l residue 118 ASN Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 89 ARG Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 49 LYS Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 40 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 78 GLU Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 68 ILE Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain u residue 77 SER Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 55 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 52 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 246 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 112 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 42 GLN l 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.142369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.126837 restraints weight = 37612.245| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 0.22 r_work: 0.3117 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 36076 Z= 0.270 Angle : 1.165 17.030 53953 Z= 0.472 Chirality : 0.100 1.138 6935 Planarity : 0.005 0.054 2985 Dihedral : 18.942 178.597 14123 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 7.72 % Allowed : 27.25 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.22), residues: 1470 helix: 0.60 (0.22), residues: 575 sheet: -0.33 (0.33), residues: 239 loop : -2.13 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG r 41 TYR 0.018 0.002 TYR m 117 PHE 0.014 0.001 PHE f 140 TRP 0.014 0.002 TRP q 60 HIS 0.004 0.001 HIS m 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.27 (36076) covalent geometry : angle 1.16503 / 0.47 (53953) hydrogen bonds : bond 0.06572 / 3.41 ( 1304) hydrogen bonds : angle 3.11409 / 1.22 ( 2630) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 177 time to evaluate : 0.690 Fit side-chains REVERT: e 204 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7230 (mt-10) REVERT: g 14 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6610 (mt0) REVERT: g 44 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7595 (ptt180) REVERT: g 91 ARG cc_start: 0.8468 (ttt-90) cc_final: 0.8179 (mtp180) REVERT: i 125 GLU cc_start: 0.8417 (tt0) cc_final: 0.8154 (tt0) REVERT: l 17 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5937 (mp0) REVERT: l 41 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7656 (mt) REVERT: p 10 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7159 (mt-10) REVERT: p 64 ARG cc_start: 0.8942 (tpm170) cc_final: 0.8695 (tpm170) REVERT: q 14 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7881 (mtp180) REVERT: q 55 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.6944 (p0) REVERT: r 40 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7128 (mtm-85) REVERT: r 66 ARG cc_start: 0.8409 (ptm160) cc_final: 0.7519 (ptp-170) REVERT: r 78 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.8017 (pt0) REVERT: u 82 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: v 54 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7849 (tttm) outliers start: 77 outliers final: 52 residues processed: 237 average time/residue: 0.7160 time to fit residues: 201.1799 Evaluate side-chains 238 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 175 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 166 GLN Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 162 GLU Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 14 GLN Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 44 ARG Chi-restraints excluded: chain g residue 56 LYS Chi-restraints excluded: chain g residue 65 GLU Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 17 GLU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain l residue 118 ASN Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 75 GLN Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 89 ARG Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 49 LYS Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 40 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 78 GLU Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 68 ILE Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain u residue 82 GLN Chi-restraints excluded: chain v residue 42 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 243 optimal weight: 8.9990 chunk 229 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 174 optimal weight: 0.0670 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 42 GLN l 27 ASN l 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.142602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.127119 restraints weight = 37646.195| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 0.22 r_work: 0.3121 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 36076 Z= 0.260 Angle : 1.157 16.933 53953 Z= 0.469 Chirality : 0.100 1.122 6935 Planarity : 0.005 0.054 2985 Dihedral : 18.942 178.561 14116 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 6.81 % Allowed : 28.46 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.22), residues: 1470 helix: 0.64 (0.23), residues: 575 sheet: -0.33 (0.33), residues: 239 loop : -2.12 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG g 79 TYR 0.018 0.002 TYR m 117 PHE 0.014 0.001 PHE f 140 TRP 0.014 0.002 TRP q 60 HIS 0.008 0.001 HIS e 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.26 (36076) covalent geometry : angle 1.15738 / 0.47 (53953) hydrogen bonds : bond 0.06515 / 3.38 ( 1304) hydrogen bonds : angle 3.10725 / 1.22 ( 2630) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 172 time to evaluate : 0.963 Fit side-chains REVERT: e 204 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7234 (mt-10) REVERT: g 14 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6631 (mt0) REVERT: g 44 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7602 (ptt180) REVERT: g 91 ARG cc_start: 0.8468 (ttt-90) cc_final: 0.8181 (mtp180) REVERT: i 125 GLU cc_start: 0.8437 (tt0) cc_final: 0.8175 (tt0) REVERT: l 17 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6001 (mp0) REVERT: l 41 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7655 (mt) REVERT: p 10 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7151 (mt-10) REVERT: p 64 ARG cc_start: 0.8930 (tpm170) cc_final: 0.8647 (tpm170) REVERT: q 14 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7882 (mtp180) REVERT: q 55 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.6957 (p0) REVERT: r 40 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7233 (mtm-85) REVERT: r 66 