Starting phenix.real_space_refine on Sat Jun 14 23:23:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc2_15960/06_2025/8bc2_15960.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc2_15960/06_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_15960/06_2025/8bc2_15960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc2_15960/06_2025/8bc2_15960.map" model { file = "/net/cci-nas-00/data/ceres_data/8bc2_15960/06_2025/8bc2_15960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc2_15960/06_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-5710/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: 5.53, 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: 3.89 Conformation dependent library (CDL) restraints added in 2.1 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: 2.15 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: 5.29 Time building geometry restraints manager: 4.64 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: 0.15 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 33.920 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.460 ------------------------------------------------------------------------------- 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 : 2.216 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: 1.2996 time to fit residues: 826.0376 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 : 1.727 ------------------------------------------------------------------------------- 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 = 0.124652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118045 restraints weight = 21910.606| |-----------------------------------------------------------------------------| 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 58.057 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 : 20.75 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.04690 ( 840) hydrogen bonds : angle 4.90086 ( 2520) covalent geometry : bond 0.00334 (16720) covalent geometry : angle 0.50429 (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 : 1.848 Fit side-chains REVERT: A 130 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7305 (mmtm) REVERT: A 157 LYS cc_start: 0.8426 (mttm) cc_final: 0.7900 (mmtt) REVERT: A 174 LYS cc_start: 0.8133 (tttm) cc_final: 0.7793 (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: 0.7844 (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: 0.7678 (tp30) cc_final: 0.7326 (tt0) REVERT: F 130 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7327 (mmtm) REVERT: F 157 LYS cc_start: 0.8358 (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: 0.8536 (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: 1.3430 time to fit residues: 462.7605 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 : 1.871 ------------------------------------------------------------------------------- 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: 0.0970 chunk 206 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.116806 restraints weight = 22329.885| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.10 r_work: 0.3284 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3280 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= 0.134 Angle : 0.469 5.318 22850 Z= 0.256 Chirality : 0.043 0.123 2610 Planarity : 0.005 0.043 2960 Dihedral : 3.664 13.065 2310 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.52 % Allowed : 20.19 % Favored : 77.30 % 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: 0.63 (0.18), residues: 2160 helix: 1.21 (0.14), residues: 1350 sheet: -1.00 (0.27), residues: 300 loop : -0.59 (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 J 200 PHE 0.011 0.001 PHE E 103 TYR 0.018 0.001 TYR C 205 ARG 0.003 0.001 ARG C 126 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 840) hydrogen bonds : angle 4.45629 ( 2520) covalent geometry : bond 0.00313 (16720) covalent geometry : angle 0.46897 (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 307 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 267 time to evaluate : 1.861 Fit side-chains REVERT: A 130 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7351 (mmtm) REVERT: A 157 LYS cc_start: 0.8396 (mttm) cc_final: 0.7859 (mmtt) REVERT: B 130 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7143 (mmtt) REVERT: C 33 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8290 (ttp) REVERT: C 157 LYS cc_start: 0.8496 (mttm) cc_final: 0.8000 (mmtt) REVERT: C 199 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7893 (mt0) REVERT: D 130 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7350 (mmtm) REVERT: D 157 LYS cc_start: 0.8444 (mttm) cc_final: 0.7897 (mmtt) REVERT: E 157 LYS cc_start: 0.8444 (mtmm) cc_final: 0.7925 (mmtt) REVERT: E 171 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7305 (mmt90) REVERT: E 174 LYS cc_start: 0.8368 (tptp) cc_final: 0.8139 (tptp) REVERT: F 49 GLU cc_start: 0.7755 (tp30) cc_final: 0.7379 (tt0) REVERT: F 130 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7381 (mmtm) REVERT: F 157 LYS cc_start: 0.8353 (mttm) cc_final: 0.7834 (mmtt) REVERT: G 130 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7155 (mmtt) REVERT: H 30 ARG cc_start: 0.7921 (ttp-110) cc_final: 0.7718 (ttp-110) REVERT: H 157 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8012 (mmtt) REVERT: H 174 LYS cc_start: 0.8242 (tmtm) cc_final: 0.7886 (tmtt) REVERT: H 199 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7877 (mt0) REVERT: I 130 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7374 (mmtm) REVERT: I 157 LYS cc_start: 0.8457 (mttm) cc_final: 0.7915 (mmtt) REVERT: J 49 GLU cc_start: 0.7912 (tp30) cc_final: 0.7306 (tt0) REVERT: J 157 LYS cc_start: 0.8393 (mtmm) cc_final: 0.7850 (mmtt) REVERT: J 171 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7358 (mmt90) REVERT: J 174 LYS cc_start: 0.8388 (tptp) cc_final: 0.8121 (tptp) outliers start: 40 outliers final: 10 residues processed: 288 average time/residue: 1.4094 time to fit residues: 449.3842 Evaluate side-chains 259 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 238 time to evaluate : 1.847 ------------------------------------------------------------------------------- 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: 0.7980 chunk 120 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 H 150 GLN I 150 GLN I 158 ASN 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 = 0.3431 r_free = 0.3431 target = 0.122598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115860 restraints weight = 22420.524| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.10 r_work: 0.3267 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16720 Z= 0.141 Angle : 0.466 5.160 22850 Z= 0.255 Chirality : 0.044 0.123 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.695 13.295 2310 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.45 % Allowed : 19.75 % 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: 1.10 (0.18), residues: 2160 helix: 1.59 (0.14), residues: 1350 sheet: -0.70 (0.28), residues: 300 loop : -0.53 (0.27), residues: 510 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 0.011 0.001 PHE I 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 0.04441 ( 840) hydrogen bonds : angle 4.36968 ( 2520) covalent geometry : bond 0.00332 (16720) covalent geometry : angle 0.46570 (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 284 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 2.009 Fit side-chains REVERT: A 130 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7386 (mmtm) REVERT: A 157 LYS cc_start: 0.8392 (mttm) cc_final: 0.7853 (mmtt) REVERT: A 174 LYS cc_start: 0.8222 (tttm) cc_final: 0.7967 (tptp) REVERT: B 130 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7155 (mmtt) REVERT: B 178 ASP cc_start: 0.8055 (m-30) cc_final: 0.7690 (m-30) REVERT: C 144 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8122 (m-30) REVERT: C 157 LYS cc_start: 0.8440 (mttm) cc_final: 0.7943 (mmtt) REVERT: C 174 LYS cc_start: 0.8364 (tttm) cc_final: 0.8136 (tttm) REVERT: C 199 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: D 130 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7339 (mmtm) REVERT: D 157 LYS cc_start: 0.8435 (mttm) cc_final: 0.7916 (mmtt) REVERT: D 178 ASP cc_start: 0.7942 (m-30) cc_final: 0.7457 (m-30) REVERT: E 140 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8406 (mt-10) REVERT: E 150 GLN cc_start: 0.8456 (tp40) cc_final: 0.8204 (mm-40) REVERT: E 157 LYS cc_start: 0.8420 (mtmm) cc_final: 0.7880 (mmtt) REVERT: E 171 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8129 (mmt90) REVERT: F 49 GLU cc_start: 0.7718 (tp30) cc_final: 0.7204 (tt0) REVERT: F 130 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7394 (mmtm) REVERT: F 157 LYS cc_start: 0.8372 (mttm) cc_final: 0.7822 (mmtt) REVERT: G 130 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7167 (mmtt) REVERT: G 171 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7189 (mmt90) REVERT: G 174 LYS cc_start: 0.8408 (tttm) cc_final: 0.8062 (tmtt) REVERT: G 178 