Starting phenix.real_space_refine on Sun May 18 07:02:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc2_15960/05_2025/8bc2_15960.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc2_15960/05_2025/8bc2_15960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bc2_15960/05_2025/8bc2_15960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc2_15960/05_2025/8bc2_15960.map" model { file = "/net/cci-nas-00/data/ceres_data/8bc2_15960/05_2025/8bc2_15960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc2_15960/05_2025/8bc2_15960.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 10540 2.51 5 N 2720 2.21 5 O 3470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16770 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1631 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "I" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 5.47, per 1000 atoms: 0.33 Number of scatterers: 16770 At special positions: 0 Unit cell: (117, 123.3, 81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 3470 8.00 N 2720 7.00 C 10540 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: 3.97 Conformation dependent library (CDL) restraints added in 2.2 seconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4100 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 10 sheets defined 60.1% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.793A pdb=" N GLY A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.537A pdb=" N LYS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 106 Processing helix chain 'A' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER A 142 " --> pdb=" O TRP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.995A pdb=" N ASP A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 200 through 216 removed outlier: 3.662A pdb=" N ASP A 204 " --> pdb=" O HIS A 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 28 through 36 removed outlier: 3.794A pdb=" N GLY B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 50 Processing helix chain 'B' and resid 68 through 81 removed outlier: 3.537A pdb=" N LYS B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 106 Processing helix chain 'B' and resid 117 through 127 removed outlier: 4.015A pdb=" N GLN B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER B 142 " --> pdb=" O TRP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.995A pdb=" N ASP B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 200 through 216 removed outlier: 3.662A pdb=" N ASP B 204 " --> pdb=" O HIS B 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.793A pdb=" N GLY C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 68 through 81 removed outlier: 3.536A pdb=" N LYS C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 106 Processing helix chain 'C' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN C 123 " --> pdb=" O SER C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER C 142 " --> pdb=" O TRP C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.996A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 183 Processing helix chain 'C' and resid 190 through 198 Processing helix chain 'C' and resid 200 through 216 removed outlier: 3.661A pdb=" N ASP C 204 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.793A pdb=" N GLY D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 68 through 81 removed outlier: 3.536A pdb=" N LYS D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 106 Processing helix chain 'D' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Proline residue: D 124 - end of helix Processing helix chain 'D' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER D 142 " --> pdb=" O TRP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 159 removed outlier: 3.995A pdb=" N ASP D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 183 Processing helix chain 'D' and resid 190 through 198 Processing helix chain 'D' and resid 200 through 216 removed outlier: 3.661A pdb=" N ASP D 204 " --> pdb=" O HIS D 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 28 through 36 removed outlier: 3.794A pdb=" N GLY E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 68 through 81 removed outlier: 3.537A pdb=" N LYS E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 106 Processing helix chain 'E' and resid 117 through 127 removed outlier: 4.015A pdb=" N GLN E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER E 142 " --> pdb=" O TRP E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 159 removed outlier: 3.996A pdb=" N ASP E 151 " --> pdb=" O THR E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 183 Processing helix chain 'E' and resid 190 through 198 Processing helix chain 'E' and resid 200 through 216 removed outlier: 3.662A pdb=" N ASP E 204 " --> pdb=" O HIS E 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 20 Processing helix chain 'F' and resid 28 through 36 removed outlier: 3.794A pdb=" N GLY F 36 " --> pdb=" O ILE F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 68 through 81 removed outlier: 3.537A pdb=" N LYS F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER F 142 " --> pdb=" O TRP F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 159 removed outlier: 3.995A pdb=" N ASP F 151 " --> pdb=" O THR F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 183 Processing helix chain 'F' and resid 190 through 198 Processing helix chain 'F' and resid 200 through 216 removed outlier: 3.663A pdb=" N ASP F 204 " --> pdb=" O HIS F 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 20 Processing helix chain 'G' and resid 28 through 36 removed outlier: 3.793A pdb=" N GLY G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 50 Processing helix chain 'G' and resid 68 through 81 removed outlier: 3.536A pdb=" N LYS G 78 " --> pdb=" O GLU G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 106 Processing helix chain 'G' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN G 123 " --> pdb=" O SER G 119 " (cutoff:3.500A) Proline residue: G 124 - end of helix Processing helix chain 'G' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER G 142 " --> pdb=" O TRP G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 159 removed outlier: 3.995A pdb=" N ASP G 151 " --> pdb=" O THR G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 183 Processing helix chain 'G' and resid 190 through 198 Processing helix chain 'G' and resid 200 through 216 removed outlier: 3.662A pdb=" N ASP G 204 " --> pdb=" O HIS G 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 28 through 36 removed outlier: 3.794A pdb=" N GLY H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 68 through 81 removed outlier: 3.537A pdb=" N LYS H 78 " --> pdb=" O GLU H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 106 Processing helix chain 'H' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN H 123 " --> pdb=" O SER H 119 " (cutoff:3.500A) Proline residue: H 124 - end of helix Processing helix chain 'H' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER H 142 " --> pdb=" O TRP H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 159 removed outlier: 3.994A pdb=" N ASP H 151 " --> pdb=" O THR H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 183 Processing helix chain 'H' and resid 190 through 198 Processing helix chain 'H' and resid 200 through 216 removed outlier: 3.662A pdb=" N ASP H 204 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 20 Processing helix chain 'I' and resid 28 through 36 removed outlier: 3.793A pdb=" N GLY I 36 " --> pdb=" O ILE I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 50 Processing helix chain 'I' and resid 68 through 81 removed outlier: 3.537A pdb=" N LYS I 78 " --> pdb=" O GLU I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 106 Processing helix chain 'I' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN I 123 " --> pdb=" O SER I 119 " (cutoff:3.500A) Proline residue: I 124 - end of helix Processing helix chain 'I' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER I 142 " --> pdb=" O TRP I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 159 removed outlier: 3.995A pdb=" N ASP I 151 " --> pdb=" O THR I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 183 Processing helix chain 'I' and resid 190 through 198 Processing helix chain 'I' and resid 200 through 216 removed outlier: 3.661A pdb=" N ASP I 204 " --> pdb=" O HIS I 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 20 Processing helix chain 'J' and resid 28 through 36 removed outlier: 3.793A pdb=" N GLY J 36 " --> pdb=" O ILE J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 50 Processing helix chain 'J' and resid 68 through 81 removed outlier: 3.537A pdb=" N LYS J 78 " --> pdb=" O GLU J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 106 Processing helix chain 'J' and resid 117 through 127 removed outlier: 4.015A pdb=" N GLN J 123 " --> pdb=" O SER J 119 " (cutoff:3.500A) Proline residue: J 124 - end of helix Processing helix chain 'J' and resid 136 through 142 removed outlier: 3.554A pdb=" N SER J 142 " --> pdb=" O TRP J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 159 removed outlier: 3.995A pdb=" N ASP J 151 " --> pdb=" O THR J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 183 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 200 through 216 removed outlier: 3.662A pdb=" N ASP J 204 " --> pdb=" O HIS J 200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 4.183A pdb=" N GLY A 24 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 25 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU A 61 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 58 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS A 89 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL A 60 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN A 111 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 88 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR A 113 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE A 90 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL A 115 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR A 110 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER A 133 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL A 112 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 132 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE A 165 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR A 188 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 167 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 6 removed outlier: 4.184A pdb=" N GLY B 24 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 25 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU B 61 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE B 58 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS B 89 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 60 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN B 111 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 88 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR B 113 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE B 90 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL B 115 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR B 110 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER B 133 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL B 112 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL B 132 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE B 165 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR B 188 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL B 167 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 6 removed outlier: 4.183A pdb=" N GLY C 24 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C 25 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU C 61 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE C 58 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS C 89 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL C 60 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ASN C 111 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE C 88 " --> pdb=" O ASN C 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR C 113 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE C 90 " --> pdb=" O THR C 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 115 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR C 110 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER C 133 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL C 112 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL C 132 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE C 165 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR C 188 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL C 167 " --> pdb=" O THR C 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.184A pdb=" N GLY D 24 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL D 25 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU D 61 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE D 58 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS D 89 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL D 60 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN D 111 " --> pdb=" O PHE D 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE D 88 " --> pdb=" O ASN D 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR D 113 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE D 90 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL D 115 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR D 110 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER D 133 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL D 112 " --> pdb=" O SER D 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL D 132 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE D 165 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR D 188 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL D 167 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 6 removed outlier: 4.183A pdb=" N GLY E 24 " --> pdb=" O TYR E 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 25 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU E 61 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE E 58 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS E 89 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL E 60 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN E 111 " --> pdb=" O PHE E 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE E 88 " --> pdb=" O ASN E 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR E 113 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE E 90 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL E 115 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR E 110 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER E 133 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL E 112 " --> pdb=" O SER E 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL E 132 " --> pdb=" O ILE E 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE E 165 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR E 188 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL E 167 " --> pdb=" O THR E 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.183A pdb=" N GLY F 24 " --> pdb=" O TYR F 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL F 25 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU F 61 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE F 58 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS F 89 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL F 60 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ASN F 111 " --> pdb=" O PHE F 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE F 88 " --> pdb=" O ASN F 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR F 113 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE F 90 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL F 115 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR F 110 