Starting phenix.real_space_refine on Tue Aug 26 01:22:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ypu_10869/08_2025/6ypu_10869.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ypu_10869/08_2025/6ypu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ypu_10869/08_2025/6ypu_10869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ypu_10869/08_2025/6ypu_10869.map" model { file = "/net/cci-nas-00/data/ceres_data/6ypu_10869/08_2025/6ypu_10869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ypu_10869/08_2025/6ypu_10869.cif" } 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-2.0-5787/lib/python3.9/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: {'RNA': 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: {'RNA': 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: 8.00, per 1000 atoms: 0.24 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 781.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 5.59 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: 14.31 Time building geometry restraints manager: 3.83 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 - 1.93: 50883 1.93 - 3.86: 2742 3.86 - 5.79: 278 5.79 - 7.72: 41 7.72 - 9.65: 9 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=" 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=" O4' G 2 612 " pdb=" C1' G 2 612 " pdb=" N9 G 2 612 " ideal model delta sigma weight residual 108.20 114.93 -6.73 1.50e+00 4.44e-01 2.01e+01 angle pdb=" C2' A 2 360 " pdb=" C1' A 2 360 " pdb=" N9 A 2 360 " ideal model delta sigma weight residual 112.00 118.14 -6.14 1.50e+00 4.44e-01 1.67e+01 angle pdb=" O3' G 2 186 " pdb=" C3' G 2 186 " pdb=" C2' G 2 186 " ideal model delta sigma weight residual 113.70 119.35 -5.65 1.50e+00 4.44e-01 1.42e+01 ... (remaining 53948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 20342 35.76 - 71.53: 2433 71.53 - 107.29: 252 107.29 - 143.05: 7 143.05 - 178.82: 11 Dihedral angle restraints: 23045 sinusoidal: 18759 harmonic: 4286 Sorted by residual: dihedral pdb=" O4' C 2 131 " pdb=" C1' C 2 131 " pdb=" N1 C 2 131 " pdb=" C2 C 2 131 " ideal model delta sinusoidal sigma weight residual -160.00 18.82 -178.82 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 2 172 " pdb=" C1' C 2 172 " pdb=" N1 C 2 172 " pdb=" C2 C 2 172 " ideal model delta sinusoidal sigma weight residual 200.00 24.73 175.27 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U 2 463 " pdb=" C1' U 2 463 " pdb=" N1 U 2 463 " pdb=" C2 U 2 463 " ideal model delta sinusoidal sigma weight residual -160.00 14.91 -174.91 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 23042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 5698 0.072 - 0.145: 1095 0.145 - 0.217: 123 0.217 - 0.290: 15 0.290 - 0.362: 4 Chirality restraints: 6935 Sorted by residual: 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 2.47 2.10 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C3' G 2 186 " pdb=" C4' G 2 186 " pdb=" O3' G 2 186 " pdb=" C2' G 2 186 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C1' G 41527 " pdb=" O4' G 41527 " pdb=" C2' G 41527 " pdb=" N9 G 41527 " both_signs ideal model delta sigma weight residual False 2.46 2.14 0.32 2.00e-01 2.50e+01 2.49e+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: 5.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 41.940 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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= 0.590 Angle : 0.989 9.647 53953 Z= 0.495 Chirality : 0.057 0.362 6935 Planarity : 0.007 0.065 2985 Dihedral : 23.552 178.817 20279 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 aren 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 covalent geometry : bond 0.01165 (36076) covalent geometry : angle 0.98852 (53953) hydrogen bonds : bond 0.13889 ( 1304) hydrogen bonds : angle 5.08144 ( 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 : 0.747 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: 0.7609 time to fit residues: 265.2039 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 : 0.685 ------------------------------------------------------------------------------- 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: 5.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 68 HIS u 70 ASN u 75 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.138747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.123315 restraints weight = 37509.940| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 0.22 r_work: 0.3064 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36076 Z= 0.180 Angle : 0.596 8.046 53953 Z= 0.312 Chirality : 0.038 0.260 6935 Planarity : 0.005 0.054 2985 Dihedral : 23.124 179.235 18047 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.17 % Favored : 94.76 % Rotamer: Outliers : 7.31 % Allowed : 23.95 % Favored : 68.74 % 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 aren not related in a simple way. whole: -2.45 (0.20), residues: 1470 helix: -0.71 (0.21), residues: 568 sheet: -0.77 (0.32), residues: 245 loop : -2.83 (0.20), residues: 657 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 0.014 0.001 PHE f 140 TRP 0.014 0.001 TRP q 60 HIS 0.005 0.001 HIS r 32 Details of bonding type rmsd covalent geometry : bond 0.00349 (36076) covalent geometry : angle 0.59570 (53953) hydrogen bonds : bond 0.06190 ( 1304) hydrogen bonds : angle 3.41967 ( 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 264 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 191 time to evaluate : 0.681 Fit side-chains REVERT: e 41 GLN cc_start: 0.7500 (tt0) cc_final: 0.7260 (tt0) REVERT: e 204 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7064 (mt-10) REVERT: i 70 LYS cc_start: 0.7870 (mtmm) cc_final: 0.7669 (mtmm) REVERT: l 17 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5950 (mp0) REVERT: p 64 ARG cc_start: 0.9025 (tpp-160) cc_final: 0.8668 (tpm170) REVERT: r 29 ARG cc_start: 0.7701 (ttm-80) cc_final: 0.7399 (ttm110) REVERT: s 25 ASP cc_start: 0.8498 (t0) cc_final: 0.8210 (t0) REVERT: s 31 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8060 (mt0) REVERT: v 54 LYS cc_start: 0.8181 (ttmm) cc_final: 0.7849 (tttm) REVERT: v 56 TYR cc_start: 0.8625 (t80) cc_final: 0.8406 (t80) outliers start: 73 outliers final: 37 residues processed: 243 average time/residue: 0.7935 time to fit residues: 226.8157 Evaluate side-chains 215 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 37 SER 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: 10.0000 chunk 162 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 209 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 96 GLN ** f 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 GLN i 42 GLN i 53 GLN l 27 ASN p 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.135310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.119833 restraints weight = 37428.607| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 0.35 r_work: 0.3024 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 36076 Z= 0.340 Angle : 0.730 8.865 53953 Z= 0.369 Chirality : 0.045 0.293 6935 Planarity : 0.006 0.058 2985 Dihedral : 23.159 179.334 17962 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 8.82 % Allowed : 24.55 % Favored : 66.63 % 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 aren not related in a simple way. whole: -2.06 (0.21), residues: 1470 helix: -0.33 (0.22), residues: 569 sheet: -0.54 (0.33), residues: 231 loop : -2.65 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG u 74 TYR 0.022 0.002 TYR m 117 PHE 0.016 0.002 PHE f 140 TRP 0.017 0.002 TRP q 60 HIS 0.005 0.001 HIS p 48 Details of bonding type rmsd covalent geometry : bond 0.00671 (36076) covalent geometry : angle 0.72967 (53953) hydrogen bonds : bond 0.07579 ( 1304) hydrogen bonds : angle 3.40012 ( 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 271 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 183 time to evaluate : 0.679 Fit side-chains REVERT: e 33 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.6091 (mmtp) REVERT: e 41 GLN cc_start: 0.7553 (tt0) cc_final: 0.7278 (tt0) REVERT: e 61 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8523 (tp40) REVERT: e 193 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5559 (mt) REVERT: e 204 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: f 14 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8381 (tp) REVERT: f 100 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7400 (tp30) REVERT: g 14 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6636 (mt0) REVERT: g 46 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: l 17 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.5969 (mp0) REVERT: p 64 ARG cc_start: 0.8944 (tpp-160) cc_final: 0.8721 (tpm170) REVERT: q 14 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7822 (mtp180) REVERT: q 55 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6826 (p0) REVERT: r 29 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7411 (ttm110) REVERT: r 40 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6930 (mtm-85) REVERT: v 54 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7897 (tttt) REVERT: v 56 TYR cc_start: 0.8666 (t80) cc_final: 0.8438 (t80) outliers start: 88 outliers final: 49 residues processed: 248 average time/residue: 0.7668 time to fit residues: 224.2494 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 : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 33 LYS 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 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 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 46 GLN 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 96 ILE 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 106 ILE 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 47 SER 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 15 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 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: 8.9990 chunk 244 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 188 optimal weight: 0.0030 chunk 111 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 overall best weight: 2.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 121 ASN i 42 GLN p 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.135467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.120618 restraints weight = 37389.729| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 0.56 r_work: 0.2917 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 36076 Z= 0.337 Angle : 0.723 8.500 53953 Z= 0.366 Chirality : 0.045 0.288 6935 Planarity : 0.006 0.059 2985 Dihedral : 23.139 179.474 17962 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.60 % Favored : 93.33 % Rotamer: Outliers : 9.62 % Allowed : 24.65 % Favored : 65.73 % 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 aren not related in a simple way. whole: -1.82 (0.21), residues: 1470 helix: -0.09 (0.22), residues: 568 sheet: -0.47 (0.33), residues: 236 loop : -2.54 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG g 79 TYR 0.022 0.002 TYR m 117 PHE 0.016 0.002 PHE f 140 TRP 0.017 0.002 TRP q 60 HIS 0.005 0.001 HIS p 48 Details