ASP cc_start: 0.8097 (m-30) cc_final: 0.7761 (m-30) REVERT: H 157 LYS cc_start: 0.8432 (mtmm) cc_final: 0.7877 (mmtt) REVERT: H 174 LYS cc_start: 0.8337 (tmtm) cc_final: 0.8090 (tttm) REVERT: H 199 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: I 130 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7367 (mmtm) REVERT: I 157 LYS cc_start: 0.8459 (mttm) cc_final: 0.7956 (mmtt) REVERT: I 178 ASP cc_start: 0.7927 (m-30) cc_final: 0.7441 (m-30) REVERT: J 140 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8430 (mt-10) REVERT: J 150 GLN cc_start: 0.8460 (tp40) cc_final: 0.8210 (mm-40) REVERT: J 157 LYS cc_start: 0.8411 (mtmm) cc_final: 0.7880 (mmtt) REVERT: J 171 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8089 (mmt90) outliers start: 39 outliers final: 11 residues processed: 269 average time/residue: 1.3845 time to fit residues: 411.5776 Evaluate side-chains 257 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 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 140 GLU 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 140 GLU 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: 3.9990 chunk 57 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.122893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116060 restraints weight = 22758.701| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.12 r_work: 0.3269 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3564 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= 0.131 Angle : 0.455 5.036 22850 Z= 0.249 Chirality : 0.043 0.122 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.648 12.930 2310 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.14 % Allowed : 18.30 % Favored : 78.55 % 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: 1.40 (0.18), residues: 2160 helix: 1.81 (0.14), residues: 1350 sheet: -0.51 (0.29), residues: 300 loop : -0.43 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 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 0.003 0.000 ARG G 211 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 840) hydrogen bonds : angle 4.26175 ( 2520) covalent geometry : bond 0.00307 (16720) covalent geometry : angle 0.45522 (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: 50 poor density : 239 time to evaluate : 1.878 Fit side-chains REVERT: A 30 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7922 (ttm170) REVERT: A 157 LYS cc_start: 0.8382 (mttm) cc_final: 0.7830 (mmtt) REVERT: B 130 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7147 (mmtt) REVERT: B 178 ASP cc_start: 0.7970 (m-30) cc_final: 0.7559 (m-30) REVERT: C 130 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8146 (tptp) REVERT: C 144 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: C 157 LYS cc_start: 0.8383 (mttm) cc_final: 0.7876 (mmtt) REVERT: C 174 LYS cc_start: 0.8263 (tttm) cc_final: 0.8032 (tttm) REVERT: C 199 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: D 122 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8747 (mt) REVERT: D 130 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7341 (mmtm) REVERT: D 157 LYS cc_start: 0.8432 (mttm) cc_final: 0.7926 (mmtt) REVERT: D 178 ASP cc_start: 0.7865 (m-30) cc_final: 0.7346 (m-30) REVERT: E 140 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: E 150 GLN cc_start: 0.8444 (tp40) cc_final: 0.8150 (mm-40) REVERT: E 157 LYS cc_start: 0.8425 (mtmm) cc_final: 0.7887 (mmtt) REVERT: E 171 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7301 (mmt90) REVERT: F 30 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7895 (ttm170) REVERT: F 49 GLU cc_start: 0.7785 (tp30) cc_final: 0.7234 (tt0) REVERT: F 157 LYS cc_start: 0.8382 (mttm) cc_final: 0.7832 (mmtt) REVERT: G 130 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7140 (mmtt) REVERT: G 171 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7213 (mmt90) REVERT: G 178 ASP cc_start: 0.8039 (m-30) cc_final: 0.7679 (m-30) REVERT: H 144 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: H 157 LYS cc_start: 0.8442 (mtmm) cc_final: 0.7891 (mmtt) REVERT: H 174 LYS cc_start: 0.8398 (tmtm) cc_final: 0.8088 (tttm) REVERT: H 199 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: I 122 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8688 (mt) REVERT: I 130 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7375 (mmtm) REVERT: I 157 LYS cc_start: 0.8455 (mttm) cc_final: 0.7954 (mmtt) REVERT: I 178 ASP cc_start: 0.7859 (m-30) cc_final: 0.7342 (m-30) REVERT: J 49 GLU cc_start: 0.7889 (tp30) cc_final: 