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER F 133 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL F 112 " --> pdb=" O SER F 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL F 132 " --> pdb=" O ILE F 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE F 165 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR F 188 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL F 167 " --> pdb=" O THR F 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 2 through 6 removed outlier: 4.184A pdb=" N GLY G 24 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL G 25 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU G 61 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE G 58 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS G 89 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL G 60 " --> pdb=" O LYS G 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN G 111 " --> pdb=" O PHE G 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE G 88 " --> pdb=" O ASN G 111 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR G 113 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE G 90 " --> pdb=" O THR G 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL G 115 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR G 110 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER G 133 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL G 112 " --> pdb=" O SER G 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL G 132 " --> pdb=" O ILE G 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE G 165 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR G 188 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL G 167 " --> pdb=" O THR G 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 2 through 6 removed outlier: 4.183A pdb=" N GLY H 24 " --> pdb=" O TYR H 3 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL H 25 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU H 61 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE H 58 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS H 89 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL H 60 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ASN H 111 " --> pdb=" O PHE H 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE H 88 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR H 113 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE H 90 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL H 115 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR H 110 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER H 133 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL H 112 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL H 132 " --> pdb=" O ILE H 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE H 165 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR H 188 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL H 167 " --> pdb=" O THR H 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 2 through 6 removed outlier: 4.183A pdb=" N GLY I 24 " --> pdb=" O TYR I 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL I 25 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU I 61 " --> pdb=" O VAL I 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE I 58 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS I 89 " --> pdb=" O ILE I 58 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL I 60 " --> pdb=" O LYS I 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN I 111 " --> pdb=" O PHE I 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE I 88 " --> pdb=" O ASN I 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR I 113 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE I 90 " --> pdb=" O THR I 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL I 115 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR I 110 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER I 133 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL I 112 " --> pdb=" O SER I 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL I 132 " --> pdb=" O ILE I 166 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE I 165 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR I 188 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL I 167 " --> pdb=" O THR I 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 2 through 6 removed outlier: 4.184A pdb=" N GLY J 24 " --> pdb=" O TYR J 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL J 25 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU J 61 " --> pdb=" O VAL J 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE J 58 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS J 89 " --> pdb=" O ILE J 58 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL J 60 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN J 111 " --> pdb=" O PHE J 86 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE J 88 " --> pdb=" O ASN J 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR J 113 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE J 90 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL J 115 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR J 110 " --> pdb=" O PHE J 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER J 133 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL J 112 " --> pdb=" O SER J 133 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL J 132 " --> pdb=" O ILE J 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE J 165 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR J 188 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL J 167 " --> pdb=" O THR J 188 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2520 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.36 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2680 1.32 - 1.44: 4730 1.44 - 1.56: 9250 1.56 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 16720 Sorted by residual: bond pdb=" CE1 HIS F 65 " pdb=" NE2 HIS F 65 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.56e+01 bond pdb=" CE1 HIS B 65 " pdb=" NE2 HIS B 65 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.52e+01 bond pdb=" CE1 HIS G 65 " pdb=" NE2 HIS G 65 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.52e+01 bond pdb=" CE1 HIS A 65 " pdb=" NE2 HIS A 65 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.52e+01 bond pdb=" CE1 HIS E 65 " pdb=" NE2 HIS E 65 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.51e+01 ... (remaining 16715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 14120 1.46 - 2.92: 6854 2.92 - 4.38: 1639 4.38 - 5.84: 217 5.84 - 7.30: 20 Bond angle restraints: 22850 Sorted by residual: angle pdb=" CA THR H 188 " pdb=" CB THR H 188 " pdb=" OG1 THR H 188 " ideal model delta sigma weight residual 109.60 102.30 7.30 1.50e+00 4.44e-01 2.37e+01 angle pdb=" CA THR D 188 " pdb=" CB THR D 188 " pdb=" OG1 THR D 188 " ideal model delta sigma weight residual 109.60 102.31 7.29 1.50e+00 4.44e-01 2.36e+01 angle pdb=" CA THR G 188 " pdb=" CB THR G 188 " pdb=" OG1 THR G 188 " ideal model delta sigma weight residual 109.60 102.31 7.29 1.50e+00 4.44e-01 2.36e+01 angle pdb=" CA THR F 188 " pdb=" CB THR F 188 " pdb=" OG1 THR F 188 " ideal model delta sigma weight residual 109.60 102.31 7.29 1.50e+00 4.44e-01 2.36e+01 angle pdb=" CA THR A 188 " pdb=" CB THR A 188 " pdb=" OG1 THR A 188 " ideal model delta sigma weight residual 109.60 102.33 7.27 1.50e+00 4.44e-01 2.35e+01 ... (remaining 22845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 8340 17.52 - 35.03: 920 35.03 - 52.55: 280 52.55 - 70.06: 120 70.06 - 87.58: 30 Dihedral angle restraints: 9690 sinusoidal: 3330 harmonic: 6360 Sorted by residual: dihedral pdb=" CD ARG H 211 " pdb=" NE ARG H 211 " pdb=" CZ ARG H 211 " pdb=" NH1 ARG H 211 " ideal model delta sinusoidal sigma weight residual 0.00 42.18 -42.18 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CD ARG E 211 " pdb=" NE ARG E 211 " pdb=" CZ ARG E 211 " pdb=" NH1 ARG E 211 " ideal model delta sinusoidal