of bonding type rmsd covalent geometry : bond 0.00665 (36076) covalent geometry : angle 0.72337 (53953) hydrogen bonds : bond 0.07452 ( 1304) hydrogen bonds : angle 3.34510 ( 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 277 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 181 time to evaluate : 0.770 Fit side-chains REVERT: e 33 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6210 (mmtp) REVERT: e 41 GLN cc_start: 0.7656 (tt0) cc_final: 0.7381 (tt0) REVERT: e 61 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8577 (tp40) REVERT: e 193 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5538 (mt) REVERT: e 204 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: f 14 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8427 (tp) REVERT: g 14 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6733 (mt0) REVERT: g 44 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7615 (ptt180) REVERT: g 46 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: g 92 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7876 (mmt90) REVERT: l 17 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5912 (mp0) REVERT: l 111 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8031 (t0) REVERT: p 64 ARG cc_start: 0.9038 (tpp-160) cc_final: 0.8794 (tpm170) REVERT: q 14 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8018 (mtp180) REVERT: q 55 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7096 (p0) REVERT: r 29 ARG cc_start: 0.7674 (ttm-80) cc_final: 0.7422 (ttm110) REVERT: r 40 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7117 (mtm-85) REVERT: v 54 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7857 (tttt) REVERT: v 56 TYR cc_start: 0.8685 (t80) cc_final: 0.8449 (t80) outliers start: 96 outliers final: 56 residues processed: 249 average time/residue: 0.7736 time to fit residues: 227.2488 Evaluate side-chains 241 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 172 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 33 LYS 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 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 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 46 GLN 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 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 54 SER 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 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 47 SER 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 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 40 ARG 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 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: 4.9990 chunk 105 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 140 optimal weight: 0.0570 chunk 171 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 42 GLN l 27 ASN p 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.138288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122716 restraints weight = 37548.037| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 0.23 r_work: 0.3059 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36076 Z= 0.165 Angle : 0.601 8.239 53953 Z= 0.314 Chirality : 0.038 0.269 6935 Planarity : 0.004 0.056 2985 Dihedral : 23.131 179.598 17961 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 8.52 % Allowed : 25.85 % Favored : 65.63 % 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 aren not related in a simple way. whole: -1.55 (0.21), residues: 1470 helix: 0.18 (0.22), residues: 574 sheet: -0.35 (0.33), residues: 239 loop : -2.45 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG g 79 TYR 0.016 0.002 TYR m 117 PHE 0.015 0.001 PHE f 140 TRP 0.014 0.001 TRP q 60 HIS 0.004 0.001 HIS m 96 Details of bonding type rmsd covalent geometry : bond 0.00321 (36076) covalent geometry : angle 0.60110 (53953) hydrogen bonds : bond 0.06292 ( 1304) hydrogen bonds : angle 3.20114 ( 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 260 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 175 time to evaluate : 0.676 Fit side-chains REVERT: e 41 GLN cc_start: 0.7503 (tt0) cc_final: 0.7270 (tt0) REVERT: e 193 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5613 (mt) REVERT: e 204 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: f 110 MET cc_start: 0.8402 (mtt) cc_final: 0.8152 (mtm) REVERT: g 14 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.6628 (mt0) REVERT: g 44 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7478 (ptt180) REVERT: i 125 GLU cc_start: 0.8499 (tt0) cc_final: 0.8214 (tt0) REVERT: l 17 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6052 (mp0) REVERT: q 14 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7898 (mtp180) REVERT: q 55 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6868 (p0) REVERT: r 29 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.7355 (ttm110) REVERT: r 40 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.7308 (mtm-85) REVERT: s 31 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8085 (mt0) REVERT: u 34 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7559 (mtt90) REVERT: v 54 LYS cc_start: 0.8171 (ttmm) cc_final: 0.7874 (tttm) REVERT: v 56 TYR cc_start: 0.8662 (t80) cc_final: 0.8418 (t80) outliers start: 85 outliers final: 56 residues processed: 241 average time/residue: 0.7592 time to fit residues: 216.4140 Evaluate side-chains 237 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 172 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 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 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 