0.7322 (tt0) REVERT: J 140 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8461 (mt-10) REVERT: J 150 GLN cc_start: 0.8445 (tp40) cc_final: 0.8151 (mm-40) REVERT: J 157 LYS cc_start: 0.8440 (mtmm) cc_final: 0.7907 (mmtt) REVERT: J 171 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7286 (mmt90) outliers start: 50 outliers final: 12 residues processed: 275 average time/residue: 1.6987 time to fit residues: 516.2987 Evaluate side-chains 260 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 2.044 ------------------------------------------------------------------------------- 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 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 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 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=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: 5.9990 chunk 209 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 150 GLN C 150 GLN D 158 ASN E 162 ASN F 162 ASN G 150 GLN H 150 GLN I 150 GLN I 158 ASN J 162 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114466 restraints weight = 22628.033| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.12 r_work: 0.3249 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3624 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= 0.157 Angle : 0.474 5.033 22850 Z= 0.259 Chirality : 0.044 0.125 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.788 13.808 2310 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.64 % Allowed : 18.36 % Favored : 78.99 % 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: 1.45 (0.18), residues: 2160 helix: 1.85 (0.14), residues: 1350 sheet: -0.46 (0.29), residues: 300 loop : -0.46 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 214 HIS 0.004 0.001 HIS G 200 PHE 0.011 0.001 PHE C 103 TYR 0.013 0.001 TYR C 205 ARG 0.003 0.001 ARG G 211 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 840) hydrogen bonds : angle 4.32362 ( 2520) covalent geometry : bond 0.00375 (16720) covalent geometry : angle 0.47394 (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 288 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 2.221 Fit side-chains REVERT: A 30 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7929 (ttm170) REVERT: A 157 LYS cc_start: 0.8380 (mttm) cc_final: 0.7834 (mmtt) REVERT: A 174 LYS cc_start: 0.8252 (tttm) cc_final: 0.8020 (tttm) REVERT: B 130 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7242 (mmtt) REVERT: B 178 ASP cc_start: 0.7998 (m-30) cc_final: 0.7599 (m-30) REVERT: C 130 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8165 (tptp) REVERT: C 144 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8114 (m-30) REVERT: C 157 LYS cc_start: 0.8393 (mttm) cc_final: 0.7889 (mmtt) REVERT: C 174 LYS cc_start: 0.8325 (tttm) cc_final: 0.8103 (tttm) REVERT: C 199 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: D 130 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7317 (mmtm) REVERT: D 157 LYS cc_start: 0.8439 (mttm) cc_final: 0.7934 (mmtt) REVERT: D 178 ASP cc_start: 0.7838 (m-30) cc_final: 0.7300 (m-30) REVERT: E 140 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8445 (mt-10) REVERT: E 150 GLN cc_start: 0.8462 (tp40) cc_final: 0.8191 (mm-40) REVERT: E 157 LYS cc_start: 0.8426 (mtmm) cc_final: 0.7895 (mmtt) REVERT: E 171 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8194 (mmt90) REVERT: F 30 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7912 (ttm170) REVERT: F 49 GLU cc_start: 0.7757 (tp30) cc_final: 0.7205 (tt0) REVERT: F 157 LYS cc_start: 0.8372 (mttm) cc_final: 0.7829 (mmtt) REVERT: F 174 LYS cc_start: 0.8403 (tttm) cc_final: 0.8198 (tmtt) REVERT: G 130 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7209 (mmtt) REVERT: G 140 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: G 171 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7146 (mmt90) REVERT: G 178 ASP cc_start: 0.8023 (m-30) cc_final: 0.7611 (m-30) REVERT: H 144 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8125 (m-30) REVERT: H 157 LYS cc_start: 0.8439 (mtmm) cc_final: 0.7893 (mmtt) REVERT: H 174 LYS cc_start: 0.8410 (tmtm) cc_final: 0.8168 (tttm) REVERT: H 199 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: I 130 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7401 (mmtm) REVERT: I 157 LYS cc_start: 0.8464 (mttm) cc_final: 0.7959 (mmtt) REVERT: I 178 ASP cc_start: 0.7825 (m-30) cc_final: 0.7295 (m-30) REVERT: J 140 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8489 (mt-10) REVERT: J 