sigma weight residual 0.00 42.15 -42.15 1 1.00e+01 1.00e-02 2.48e+01 dihedral pdb=" CD ARG A 211 " pdb=" NE ARG A 211 " pdb=" CZ ARG A 211 " pdb=" NH1 ARG A 211 " ideal model delta sinusoidal sigma weight residual 0.00 42.14 -42.14 1 1.00e+01 1.00e-02 2.48e+01 ... (remaining 9687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 730 0.048 - 0.096: 883 0.096 - 0.144: 699 0.144 - 0.192: 218 0.192 - 0.240: 80 Chirality restraints: 2610 Sorted by residual: chirality pdb=" CA VAL E 132 " pdb=" N VAL E 132 " pdb=" C VAL E 132 " pdb=" CB VAL E 132 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA VAL C 132 " pdb=" N VAL C 132 " pdb=" C VAL C 132 " pdb=" CB VAL C 132 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA VAL B 132 " pdb=" N VAL B 132 " pdb=" C VAL B 132 " pdb=" CB VAL B 132 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2607 not shown) Planarity restraints: 2960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 211 " 0.728 9.50e-02 1.11e+02 3.26e-01 6.49e+01 pdb=" NE ARG G 211 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG G 211 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG G 211 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 211 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 211 " 0.728 9.50e-02 1.11e+02 3.26e-01 6.48e+01 pdb=" NE ARG A 211 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 211 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 211 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 211 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 211 " -0.728 9.50e-02 1.11e+02 3.26e-01 6.48e+01 pdb=" NE ARG J 211 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG J 211 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG J 211 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG J 211 " -0.022 2.00e-02 2.50e+03 ... (remaining 2957 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4520 2.83 - 3.35: 18104 3.35 - 3.86: 31591 3.86 - 4.38: 38884 4.38 - 4.90: 60221 Nonbonded interactions: 153320 Sorted by model distance: nonbonded pdb=" O LEU E 170 " pdb=" O HOH E 301 " model vdw 2.311 3.040 nonbonded pdb=" O LEU D 170 " pdb=" O HOH D 301 " model vdw 2.311 3.040 nonbonded pdb=" O LEU A 170 " pdb=" O HOH A 301 " model vdw 2.311 3.040 nonbonded pdb=" O LEU J 170 " pdb=" O HOH J 301 " model vdw 2.311 3.040 nonbonded pdb=" O LEU I 170 " pdb=" O HOH I 301 " model vdw 2.311 3.040 ... (remaining 153315 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 33.390 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 0.046 16720 Z= 0.899 Angle : 1.656 7.297 22850 Z= 1.286 Chirality : 0.097 0.240 2610 Planarity : 0.029 0.326 2960 Dihedral : 18.310 87.581 5590 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 13.21 % Allowed : 15.09 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.13), residues: 2160 helix: -3.13 (0.09), residues: 1270 sheet: -3.08 (0.20), residues: 300 loop : -1.80 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 138 HIS 0.003 0.001 HIS I 200 PHE 0.010 0.001 PHE F 131 TYR 0.022 0.002 TYR D 15 ARG 0.004 0.001 ARG F 14 Details of bonding type rmsd hydrogen bonds : bond 0.25111 ( 840) hydrogen bonds : angle 9.94100 ( 2520) covalent geometry : bond 0.01190 (16720) covalent geometry : angle 1.65599 (22850) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 474 time to evaluate : 1.732 Fit side-chains REVERT: A 204 ASP cc_start: 0.8135 (m-30) cc_final: 0.7902 (m-30) REVERT: C 6 ASP cc_start: 0.8441 (t0) cc_final: 0.8200 (t0) REVERT: J 122 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8117 (tt) outliers start: 210 outliers final: 3 residues processed: 573 average time/residue: 1.2289 time to fit residues: 781.6951 Evaluate side-chains 268 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 264 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain J residue 122 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 34 ASN A 63 ASN A 120 GLN A 162 ASN A 172 ASN A 175 GLN A 200 HIS A 212 ASN B 19 ASN B 65 HIS B 85 ASN B 150 GLN B 172 ASN B 200 HIS B 212 ASN C 19 ASN C 65 HIS C 85 ASN C 120 GLN C 150 GLN C 172 ASN C 175 GLN C 200 HIS C 212 ASN C 216 ASN D 65 HIS D 120 GLN D 150 GLN D 172 ASN D 200 HIS E 65 HIS E 120 GLN E 150 GLN E 172 ASN E 200 HIS F 19 ASN F 34 ASN F 63 ASN F 85 ASN F 120 GLN F 150 GLN F 162 ASN F 172 ASN F 175 GLN F 200 HIS F 212 ASN G 19 ASN G 65 HIS G 85 ASN G 150 GLN G 172 ASN G 200 HIS G 212 ASN H 19 ASN H 65 HIS H 85 ASN H 150 GLN H 172 ASN H 175 GLN H 200 HIS H 212 ASN H 216 ASN I 65 HIS I 120 GLN I 150 GLN I 172 ASN I 200 HIS J 63 ASN J 65 HIS J 120 GLN J 150 GLN J 158 ASN J 172 ASN J 200 HIS Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118041 restraints weight = 21911.008| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.11 r_work: 0.3317 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16720 Z= 0.143 Angle : 0.504 5.575 22850 Z= 0.277 Chirality : 0.043 0.119 2610 Planarity : 0.006 0.069 2960 Dihedral : 4.518 58.055 2318 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.20 % Allowed : 20.82 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.17), residues: 2160 helix: -0.08 (0.13), residues: 1340 sheet: -1.59 (0.24), residues: 300 loop : -1.28 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 138 HIS 0.006 0.002 HIS E 200 PHE 0.011 0.001 PHE A 103 TYR 0.015 0.001 TYR J 205 ARG 0.005 0.001 ARG J 126 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 840) hydrogen bonds : angle 4.90082 ( 2520) covalent geometry : bond 0.00334 (16720) covalent geometry : angle 0.50430 (22850) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 290 time to evaluate : 1.989 Fit side-chains REVERT: A 130 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7305 (mmtm) REVERT: A 157 LYS cc_start: 0.8427 (mttm) cc_final: 0.7900 (mmtt) REVERT: A 174 LYS cc_start: 0.8135 (tttm) cc_final: 0.7795 (tmtt) REVERT: C 174 LYS cc_start: 0.8181 (tttm) cc_final: 0.7964 (tttm) REVERT: C 199 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7843 (mt0) REVERT: E 157 LYS cc_start: 0.8389 (mtmm) cc_final: 0.7867 (mmtt) REVERT: E 171 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7303 (mmt90) REVERT: F 49 GLU cc_start: 0.7679 (tp30) cc_final: 0.7327 (tt0) REVERT: F 130 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7327 (mmtm) REVERT: F 157 LYS cc_start: 0.8359 (mttm) cc_final: 0.7811 (mmtt) REVERT: G 171 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7252 (mmt90) REVERT: H 33 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8264 (ttp) REVERT: H 199 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7853 (mt0) REVERT: J 157 LYS cc_start: 0.8401 (mtmm) cc_final: 0.7881 (mmtt) REVERT: J 171 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7314 (mmt90) outliers start: 35 outliers final: 2 residues processed: 311 average time/residue: 1.3175 time to fit residues: 454.2620 Evaluate side-chains 269 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 259 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain C residue 199 GLN Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 171 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 134 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 162 ASN B 34 ASN B 150 GLN C 150 GLN D 34 ASN D 150 GLN D 158 ASN E 150 GLN E 158 ASN F 158 ASN F 162 ASN G 34 ASN G 150 GLN H 150 GLN I 34 ASN I 150 GLN I 158 ASN J 150 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117599 restraints weight = 22245.886| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.10 r_work: 0.3293 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16720 Z= 0.124 Angle : 0.458 5.250 22850 Z= 0.250 Chirality : 0.043 0.122 2610 Planarity : 0.005 0.042 2960 Dihedral : 3.596 12.681 2310 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.39 % Allowed : 20.44 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.18), residues: 2160 helix: 1.26 (0.14), residues: 1350 sheet: -0.98 (0.27), residues: 300 loop : -0.54 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 