26 ILE Chi-restraints excluded: chain g residue 44 ARG 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 19 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 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 15 LEU 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 47 SER Chi-restraints excluded: chain m residue 52 VAL 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 8 THR 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 31 GLN Chi-restraints excluded: chain s residue 47 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 207 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 245 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 173 optimal weight: 0.0000 chunk 198 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 42 GLN i 53 GLN l 27 ASN p 62 GLN u 20 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.141266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.125152 restraints weight = 37519.597| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 0.23 r_work: 0.3098 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36076 Z= 0.143 Angle : 0.535 8.084 53953 Z= 0.279 Chirality : 0.035 0.235 6935 Planarity : 0.004 0.050 2985 Dihedral : 22.917 179.960 17961 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 6.41 % Allowed : 27.66 % 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 aren not related in a simple way. whole: -1.09 (0.22), residues: 1470 helix: 0.63 (0.23), residues: 572 sheet: -0.29 (0.33), residues: 244 loop : -2.18 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG g 79 TYR 0.011 0.001 TYR m 117 PHE 0.012 0.001 PHE f 140 TRP 0.011 0.001 TRP q 60 HIS 0.003 0.001 HIS m 96 Details of bonding type rmsd covalent geometry : bond 0.00276 (36076) covalent geometry : angle 0.53528 (53953) hydrogen bonds : bond 0.05550 ( 1304) hydrogen bonds : angle 2.97435 ( 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 239 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 175 time to evaluate : 0.694 Fit side-chains REVERT: e 204 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7013 (mt-10) REVERT: g 45 ARG cc_start: 0.8762 (mtp85) cc_final: 0.8555 (mtp85) REVERT: i 125 GLU cc_start: 0.8476 (tt0) cc_final: 0.8182 (tt0) REVERT: m 70 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7838 (mt-10) REVERT: p 61 ASN cc_start: 0.8318 (p0) cc_final: 0.7610 (m110) REVERT: q 14 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7776 (mtp180) REVERT: r 40 ARG cc_start: 0.7527 (mmm-85) cc_final: 0.7239 (mtm-85) REVERT: u 34 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7667 (mtt90) REVERT: v 54 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7884 (tttm) outliers start: 64 outliers final: 37 residues processed: 223 average time/residue: 0.8115 time to fit residues: 212.2186 Evaluate side-chains 208 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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 18 VAL Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain l residue 108 SER 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 21 VAL Chi-restraints excluded: chain m residue 31 ARG 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 q residue 14 ARG 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 30 VAL Chi-restraints excluded: chain r residue 38 SER Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain v residue 42 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 24 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 102 ASN i 42 GLN l 63 GLN p 35 GLN p 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.137002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.121634 restraints weight = 37441.861| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 0.27 r_work: 0.3041 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 36076 Z= 0.272 Angle : 0.653 7.944 53953 Z= 0.333 Chirality : 0.041 0.274 6935 Planarity : 0.005 0.054 2985 Dihedral : 22.972 179.856 17940 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.60 % Favored : 93.33 % Rotamer: Outliers : 7.01 % Allowed : 27.35 % Favored : 65.63 % 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 aren not related in a simple way. whole: -1.14 (0.22), residues: 1470 helix: 0.55 (0.23), residues: 572 sheet: -0.25 (0.34), residues: 232 loop : -2.16 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG m 56 TYR 0.018 0.002 TYR m 117 PHE 0.015 0.002 PHE f 140 TRP 0.013 0.002 TRP q 60 HIS 0.004 0.001 HIS p 48 Details of bonding type rmsd covalent geometry : bond 0.00537 (36076) covalent geometry : angle 0.65341 (53953) hydrogen bonds : bond 0.06854 ( 1304) hydrogen bonds : angle 3.12735 ( 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 242 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 172 time to evaluate : 0.679 Fit side-chains REVERT: e 204 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: f 14 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8367 (tp) REVERT: g 45 ARG cc_start: 0.8790 (mtp85) cc_final: 0.8587 (mtp85) REVERT: l 41 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7695 (mt) REVERT: q 1 MET cc_start: 0.8323 (ttm) cc_final: 0.8088 (ttm) REVERT: q 14 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7886 (mtp180) REVERT: r 78 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8045 (pt0) REVERT: v 54 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7897 (tttm) outliers start: 70 outliers final: 47 residues processed: 229 average time/residue: 0.7725 time to fit residues: 208.9498 Evaluate side-chains 220 