150 GLN cc_start: 0.8448 (tp40) cc_final: 0.8173 (mm-40) REVERT: J 157 LYS cc_start: 0.8452 (mtmm) cc_final: 0.7916 (mmtt) REVERT: J 171 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8159 (mmt90) outliers start: 42 outliers final: 14 residues processed: 275 average time/residue: 1.4400 time to fit residues: 437.9387 Evaluate side-chains 261 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 1.738 ------------------------------------------------------------------------------- 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 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 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 130 LYS Chi-restraints excluded: chain G residue 140 GLU 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 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: 0.0020 chunk 10 optimal weight: 0.0010 chunk 142 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 201 optimal weight: 0.0980 chunk 145 optimal weight: 0.2980 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 34 ASN B 150 GLN C 150 GLN C 158 ASN E 162 ASN F 162 ASN H 150 GLN H 158 ASN I 150 GLN J 162 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118165 restraints weight = 22298.830| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.14 r_work: 0.3315 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16720 Z= 0.092 Angle : 0.424 4.961 22850 Z= 0.231 Chirality : 0.042 0.119 2610 Planarity : 0.004 0.036 2960 Dihedral : 3.405 12.042 2310 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.82 % Allowed : 19.43 % 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: 1.81 (0.18), residues: 2160 helix: 2.06 (0.14), residues: 1360 sheet: -0.29 (0.30), residues: 300 loop : -0.15 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 214 HIS 0.001 0.000 HIS F 31 PHE 0.008 0.001 PHE F 131 TYR 0.013 0.001 TYR C 205 ARG 0.002 0.000 ARG H 211 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 840) hydrogen bonds : angle 3.95697 ( 2520) covalent geometry : bond 0.00202 (16720) covalent geometry : angle 0.42415 (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 270 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 1.523 Fit side-chains REVERT: A 30 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7895 (ttm170) REVERT: A 157 LYS cc_start: 0.8372 (mttm) cc_final: 0.7820 (mmtt) REVERT: B 130 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7122 (mmtt) REVERT: C 144 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: C 157 LYS cc_start: 0.8346 (mttm) cc_final: 0.7844 (mmtt) REVERT: C 174 LYS cc_start: 0.8383 (tttm) cc_final: 0.8076 (tttm) REVERT: D 122 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8574 (mt) REVERT: D 157 LYS cc_start: 0.8458 (mttm) cc_final: 0.7933 (mmtt) REVERT: D 178 ASP cc_start: 0.7777 (m-30) cc_final: 0.7260 (m-30) REVERT: E 49 GLU cc_start: 0.7858 (tp30) cc_final: 0.7287 (tt0) REVERT: E 140 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: E 150 GLN cc_start: 0.8444 (tp40) cc_final: 0.8164 (mm-40) REVERT: E 157 LYS cc_start: 0.8413 (mtmm) cc_final: 0.7877 (mmtt) REVERT: F 30 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7865 (ttm170) REVERT: F 49 GLU cc_start: 0.7732 (tp30) cc_final: 0.7216 (tt0) REVERT: F 157 LYS cc_start: 0.8373 (mttm) cc_final: 0.7837 (mmtt) REVERT: G 130 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7104 (mmtt) REVERT: G 178 ASP cc_start: 0.7804 (m-30) cc_final: 0.7363 (m-30) REVERT: H 144 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8040 (m-30) REVERT: H 157 LYS cc_start: 0.8406 (mtmm) cc_final: 0.7877 (mmtt) REVERT: H 174 LYS cc_start: 0.8406 (tmtm) cc_final: 0.8057 (tttm) REVERT: I 122 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8546 (mt) REVERT: I 157 LYS cc_start: 0.8453 (mttm) cc_final: 0.7935 (mmtt) REVERT: I 178 ASP cc_start: 0.7711 (m-30) cc_final: 0.7226 (m-30) REVERT: J 49 GLU cc_start: 0.7874 (tp30) cc_final: 0.7310 (tt0) REVERT: J 140 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8443 (mt-10) REVERT: J 150 GLN cc_start: 0.8456 (tp40) cc_final: 0.8184 (mm-40) REVERT: J 157 LYS cc_start: 0.8401 (mtmm) cc_final: 0.7851 (mmtt) outliers start: 29 outliers final: 5 residues processed: 262 average time/residue: 1.4120 time to fit residues: 408.7982 Evaluate side-chains 244 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 229 time to evaluate : 1.927 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain D residue 144 ASP 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 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 