214 HIS 0.004 0.001 HIS E 200 PHE 0.010 0.001 PHE E 103 TYR 0.019 0.001 TYR C 205 ARG 0.003 0.001 ARG C 126 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 840) hydrogen bonds : angle 4.40144 ( 2520) covalent geometry : bond 0.00286 (16720) covalent geometry : angle 0.45788 (22850) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 267 time to evaluate : 1.814 Fit side-chains REVERT: A 130 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7357 (mmtm) REVERT: A 157 LYS cc_start: 0.8394 (mttm) cc_final: 0.7861 (mmtt) REVERT: B 130 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7102 (mmtt) REVERT: C 33 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8308 (ttp) REVERT: C 157 LYS cc_start: 0.8488 (mttm) cc_final: 0.7989 (mmtt) REVERT: C 174 LYS cc_start: 0.8247 (tttm) cc_final: 0.8010 (tttm) REVERT: C 199 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7891 (mt0) REVERT: D 130 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7345 (mmtm) REVERT: D 157 LYS cc_start: 0.8448 (mttm) cc_final: 0.7895 (mmtt) REVERT: D 162 ASN cc_start: 0.7759 (m-40) cc_final: 0.7557 (m110) REVERT: E 49 GLU cc_start: 0.7887 (tp30) cc_final: 0.7343 (tt0) REVERT: E 157 LYS cc_start: 0.8439 (mtmm) cc_final: 0.7923 (mmtt) REVERT: E 171 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7315 (mmt90) REVERT: F 49 GLU cc_start: 0.7748 (tp30) cc_final: 0.7374 (tt0) REVERT: F 130 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7372 (mmtm) REVERT: F 157 LYS cc_start: 0.8340 (mttm) cc_final: 0.7825 (mmtt) REVERT: G 130 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7146 (mmtt) REVERT: H 157 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8013 (mmtt) REVERT: H 174 LYS cc_start: 0.8258 (tmtm) cc_final: 0.7870 (tmtt) REVERT: H 199 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7880 (mt0) REVERT: I 130 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7365 (mmtm) REVERT: I 157 LYS cc_start: 0.8476 (mttm) cc_final: 0.7907 (mmtt) REVERT: J 49 GLU cc_start: 0.7892 (tp30) cc_final: 0.7281 (tt0) REVERT: J 157 LYS cc_start: 0.8394 (mtmm) cc_final: 0.7847 (mmtt) REVERT: J 171 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7310 (mmt90) REVERT: J 174 LYS cc_start: 0.8384 (tptp) cc_final: 0.8167 (tptp) outliers start: 38 outliers final: 10 residues processed: 289 average time/residue: 1.3309 time to fit residues: 426.7968 Evaluate side-chains 263 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain C residue 33 MET Chi-restraints excluded: chain C residue 199 GLN Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 171 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 119 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 162 ASN B 150 GLN C 150 GLN D 150 GLN D 158 ASN E 150 GLN E 162 ASN F 158 ASN F 162 ASN G 150 GLN G 158 ASN H 150 GLN I 150 GLN ** I 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 GLN J 162 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115104 restraints weight = 22482.140| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.11 r_work: 0.3257 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16720 Z= 0.155 Angle : 0.484 5.881 22850 Z= 0.264 Chirality : 0.044 0.126 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.776 13.755 2310 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.89 % Allowed : 19.31 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.18), residues: 2160 helix: 1.63 (0.14), residues: 1340 sheet: -0.72 (0.28), residues: 300 loop : -0.53 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 214 HIS 0.004 0.001 HIS E 200 PHE 0.013 0.001 PHE E 103 TYR 0.015 0.001 TYR C 205 ARG 0.003 0.001 ARG G 211 Details of bonding type rmsd hydrogen bonds : bond 0.04657 ( 840) hydrogen bonds : angle 4.42920 ( 2520) covalent geometry : bond 0.00370 (16720) covalent geometry : angle 0.48374 (22850) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 1.760 Fit side-chains REVERT: A 130 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7370 (mmtm) REVERT: A 157 LYS cc_start: 0.8394 (mttm) cc_final: 0.7848 (mmtt) REVERT: B 130 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7219 (mmtt) REVERT: B 140 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: B 178 ASP cc_start: 0.8048 (m-30) cc_final: 0.7686 (m-30) REVERT: C 33 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8313 (ttp) REVERT: C 144 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8131 (m-30) REVERT: C 157 LYS cc_start: 0.8395 (mttm) cc_final: 0.7878 (mmtt) REVERT: C 199 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: D 130 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7355 (mmtm) REVERT: D 157 LYS cc_start: 0.8456 (mttm) cc_final: 0.7941 (mmtt) REVERT: D 162 ASN cc_start: 0.7783 (m-40) cc_final: 0.7579 (m110) REVERT: D 178 ASP cc_start: 0.7939 (m-30) cc_final: 0.7458 (m-30) REVERT: E 150 GLN cc_start: 0.8454 (tp40) cc_final: 0.8212 (mm-40) REVERT: E 157 LYS cc_start: 0.8440 (mtmm) cc_final: 0.7902 (mmtt) REVERT: E 171 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8056 (mmt90) REVERT: F 49 GLU cc_start: 0.7724 (tp30) cc_final: 0.7206 (tt0) REVERT: F 130 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7405 (mmtm) REVERT: F 157 LYS cc_start: 0.8378 (mttm) cc_final: 0.7827 (mmtt) REVERT: G 130 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7193 (mmtt) REVERT: G 171 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7194 (mmt90) REVERT: H 157 LYS cc_start: 0.8438 (mtmm) cc_final: 0.7890 (mmtt) REVERT: H 174 LYS cc_start: 0.8372 (tmtm) cc_final: 0.7912 (tmtt) REVERT: H 199 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: I 130 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7403 (mmtm) REVERT: I 157 LYS cc_start: 0.8453 (mttm) cc_final: 0.7944 (mmtt) REVERT: I 178 ASP cc_start: 0.7919 (m-30) cc_final: 0.7433 (m-30) REVERT: J 150 GLN cc_start: 0.8463 (tp40) cc_final: 0.8210 (mm-40) REVERT: J 157 LYS cc_start: 0.8413 (mtmm) cc_final: 0.7898 (mmtt) REVERT: J 171 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8055 (mmt90) outliers start: 46 outliers final: 11 residues processed: 278 average time/residue: 1.2973 time to fit residues: 400.1474 Evaluate side-chains 258 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain C residue 33 MET Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 199 GLN Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 171 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 197 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 150 GLN C 150 GLN D 150 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN F 162 ASN G 150 GLN H 150 GLN I 150 GLN ** I 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116162 restraints weight = 22764.748| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.12 r_work: 0.3273 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16720 Z= 0.126 Angle : 0.454 5.068 22850 Z= 0.248 Chirality : 0.043 0.122 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.631 12.769 2310 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.96 % Allowed : 18.62 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.18), residues: 2160 helix: 1.81 (0.14), residues: 1350 sheet: -0.53 (0.29), residues: 300 loop : -0.40 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 214 HIS 0.003 0.001 HIS G 200 PHE 0.010 0.001 PHE D 103 TYR 0.014 0.001 TYR C 205 ARG 0.002 0.000 ARG G 211 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 840) hydrogen bonds : angle 4.25056 ( 2520) covalent geometry : bond 0.00296 (16720) covalent geometry : angle 0.45396 (22850) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 242 time to evaluate : 1.864 Fit side-chains REVERT: A 30 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7904 (ttm170) REVERT: A 157 LYS cc_start: 0.8390 (mttm) cc_final: 0.7834 (mmtt) REVERT: A 174 LYS cc_start: 0.8302 (tttm) cc_final: 0.8033 (tmtt) REVERT: B 130 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7172 (mmtt) REVERT: B 178 ASP cc_start: 0.7967 (m-30) cc_final: 0.7566 (m-30) REVERT: C 130 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8137 (tptp) REVERT: C 144 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: C 157 LYS cc_start: 0.8380 (mttm) cc_final: 0.7876 (mmtt) REVERT: C 174 LYS cc_start: 0.8338 (tttm) cc_final: 0.7866 (tmtt) REVERT: C 199 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7930 (mt0) REVERT: D 122 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8687 (mt) REVERT: D 130 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7330 (mmtm) REVERT: D 157 LYS cc_start: 0.8454 (mttm) cc_final: 0.7938 (mmtt) REVERT: D 178 ASP cc_start: 0.7857 (m-30) cc_final: 0.7325 (m-30) REVERT: E 49 GLU cc_start: 0.7884 (tp30) cc_final: 0.7340 (tt0) REVERT: E 140 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8392 (mt-10) REVERT: E 150 GLN cc_start: 0.8452 (tp40) cc_final: 0.8158 (mm-40) REVERT: E 157 LYS cc_start: 0.8427 (mtmm) cc_final: 0.7889 (mmtt) REVERT: E 171 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7280 (mmt90) REVERT: F 30 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7891 (ttm170) REVERT: F 49 GLU cc_start: 0.7791 (tp30) cc_final: 0.7232 (tt0) REVERT: F 157 LYS cc_start: 0.8377 (mttm) cc_final: 0.7833 (mmtt) REVERT: G 130 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7140 (mmtt) REVERT: G 171 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7231 (mmt90) REVERT: G 174 LYS cc_start: 0.8399 (tttm) cc_final: 0.7955 (tmtt) REVERT: G 178 ASP cc_start: 0.7996 (m-30) cc_final: 0.7650 (m-30) REVERT: H 130 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8147 (tptp) REVERT: H 144 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8234 (m-30) REVERT: H 157 LYS cc_start: 0.8443 (mtmm) cc_final: 0.7895 (mmtt) REVERT: H 174 LYS cc_start: 0.8375 (tmtm) cc_final: 0.8066 (tttm) REVERT: H 199 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7933 (mt0) REVERT: I 122 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8631 (mt) REVERT: I 130 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7388 (mmtm) REVERT: I 157 LYS cc_start: 0.8466 (mttm) cc_final: 0.7942 (mmtt) REVERT: I 178 ASP cc_start: 0.7845 (m-30) cc_final: 0.7307 (m-30) REVERT: J 49 GLU cc_start: 0.7884 (tp30) cc_final: 0.7319 (tt0) REVERT: J 140 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8423 (mt-10) REVERT: J 150 GLN cc_start: 0.8473 (tp40) cc_final: 0.8176 (mm-40) REVERT: J 157 LYS cc_start: 0.8434 (mtmm) cc_final: 0.7905 (mmtt) REVERT: J 171 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7258 (mmt90) outliers start: 47 outliers final: 14 residues processed: 275 average time/residue: 1.3356 time to fit residues: 406.5407 Evaluate side-chains 262 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 199 GLN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 130 LYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 140 GLU Chi-restraints excluded: chain J residue 171 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 150 GLN C 150 GLN D 158 ASN E 162 ASN F 162 ASN G 150 GLN H 150 GLN I 158 ASN J 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115185 restraints weight = 22643.061| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.12 r_work: 0.3258 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16720 Z= 0.143 Angle : 0.464 6.006 22850 Z= 0.253 Chirality : 0.044 0.122 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.711 13.325 2310 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.14 % Allowed : 18.11 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.18), residues: 2160 helix: 1.88 (0.14), residues: 1350 sheet: -0.45 (0.29), residues: 300 loop : -0.41 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 214 HIS 0.003 0.001 HIS G 200 PHE 0.010 0.001 PHE H 103 TYR 0.013 0.001 TYR C 205 ARG 0.003 0.000 ARG G 211 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 840) hydrogen bonds : angle 4.25975 ( 2520) covalent geometry : bond 0.00339 (16720) covalent geometry : angle 0.46433 (22850) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 241 time to evaluate : 2.024 Fit side-chains REVERT: A 30 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7928 (ttm170) REVERT: A 157 LYS cc_start: 0.8377 (mttm) cc_final: 0.7826 (mmtt) REVERT: B 130 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7196 (mmtt) REVERT: B 178 ASP cc_start: 0.7984 (m-30) cc_final: 0.7574 (m-30) REVERT: C 130 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8163 (tptp) REVERT: C 144 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8116 (m-30) REVERT: C 157 LYS cc_start: 0.8391 (mttm) cc_final: 0.7883 (mmtt) REVERT: C 199 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: D 122 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8714 (mt) REVERT: D 130 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7348 (mmtm) REVERT: D 157 LYS cc_start: 0.8440 (mttm) cc_final: 0.7940 (mmtt) REVERT: D 178 ASP cc_start: 0.7852 (m-30) cc_final: 0.7336 (m-30) REVERT: E 130 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7453 (mtpp) REVERT: E 140 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8461 (mt-10) REVERT: E 150 GLN cc_start: 0.8470 (tp40) cc_final: 0.8192 (mm-40) REVERT: E 157 LYS cc_start: 0.8447 (mtmm) cc_final: 0.7903 (mmtt) REVERT: E 171 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8170 (mmt90) REVERT: F 30 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7909 (ttm170) REVERT: F 49 GLU cc_start: 0.7765 (tp30) cc_final: 0.7217 (tt0) REVERT: F 157 LYS cc_start: 0.8386 (mttm) cc_final: 0.7840 (mmtt) REVERT: G 130 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7098 (mmtt) REVERT: G 140 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: G 171 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7203 (mmt90) REVERT: G 178 ASP cc_start: 0.8044 (m-30) cc_final: 0.7689 (m-30) REVERT: H 130 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8179 (tptp) REVERT: H 144 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8240 (m-30) REVERT: H 157 LYS cc_start: 0.8447 (mtmm) cc_final: 0.7900 (mmtt) REVERT: H 174 LYS cc_start: 0.8390 (tmtm) cc_final: 0.8066 (tttm) REVERT: H 199 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7908 (mt0) REVERT: I 122 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8698 (mt) REVERT: I 130 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7390 (mmtm) REVERT: I 157 LYS cc_start: 0.8459 (mttm) cc_final: 0.7951 (mmtt) REVERT: I 178 ASP cc_start: 0.7830 (m-30) cc_final: 0.7312 (m-30) REVERT: J 140 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8478 (mt-10) REVERT: J 150 GLN cc_start: 0.8445 (tp40) cc_final: 0.8168 (mm-40) REVERT: J 157 LYS cc_start: 0.8440 (mtmm) cc_final: 0.7908 (mmtt) REVERT: J 171 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7108 (mmt90) outliers start: 50 outliers final: 15 residues processed: 275 average time/residue: 1.3460 time to fit residues: 409.6245 Evaluate side-chains 264 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 199 GLN Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 130 LYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 140 GLU Chi-restraints excluded: chain J residue 171 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 26 optimal weight: 0.0370 chunk 10 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 145 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 150 GLN C 150 GLN D 150 GLN E 162 ASN F 162 ASN H 150 GLN J 162 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.122473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115392 restraints weight = 22128.456| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.14 r_work: 0.3275 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16720 Z= 0.117 Angle : 0.449 6.538 22850 Z= 0.245 Chirality : 0.043 0.120 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.579 12.318 2310 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.33 % Allowed : 18.87 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.18), residues: 2160 helix: 2.02 (0.14), residues: 