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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 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 18 VAL 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 94 HIS 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 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 15 LEU 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 22 THR Chi-restraints excluded: chain q residue 14 ARG 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 38 SER 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 37 SER Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain v residue 42 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 52 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 227 optimal weight: 0.0040 chunk 245 optimal weight: 1.9990 chunk 246 optimal weight: 0.1980 chunk 130 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 192 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 41 GLN i 42 GLN l 27 ASN l 63 GLN p 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.139834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.124096 restraints weight = 37521.043| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 0.22 r_work: 0.3081 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36076 Z= 0.151 Angle : 0.561 8.045 53953 Z= 0.293 Chirality : 0.036 0.247 6935 Planarity : 0.004 0.052 2985 Dihedral : 22.938 179.187 17940 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.51 % Allowed : 28.76 % Favored : 65.73 % 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 aren not related in a simple way. whole: -0.92 (0.22), residues: 1470 helix: 0.76 (0.23), residues: 571 sheet: -0.23 (0.33), residues: 244 loop : -2.05 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG r 41 TYR 0.012 0.001 TYR m 117 PHE 0.012 0.001 PHE f 140 TRP 0.013 0.001 TRP q 60 HIS 0.003 0.001 HIS m 96 Details of bonding type rmsd covalent geometry : bond 0.00291 (36076) covalent geometry : angle 0.56130 (53953) hydrogen bonds : bond 0.05866 ( 1304) hydrogen bonds : angle 3.01130 ( 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 225 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 0.721 Fit side-chains REVERT: e 33 LYS cc_start: 0.6746 (OUTLIER) cc_final: 0.6237 (tptt) REVERT: e 204 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7064 (mt-10) REVERT: g 45 ARG cc_start: 0.8778 (mtp85) cc_final: 0.8559 (mtp85) REVERT: i 125 GLU cc_start: 0.8489 (tt0) cc_final: 0.8221 (tt0) REVERT: l 41 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7643 (mt) REVERT: q 1 MET cc_start: 0.8266 (ttm) cc_final: 0.8065 (ttm) REVERT: q 14 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7808 (mtp180) REVERT: r 78 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.8013 (pt0) REVERT: u 34 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7632 (mtt90) REVERT: v 54 LYS cc_start: 0.8200 (ttmm) cc_final: 0.7873 (tttm) outliers start: 55 outliers final: 39 residues processed: 214 average time/residue: 0.7993 time to fit residues: 200.8345 Evaluate side-chains 213 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 33 LYS Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 103 VAL 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 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 18 VAL Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 70 THR 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 106 ILE Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain l residue 128 VAL 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 52 VAL Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 38 SER 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 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: 4.9990 chunk 4 optimal weight: 3.9990 chunk 128 optimal weight: 0.1980 chunk 162 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 41 GLN i 42 GLN l 63 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 = 0.3470 r_free = 0.3470 target = 0.137353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.121888 restraints weight = 37387.226| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 0.27 r_work: 0.3046 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 36076 Z= 0.254 Angle : 0.633 8.025 53953 Z= 0.324 Chirality : 0.040 0.270 6935 Planarity : 0.005 0.063 2985 Dihedral : 22.937 179.697 17939 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.26 % Favored : 93.67 % Rotamer: Outliers : 6.21 % Allowed : 28.36 % Favored : 65.43 % 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 aren not related in a simple way. whole: -1.00 (0.22), residues: 1470 helix: 0.70 (0.23), residues: 572 sheet: -0.24 (0.33), residues: 239 loop : -2.10 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG g 79 TYR 0.017 0.002 TYR m 117 PHE 0.015 0.002 PHE f 140 TRP 0.013 0.002 TRP q 60 HIS 0.004 0.001 HIS m 96 Details of bonding type rmsd covalent geometry : bond 0.00500 (36076) covalent geometry : angle 0.63330 (53953) hydrogen bonds : bond 0.06626 ( 1304) hydrogen bonds : angle 3.09320 ( 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 232 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 170 time to evaluate : 0.712 Fit side-chains REVERT: e 33 LYS cc_start: 0.6704 (OUTLIER) cc_final: 0.6209 (tptt) REVERT: e 204 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7092 (mt-10) REVERT: i 125 GLU cc_start: 0.8523 (tt0) cc_final: 0.8253 (tt0) REVERT: l 41 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7649 (mt) REVERT: p 10 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: q 14 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7876 (mtp180) REVERT: r 78 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8027 (pt0) REVERT: v 54 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7901 (tttm) outliers start: 62 outliers final: 46 residues processed: 221 average time/residue: 0.7912 time to fit residues: 205.8585 Evaluate side-chains 220 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 33 LYS Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 103 VAL 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 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 56 LYS Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 70 THR 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 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 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 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 38 SER 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 37 SER Chi-restraints excluded: chain u residue 74 ARG 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: 4.9990 chunk 189 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 103 optimal weight: 0.1980 chunk 93 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 41 GLN i 42 GLN l 27 ASN l 63 GLN p 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.136869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.121944 restraints weight = 37602.810| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 0.52 r_work: 0.2926 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 36076 Z= 0.276 Angle : 0.656 8.092 53953 Z= 0.335 Chirality : 0.041 0.274 6935 Planarity : 0.005 0.053 2985 Dihedral : 22.959 179.916 17939 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.65 % Favored : 94.29 % Rotamer: Outliers : 6.11 % Allowed : 28.16 % Favored : 65.73 % 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 aren not related in a simple way. whole: -1.04 (0.22), residues: 1470 helix: 0.62 (0.23), residues: 574 sheet: -0.24 (0.34), residues: 232 loop : -2.08 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG g 79 TYR 0.018 0.002 TYR m 117 PHE 0.015 0.002 PHE f 140 TRP 0.013 0.002 TRP q 60 HIS 0.004 0.001 HIS m 96 Details of bonding type rmsd covalent geometry : bond 0.00544 (36076) covalent geometry : angle 0.65650 (53953) hydrogen bonds : bond 0.06835 ( 1304) hydrogen bonds : angle 3.12630 ( 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 229 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 0.624 Fit side-chains REVERT: e 33 LYS cc_start: 0.6765 (OUTLIER) cc_final: 0.6200 (tptt) REVERT: e 204 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: i 125 GLU cc_start: 0.8583 (tt0) cc_final: 0.8318 (tt0) REVERT: l 41 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7710 (mt) REVERT: p 10 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: p 64 ARG cc_start: 0.9086 (tpm170) cc_final: 0.8842 (tpt170) REVERT: q 14 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8030 (mtp180) REVERT: u 34 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7646 (mtt90) REVERT: v 54 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7860 (tttm) outliers start: 61 outliers final: 50 residues processed: 217 average time/residue: 0.7798 time to fit residues: 200.5244 Evaluate side-chains 224 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 168 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 33 LYS Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 103 VAL 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 18 VAL 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 94 HIS Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain i residue 112 MET 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 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 47 SER 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 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 38 SER 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 34 ARG Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain u residue 74 ARG 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: 0.6980 chunk 60 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 214 optimal weight: 0.7980 chunk 116 optimal weight: 20.0000 chunk 176 optimal weight: 0.9990 chunk 224 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 246 optimal weight: 0.0270 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 41 GLN i 42 GLN l 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.140150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.124853 restraints weight = 37493.978| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 0.21 r_work: 0.3095 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 36076 Z= 0.122 Angle : 0.575 10.914 53953 Z= 0.297 Chirality : 0.035 0.255 6935 Planarity : 0.004 0.054 2985 Dihedral : 22.978 178.806 17939 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.01 % Allowed : 29.76 % Favored : 65.23 % 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 aren not related in a simple way. whole: -0.81 (0.22), residues: 1470 helix: 0.86 (0.23), residues: 569 sheet: -0.09 (0.34), residues: 234 loop : -2.00 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG g 79 TYR 0.013 0.001 TYR m 117 PHE 0.013 0.001 PHE f 140 TRP 0.014 0.002 TRP q 60 HIS 0.004 0.001 HIS g 58 Details of bonding type rmsd covalent geometry : bond 0.00232 (36076) covalent geometry : angle 0.57501 (53953) hydrogen bonds : bond 0.05801 ( 1304) hydrogen bonds : angle 3.02392 ( 2630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9450.88 seconds wall clock time: 162 minutes 40.29 seconds (9760.29 seconds total)