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: 0.8980 chunk 143 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 C 158 ASN D 150 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN F 162 ASN G 150 GLN H 150 GLN H 158 ASN I 150 GLN J 162 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115284 restraints weight = 22320.062| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.13 r_work: 0.3270 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16720 Z= 0.132 Angle : 0.463 6.923 22850 Z= 0.252 Chirality : 0.043 0.120 2610 Planarity : 0.004 0.036 2960 Dihedral : 3.600 12.436 2310 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.14 % Allowed : 18.68 % 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: 1.80 (0.18), residues: 2160 helix: 2.11 (0.14), residues: 1350 sheet: -0.31 (0.30), residues: 300 loop : -0.27 (0.27), residues: 510 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 0.010 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 0.04168 ( 840) hydrogen bonds : angle 4.11082 ( 2520) covalent geometry : bond 0.00312 (16720) covalent geometry : angle 0.46262 (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 271 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 237 time to evaluate : 1.759 Fit side-chains REVERT: A 30 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7917 (ttm170) REVERT: A 157 LYS cc_start: 0.8387 (mttm) cc_final: 0.7824 (mmtt) REVERT: A 174 LYS cc_start: 0.8258 (tttm) cc_final: 0.8038 (tptp) REVERT: B 130 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7141 (mmtt) REVERT: C 144 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: C 157 LYS cc_start: 0.8403 (mttm) cc_final: 0.7907 (mmtt) REVERT: C 174 LYS cc_start: 0.8398 (tttm) cc_final: 0.8140 (tttm) REVERT: C 199 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: D 122 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8676 (mt) REVERT: D 157 LYS cc_start: 0.8433 (mttm) cc_final: 0.7931 (mmtt) REVERT: D 178 ASP cc_start: 0.7761 (m-30) cc_final: 0.7264 (m-30) REVERT: E 49 GLU cc_start: 0.7905 (tp30) cc_final: 0.7343 (tt0) REVERT: E 140 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8420 (mt-10) REVERT: E 150 GLN cc_start: 0.8448 (tp40) cc_final: 0.8170 (mm-40) REVERT: E 157 LYS cc_start: 0.8447 (mtmm) cc_final: 0.7888 (mmtt) REVERT: F 30 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7888 (ttm170) REVERT: F 49 GLU cc_start: 0.7729 (tp30) cc_final: 0.7165 (tt0) REVERT: F 157 LYS cc_start: 0.8389 (mttm) cc_final: 0.7846 (mmtt) REVERT: G 130 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7160 (mmtt) REVERT: G 171 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7237 (mmt90) REVERT: H 144 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8062 (m-30) REVERT: H 157 LYS cc_start: 0.8437 (mtmm) cc_final: 0.7891 (mmtt) REVERT: H 174 LYS cc_start: 0.8471 (tmtm) cc_final: 0.8114 (tttm) REVERT: H 199 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: I 122 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8657 (mt) REVERT: I 157 LYS cc_start: 0.8462 (mttm) cc_final: 0.7946 (mmtt) REVERT: I 178 ASP cc_start: 0.7766 (m-30) cc_final: 0.7281 (m-30) REVERT: J 49 GLU cc_start: 0.7888 (tp30) cc_final: 0.7339 (tt0) REVERT: J 140 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8521 (mt-10) REVERT: J 150 GLN cc_start: 0.8436 (tp40) cc_final: 0.8160 (mm-40) REVERT: J 157 LYS cc_start: 0.8403 (mtmm) cc_final: 0.7847 (mmtt) outliers start: 34 outliers final: 11 residues processed: 265 average time/residue: 1.7045 time to fit residues: 500.4652 Evaluate side-chains 251 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 1.957 ------------------------------------------------------------------------------- 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 C residue 199 GLN Chi-restraints excluded: chain D residue 40 LEU 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 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 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 H residue 199 GLN 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 140 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 170 optimal weight: 0.0040 chunk 47 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 C 158 ASN D 150 GLN E 162 ASN F 162 ASN G 150 GLN H 150 GLN H 158 ASN I 150 GLN J 162 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115902 restraints weight = 22094.237| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.14 r_work: 0.3285 