1350 sheet: -0.38 (0.29), residues: 300 loop : -0.31 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 214 HIS 0.002 0.001 HIS G 200 PHE 0.009 0.001 PHE C 103 TYR 0.013 0.001 TYR C 205 ARG 0.002 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 840) hydrogen bonds : angle 4.12584 ( 2520) covalent geometry : bond 0.00272 (16720) covalent geometry : angle 0.44861 (22850) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 2.036 Fit side-chains REVERT: A 30 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7909 (ttm170) REVERT: A 157 LYS cc_start: 0.8384 (mttm) cc_final: 0.7828 (mmtt) REVERT: A 174 LYS cc_start: 0.8176 (tttm) cc_final: 0.7921 (tmtt) REVERT: B 130 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7149 (mmtt) REVERT: B 178 ASP cc_start: 0.7831 (m-30) cc_final: 0.7392 (m-30) REVERT: C 144 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8114 (m-30) REVERT: C 157 LYS cc_start: 0.8385 (mttm) cc_final: 0.7873 (mmtt) REVERT: C 174 LYS cc_start: 0.8300 (tttm) cc_final: 0.7887 (tmtt) REVERT: D 122 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8652 (mt) REVERT: D 157 LYS cc_start: 0.8456 (mttm) cc_final: 0.7935 (mmtt) REVERT: D 178 ASP cc_start: 0.7829 (m-30) cc_final: 0.7305 (m-30) REVERT: E 130 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7433 (mtpp) REVERT: E 140 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8446 (mt-10) REVERT: E 150 GLN cc_start: 0.8465 (tp40) cc_final: 0.8184 (mm-40) REVERT: E 157 LYS cc_start: 0.8419 (mtmm) cc_final: 0.7876 (mmtt) REVERT: E 171 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7359 (mmt90) REVERT: F 30 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7882 (ttm170) REVERT: F 49 GLU cc_start: 0.7738 (tp30) cc_final: 0.7176 (tt0) REVERT: F 157 LYS cc_start: 0.8386 (mttm) cc_final: 0.7835 (mmtt) REVERT: G 130 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7117 (mmtt) REVERT: G 140 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: G 171 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7220 (mmt90) REVERT: G 178 ASP cc_start: 0.7925 (m-30) cc_final: 0.7563 (m-30) REVERT: H 130 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8157 (tptp) REVERT: H 144 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8258 (m-30) REVERT: H 157 LYS cc_start: 0.8434 (mtmm) cc_final: 0.7891 (mmtt) REVERT: H 174 LYS cc_start: 0.8420 (tmtm) cc_final: 0.8197 (tttm) REVERT: I 122 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8605 (mt) REVERT: I 130 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7347 (mmtm) REVERT: I 157 LYS cc_start: 0.8468 (mttm) cc_final: 0.7939 (mmtt) REVERT: I 178 ASP cc_start: 0.7820 (m-30) cc_final: 0.7309 (m-30) REVERT: J 49 GLU cc_start: 0.7873 (tp30) cc_final: 0.7311 (tt0) REVERT: J 140 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8471 (mt-10) REVERT: J 150 GLN cc_start: 0.8449 (tp40) cc_final: 0.8166 (mm-40) REVERT: J 157 LYS cc_start: 0.8444 (mtmm) cc_final: 0.7902 (mmtt) outliers start: 37 outliers final: 13 residues processed: 261 average time/residue: 1.3581 time to fit residues: 393.1589 Evaluate side-chains 254 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 130 LYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 140 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 66 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 192 optimal weight: 0.6980 chunk 176 optimal weight: 0.0570 chunk 52 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 136 optimal weight: 0.0060 overall best weight: 0.4514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 150 GLN C 150 GLN D 150 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN F 162 ASN H 150 GLN I 150 GLN J 162 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116945 restraints weight = 21895.045| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.13 r_work: 0.3299 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16720 Z= 0.102 Angle : 0.437 7.479 22850 Z= 0.237 Chirality : 0.042 0.119 2610 Planarity : 0.004 0.036 2960 Dihedral : 3.463 11.879 2310 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.82 % Allowed : 19.31 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.18), residues: 2160 helix: 2.08 (0.14), residues: 1360 sheet: -0.28 (0.30), residues: 300 loop : -0.18 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 214 HIS 0.001 0.001 HIS G 200 PHE 0.008 0.001 PHE G 103 TYR 0.013 0.001 TYR C 205 ARG 0.002 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 840) hydrogen bonds : angle 3.97621 ( 2520) covalent geometry : bond 0.00231 (16720) covalent geometry : angle 0.43658 (22850) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 2.001 Fit side-chains REVERT: A 30 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7903 (ttm170) REVERT: A 157 LYS cc_start: 0.8389 (mttm) cc_final: 0.7829 (mmtt) REVERT: A 174 LYS cc_start: 0.8072 (tttm) cc_final: 0.7864 (tttm) REVERT: B 130 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7095 (mmtt) REVERT: C 144 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: C 157 LYS cc_start: 0.8402 (mttm) cc_final: 0.7903 (mmtt) REVERT: D 122 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8634 (mt) REVERT: D 157 LYS cc_start: 0.8465 (mttm) cc_final: 0.7950 (mmtt) REVERT: D 178 ASP cc_start: 0.7730 (m-30) cc_final: 0.7206 (m-30) REVERT: E 49 GLU cc_start: 0.7873 (tp30) cc_final: 0.7306 (tt0) REVERT: E 130 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7404 (mtpp) REVERT: E 140 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8462 (mt-10) REVERT: E 150 GLN cc_start: 0.8408 (tp40) cc_final: 0.8165 (mm-40) REVERT: E 157 LYS cc_start: 0.8385 (mtmm) cc_final: 0.7836 (mmtt) REVERT: F 30 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7879 (ttm170) REVERT: F 49 GLU cc_start: 0.7746 (tp30) cc_final: 0.7191 (tt0) REVERT: F 157 LYS cc_start: 0.8378 (mttm) cc_final: 0.7828 (mmtt) REVERT: G 130 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7092 (mmtt) REVERT: G 174 LYS cc_start: 0.8322 (tttm) cc_final: 0.7856 (tmtt) REVERT: G 178 ASP cc_start: 0.7813 (m-30) cc_final: 0.7497 (m-30) REVERT: H 144 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: H 157 LYS cc_start: 0.8422 (mtmm) cc_final: 0.7894 (mmtt) REVERT: H 174 LYS cc_start: 0.8381 (tmtm) cc_final: 0.8034 (tttm) REVERT: I 122 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8626 (mt) REVERT: I 157 LYS cc_start: 0.8461 (mttm) cc_final: 0.7937 (mmtt) REVERT: I 178 ASP cc_start: 0.7726 (m-30) cc_final: 0.7212 (m-30) REVERT: J 49 GLU cc_start: 0.7863 (tp30) cc_final: 0.7300 (tt0) REVERT: J 140 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8447 (mt-10) REVERT: J 150 GLN cc_start: 0.8435 (tp40) cc_final: 0.8187 (mm-40) REVERT: J 157 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7839 (mmtt) REVERT: J 171 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8219 (mmt90) outliers start: 29 outliers final: 8 residues processed: 260 average time/residue: 1.3528 time to fit residues: 390.3042 Evaluate side-chains 248 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 140 GLU Chi-restraints excluded: chain J residue 171 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 101 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 170 optimal weight: 0.0020 chunk 47 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 150 GLN C 150 GLN D 150 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN F 162 ASN H 150 GLN I 150 GLN J 162 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115821 restraints weight = 22068.258| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.14 r_work: 0.3283 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16720 Z= 0.117 Angle : 0.455 7.960 22850 Z= 0.247 Chirality : 0.043 0.120 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.542 12.165 2310 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.14 % Allowed : 18.74 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.18), residues: 2160 helix: 2.09 (0.14), residues: 1360 sheet: -0.30 (0.30), residues: 300 loop : -0.19 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 214 HIS 0.002 0.001 HIS G 200 PHE 0.009 0.001 PHE H 103 TYR 0.012 0.001 TYR C 205 ARG 0.002 0.000 ARG G 211 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 840) hydrogen bonds : angle 4.03038 ( 2520) covalent geometry : bond 0.00270 (16720) covalent geometry : angle 0.45468 (22850) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 1.795 Fit side-chains REVERT: A 30 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7915 (ttm170) REVERT: A 157 LYS cc_start: 0.8376 (mttm) cc_final: 0.7827 (mmtt) REVERT: B 130 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7127 (mmtt) REVERT: B 178 ASP cc_start: 0.7739 (m-30) cc_final: 0.7360 (m-30) REVERT: C 144 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: C 157 LYS cc_start: 0.8403 (mttm) cc_final: 0.7908 (mmtt) REVERT: C 174 LYS cc_start: 0.8315 (tttm) cc_final: 0.7779 (ttpp) REVERT: D 122 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8672 (mt) REVERT: D 157 LYS cc_start: 0.8459 (mttm) cc_final: 0.7952 (mmtt) REVERT: D 178 ASP cc_start: 0.7744 (m-30) cc_final: 0.7244 (m-30) REVERT: E 49 GLU cc_start: 0.7871 (tp30) cc_final: 0.7313 (tt0) REVERT: E 130 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7423 (mtpp) REVERT: E 140 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8496 (mt-10) REVERT: E 150 GLN cc_start: 0.8405 (tp40) cc_final: 0.8136 (mm-40) REVERT: E 157 LYS cc_start: 0.8419 (mtmm) cc_final: 0.7847 (mmtt) REVERT: F 30 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7896 (ttm170) REVERT: F 49 GLU cc_start: 0.7726 (tp30) cc_final: 0.7181 (tt0) REVERT: F 157 LYS cc_start: 0.8374 (mttm) cc_final: 0.7827 (mmtt) REVERT: G 94 GLU cc_start: 0.8466 (tp30) cc_final: 0.8227 (tp30) REVERT: G 130 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7101 (mmtt) REVERT: G 171 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7219 (mmt90) REVERT: H 144 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8254 (m-30) REVERT: H 157 LYS cc_start: 0.8427 (mtmm) cc_final: 0.7895 (mmtt) REVERT: H 174 LYS cc_start: 0.8428 (tmtm) cc_final: 0.8077 (tttm) REVERT: I 122 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8646 (mt) REVERT: I 157 LYS cc_start: 0.8476 (mttm) cc_final: 0.7953 (mmtt) REVERT: I 178 ASP cc_start: 0.7725 (m-30) cc_final: 0.7238 (m-30) REVERT: J 49 GLU cc_start: 0.7860 (tp30) cc_final: 0.7303 (tt0) REVERT: J 140 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8507 (mt-10) REVERT: J 150 GLN cc_start: 0.8451 (tp40) cc_final: 0.8175 (mm-40) REVERT: J 157 LYS cc_start: 0.8411 (mtmm) cc_final: 0.7848 (mmtt) REVERT: J 171 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8223 (mmt90) outliers start: 34 outliers final: 16 residues processed: 262 average time/residue: 1.3856 time to fit residues: 400.8848 Evaluate side-chains 259 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 140 GLU Chi-restraints excluded: chain J residue 171 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 72 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 176 optimal weight: 0.0770 chunk 197 optimal weight: 3.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 150 GLN C 150 GLN D 150 GLN E 162 ASN F 162 ASN H 150 GLN I 150 GLN J 162 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117670 restraints weight = 22288.053| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.13 r_work: 0.3296 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16720 Z= 0.109 Angle : 0.452 7.238 22850 Z= 0.245 Chirality : 0.042 0.120 2610 Planarity : 0.004 0.036 2960 Dihedral : 3.502 12.077 2310 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.89 % Allowed : 18.93 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.18), residues: 2160 helix: 2.12 (0.14), residues: 1360 sheet: -0.26 (0.30), residues: 300 loop : -0.16 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 214 HIS 0.002 0.001 HIS C 31 PHE 0.008 0.001 PHE H 103 TYR 0.012 0.001 TYR C 205 ARG 0.002 0.000 ARG F 171 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 840) hydrogen bonds : angle 3.96931 ( 2520) covalent geometry : bond 0.00251 (16720) covalent geometry : angle 0.45161 (22850) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 1.722 Fit side-chains REVERT: A 30 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7911 (ttm170) REVERT: A 157 LYS cc_start: 0.8378 (mttm) cc_final: 0.7837 (mmtt) REVERT: A 174 LYS cc_start: 0.8091 (tttm) cc_final: 0.7794 (tptp) REVERT: B 130 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7101 (mmtt) REVERT: B 178 ASP cc_start: 0.7604 (m-30) cc_final: 0.7330 (m-30) REVERT: C 144 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: C 157 LYS cc_start: 0.8414 (mttm) cc_final: 0.7929 (mmtt) REVERT: D 122 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8656 (mt) REVERT: D 157 LYS cc_start: 0.8454 (mttm) cc_final: 0.7949 (mmtt) REVERT: D 178 ASP cc_start: 0.7713 (m-30) cc_final: 0.7223 (m-30) REVERT: E 49 GLU cc_start: 0.7870 (tp30) cc_final: 0.7313 (tt0) REVERT: E 130 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7419 (mtpp) REVERT: E 140 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8515 (mt-10) REVERT: E 150 GLN cc_start: 0.8406 (tp40) cc_final: 0.8162 (mm-40) REVERT: E 157 LYS cc_start: 0.8420 (mtmm) cc_final: 0.7858 (mmtt) REVERT: F 30 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7889 (ttm170) REVERT: F 49 GLU cc_start: 0.7766 (tp30) cc_final: 0.7240 (tt0) REVERT: F 157 LYS cc_start: 0.8371 (mttm) cc_final: 0.7829 (mmtt) REVERT: G 130 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7085 (mmtt) REVERT: G 178 ASP cc_start: 0.7659 (m-30) cc_final: 0.7375 (m-30) REVERT: H 144 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8253 (m-30) REVERT: H 157 LYS cc_start: 0.8425 (mtmm) cc_final: 0.7900 (mmtt) REVERT: H 174 LYS cc_start: 0.8438 (tmtm) cc_final: 0.8131 (tttm) REVERT: I 122 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8634 (mt) REVERT: I 157 LYS cc_start: 0.8465 (mttm) cc_final: 0.7949 (mmtt) REVERT: I 178 ASP cc_start: 0.7659 (m-30) cc_final: 0.7151 (m-30) REVERT: J 49 GLU cc_start: 0.7862 (tp30) cc_final: 0.7303 (tt0) REVERT: J 140 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8489 (mt-10) REVERT: J 150 GLN cc_start: 0.8438 (tp40) cc_final: 0.8187 (mm-40) REVERT: J 157 LYS cc_start: 0.8408 (mtmm) cc_final: 0.7851 (mmtt) outliers start: 30 outliers final: 15 residues processed: 259 average time/residue: 1.3721 time to fit residues: 393.1734 Evaluate side-chains 255 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 140 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 86 optimal weight: 0.3980 chunk 140 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 188 optimal weight: 0.6980 chunk 180 optimal weight: 0.1980 chunk 171 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 150 GLN C 150 GLN D 150 GLN E 162 ASN F 162 ASN H 150 GLN I 150 GLN J 162 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118081 restraints weight = 22269.311| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.13 r_work: 0.3302 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16720 Z= 0.105 Angle : 0.449 8.081 22850 Z= 0.243 Chirality : 0.042 0.119 2610 Planarity : 0.004 0.036 2960 Dihedral : 3.485 11.917 2310 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.82 % Allowed : 18.93 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.18), residues: 2160 helix: 2.13 (0.14), residues: 1360 sheet: -0.26 (0.30), residues: 300 loop : -0.13 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 214 HIS 0.002 0.001 HIS C 31 PHE 0.007 0.001 PHE H 103 TYR 0.012 0.001 TYR C 205 ARG 0.002 0.000 ARG F 171 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 840) hydrogen bonds : angle 3.93982 ( 2520) covalent geometry : bond 0.00240 (16720) covalent geometry : angle 0.44852 (22850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10531.92 seconds wall clock time: 182 minutes 27.46 seconds (10947.46 seconds total)