ARG cc_start: 0.8381 (ptm160) cc_final: 0.7501 (ptp-170) REVERT: r 78 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8022 (pt0) REVERT: u 34 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7607 (mtt90) REVERT: u 82 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7681 (mt0) REVERT: v 54 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7855 (tttm) outliers start: 68 outliers final: 51 residues processed: 222 average time/residue: 0.7534 time to fit residues: 198.0161 Evaluate side-chains 233 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 170 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 166 GLN Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 14 GLN Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 44 ARG Chi-restraints excluded: chain g residue 56 LYS Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 77 LEU Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 17 GLU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain l residue 118 ASN Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 89 ARG Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 49 LYS Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 40 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 78 GLU Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 68 ILE Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain u residue 82 GLN Chi-restraints excluded: chain v residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 47 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 122 optimal weight: 0.0270 chunk 103 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 overall best weight: 2.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 102 ASN i 42 GLN l 27 ASN l 63 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.140434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.124359 restraints weight = 37812.407| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 0.23 r_work: 0.3092 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 36076 Z= 0.329 Angle : 1.242 17.643 53953 Z= 0.503 Chirality : 0.107 1.252 6935 Planarity : 0.005 0.056 2985 Dihedral : 18.977 178.870 14116 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.80 % Favored : 93.13 % Rotamer: Outliers : 6.51 % Allowed : 28.66 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.22), residues: 1470 helix: 0.49 (0.22), residues: 576 sheet: -0.33 (0.33), residues: 232 loop : -2.13 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG g 79 TYR 0.020 0.002 TYR m 117 PHE 0.015 0.002 PHE f 140 TRP 0.015 0.002 TRP q 60 HIS 0.006 0.001 HIS e 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.33 (36076) covalent geometry : angle 1.24188 / 0.50 (53953) hydrogen bonds : bond 0.07029 / 3.65 ( 1304) hydrogen bonds : angle 3.19256 / 1.25 ( 2630) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 171 time to evaluate : 0.668 Fit side-chains REVERT: e 204 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: g 14 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6657 (mt0) REVERT: g 44 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7637 (ptt180) REVERT: g 91 ARG cc_start: 0.8505 (ttt-90) cc_final: 0.8122 (ttp-170) REVERT: i 125 GLU cc_start: 0.8531 (tt0) cc_final: 0.8304 (tt0) REVERT: l 41 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7685 (mt) REVERT: p 10 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7070 (mt-10) REVERT: p 64 ARG cc_start: 0.8971 (tpm170) cc_final: 0.8630 (tpm170) REVERT: q 14 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7898 (mtp180) REVERT: q 55 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6972 (p0) REVERT: r 40 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7217 (mtm-85) REVERT: r 66 ARG cc_start: 0.8422 (ptm160) cc_final: 0.7511 (ptp-170) REVERT: r 78 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: u 34 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7591 (mtt90) REVERT: u 82 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7744 (mt0) REVERT: v 54 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7884 (tttm) outliers start: 65 outliers final: 50 residues processed: 221 average time/residue: 0.7063 time to fit residues: 184.9779 Evaluate side-chains 229 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 166 GLN Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 162 GLU Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 14 GLN Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 44 ARG Chi-restraints excluded: chain g residue 56 LYS Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain l residue 118 ASN Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 75 GLN Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 89 ARG Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 49 LYS Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 40 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 78 GLU Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 68 ILE Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain u residue 82 GLN Chi-restraints excluded: chain v residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 234 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 116 optimal weight: 20.0000 chunk 176 optimal weight: 0.8980 chunk 224 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 42 GLN l 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.143214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.127837 restraints weight = 37632.981| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 0.22 r_work: 0.3139 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36076 Z= 0.213 Angle : 1.144 16.482 53953 Z= 0.463 Chirality : 0.098 1.094 6935 Planarity : 0.005 0.079 2985 Dihedral : 19.024 179.717 14116 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 5.71 % Allowed : 29.86 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.22), residues: 1470 helix: 0.65 (0.22), residues: 575 sheet: -0.22 (0.33), residues: 236 loop : -2.11 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG g 79 TYR 0.017 0.001 TYR m 117 PHE 0.014 0.001 PHE f 140 TRP 0.016 0.002 TRP q 60 HIS 0.006 0.001 HIS e 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 (36076) covalent geometry : angle 1.14400 / 0.46 (53953) hydrogen bonds : bond 0.06300 / 3.26 ( 1304) hydrogen bonds : angle 3.11159 / 1.22 ( 2630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9163.21 seconds wall clock time: 157 minutes 16.33 seconds (9436.33 seconds total)