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3732 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= 0.114 Angle : 0.441 4.972 22850 Z= 0.241 Chirality : 0.043 0.120 2610 Planarity : 0.004 0.036 2960 Dihedral : 3.534 12.414 2310 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.45 % Allowed : 18.93 % Favored : 79.62 % 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: 1.86 (0.18), residues: 2160 helix: 2.14 (0.14), residues: 1350 sheet: -0.27 (0.30), residues: 300 loop : -0.21 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 214 HIS 0.002 0.001 HIS C 31 PHE 0.008 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 0.03881 ( 840) hydrogen bonds : angle 4.02425 ( 2520) covalent geometry : bond 0.00265 (16720) covalent geometry : angle 0.44145 (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 259 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 1.907 Fit side-chains REVERT: A 30 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7927 (ttm170) REVERT: A 157 LYS cc_start: 0.8374 (mttm) cc_final: 0.7819 (mmtt) REVERT: A 174 LYS cc_start: 0.8279 (tttm) cc_final: 0.7871 (tptp) REVERT: B 130 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7142 (mmtt) REVERT: B 178 ASP cc_start: 0.7725 (m-30) cc_final: 0.7371 (m-30) REVERT: C 144 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: C 157 LYS cc_start: 0.8395 (mttm) cc_final: 0.7904 (mmtt) REVERT: C 174 LYS cc_start: 0.8377 (tttm) cc_final: 0.8132 (tttm) REVERT: C 199 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7810 (mt0) REVERT: D 122 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8661 (mt) REVERT: D 157 LYS cc_start: 0.8459 (mttm) cc_final: 0.7942 (mmtt) REVERT: D 178 ASP cc_start: 0.7719 (m-30) cc_final: 0.7244 (m-30) REVERT: E 49 GLU cc_start: 0.7880 (tp30) cc_final: 0.7317 (tt0) REVERT: E 140 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8419 (mt-10) REVERT: E 150 GLN cc_start: 0.8463 (tp40) cc_final: 0.8189 (mm-40) REVERT: E 157 LYS cc_start: 0.8414 (mtmm) cc_final: 0.7853 (mmtt) REVERT: F 30 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7886 (ttm170) REVERT: F 49 GLU cc_start: 0.7705 (tp30) cc_final: 0.7160 (tt0) REVERT: F 157 LYS cc_start: 0.8377 (mttm) cc_final: 0.7842 (mmtt) REVERT: G 130 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7129 (mmtt) REVERT: H 157 LYS cc_start: 0.8431 (mtmm) cc_final: 0.7902 (mmtt) REVERT: H 174 LYS cc_start: 0.8431 (tmtm) cc_final: 0.8180 (tttm) REVERT: H 199 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7862 (mt0) REVERT: I 122 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8650 (mt) REVERT: I 157 LYS cc_start: 0.8474 (mttm) cc_final: 0.7950 (mmtt) REVERT: I 178 ASP cc_start: 0.7705 (m-30) cc_final: 0.7209 (m-30) REVERT: J 49 GLU cc_start: 0.7885 (tp30) cc_final: 0.7338 (tt0) REVERT: J 140 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8484 (mt-10) REVERT: J 150 GLN cc_start: 0.8446 (tp40) cc_final: 0.8173 (mm-40) REVERT: J 157 LYS cc_start: 0.8403 (mtmm) cc_final: 0.7846 (mmtt) outliers start: 23 outliers final: 10 residues processed: 255 average time/residue: 1.4208 time to fit residues: 400.3971 Evaluate side-chains 251 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 1.774 ------------------------------------------------------------------------------- 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 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 144 ASP Chi-restraints excluded: chain E residue 48 SER 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 130 LYS Chi-restraints excluded: chain H residue 48 SER 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 J residue 140 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 72 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 96 optimal weight: 0.0670 chunk 169 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 C 158 ASN D 150 GLN E 162 ASN F 162 ASN G 150 GLN H 150 GLN H 158 ASN I 150 GLN J 162 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116752 restraints weight = 22357.888| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.12 r_work: 0.3283 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3739 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= 0.118 Angle : 0.453 6.796 22850 Z= 0.247 Chirality : 0.043 0.120 2610 Planarity : 0.004 0.036 2960 Dihedral : 3.563 12.216 2310 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.64 % Allowed : 18.87 % Favored : 79.50 % 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: 1.85 (0.18), residues: 2160 helix: 2.14 (0.14), residues: 1350 sheet: -0.27 (0.30), residues: 300 loop : -0.22 (0.28), 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 0.008 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 0.03961 ( 840) hydrogen bonds : angle 4.03982 ( 2520) covalent geometry : bond 0.00274 (16720) covalent geometry : angle 0.45261 (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 261 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 2.644 Fit side-chains REVERT: A 30 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7927 (ttm170) REVERT: A 157 LYS cc_start: 0.8375 (mttm) cc_final: 0.7839 (mmtt) REVERT: B 130 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7185 (mmtt) REVERT: B 178 ASP cc_start: 0.7621 (m-30) cc_final: 0.7376 (m-30) REVERT: C 157 LYS cc_start: 0.8416 (mttm) cc_final: 0.7935 (mmtt) REVERT: C 174 LYS cc_start: 0.8349 (tttm) cc_final: 0.8126 (tttm) REVERT: C 199 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7826 (mt0) REVERT: D 122 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8679 (mt) REVERT: D 157 LYS cc_start: 0.8458 (mttm) cc_final: 0.7958 (mmtt) REVERT: D 178 ASP cc_start: 0.7780 (m-30) cc_final: 0.7324 (m-30) REVERT: E 49 GLU cc_start: 0.7881 (tp30) cc_final: 0.7336 (tt0) REVERT: E 140 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8423 (mt-10) REVERT: E 150 GLN cc_start: 0.8458 (tp40) cc_final: 0.8206 (mm-40) REVERT: E 157 LYS cc_start: 0.8408 (mtmm) cc_final: 0.7861 (mmtt) REVERT: F 30 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7898 (ttm170) REVERT: F 157 LYS cc_start: 0.8387 (mttm) cc_final: 0.7852 (mmtt) REVERT: G 130 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7171 (mmtt) REVERT: G 171 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7189 (mmt90) REVERT: G 178 ASP cc_start: 0.7666 (m-30) cc_final: 0.7367 (m-30) REVERT: H 157 LYS cc_start: 0.8430 (mtmm) cc_final: 0.7902 (mmtt) REVERT: H 174 LYS cc_start: 0.8442 (tmtm) cc_final: 0.8088 (tttm) REVERT: H 199 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: I 122 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8665 (mt) REVERT: I 157 LYS cc_start: 0.8489 (mttm) cc_final: 0.7974 (mmtt) REVERT: I 178 ASP cc_start: 0.7766 (m-30) cc_final: 0.7272 (m-30) REVERT: J 49 GLU cc_start: 0.7897 (tp30) cc_final: 0.7358 (tt0) REVERT: J 140 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8481 (mt-10) REVERT: J 150 GLN cc_start: 0.8440 (tp40) cc_final: 0.8189 (mm-40) REVERT: J 157 LYS cc_start: 0.8396 (mtmm) cc_final: 0.7852 (mmtt) outliers start: 26 outliers final: 14 residues processed: 257 average time/residue: 1.4538 time to fit residues: 412.1849 Evaluate side-chains 256 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 1.721 ------------------------------------------------------------------------------- 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 158 ASN 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 144 ASP Chi-restraints excluded: chain E residue 48 SER 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 130 LYS Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain H residue 199 GLN 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 140 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 86 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 24 optimal weight: 0.0170 chunk 22 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 188 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 G 150 GLN H 150 GLN I 150 GLN J 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116822 restraints weight = 22364.487| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.12 r_work: 0.3285 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3760 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= 0.119 Angle : 0.458 7.782 22850 Z= 0.249 Chirality : 0.043 0.120 2610 Planarity : 0.004 0.036 2960 Dihedral : 3.570 12.545 2310 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.51 % Allowed : 18.99 % Favored : 79.50 % 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: 1.85 (0.18), residues: 2160 helix: 2.13 (0.14), residues: 1350 sheet: -0.27 (0.30), residues: 300 loop : -0.21 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 214 HIS 0.002 0.001 HIS C 31 PHE 0.008 0.001 PHE C 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 0.03963 ( 840) hydrogen bonds : angle 4.03753 ( 2520) covalent geometry : bond 0.00278 (16720) covalent geometry : angle 0.45799 (22850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11691.53 seconds wall clock time: 203 minutes 53.79 seconds (12233.79 seconds total)