Starting phenix.real_space_refine on Sun Aug 24 03:26:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc2_15960/08_2025/8bc2_15960.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc2_15960/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8bc2_15960/08_2025/8bc2_15960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc2_15960/08_2025/8bc2_15960.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bc2_15960/08_2025/8bc2_15960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc2_15960/08_2025/8bc2_15960.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 8, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1} 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: B, C, D, E, F, G, H, I, J Time building chain proxies: 2.23, per 1000 atoms: 0.13 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: 1.71 Conformation dependent library (CDL) restraints added in 717.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.65 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: 3.21 Time building geometry restraints manager: 2.14 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.340 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.950 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.004 0.001 ARG F 14 TYR 0.022 0.002 TYR D 15 PHE 0.010 0.001 PHE F 131 TRP 0.005 0.001 TRP B 138 HIS 0.003 0.001 HIS I 200 Details of bonding type rmsd covalent geometry : bond 0.01190 (16720) covalent geometry : angle 1.65599 (22850) hydrogen bonds : bond 0.25111 ( 840) hydrogen bonds : angle 9.94100 ( 2520) *********************** 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 : 0.517 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: 0.6169 time to fit residues: 391.4302 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 : 0.571 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.124115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117510 restraints weight = 21934.529| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.11 r_work: 0.3309 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2789 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= 0.148 Angle : 0.507 5.592 22850 Z= 0.280 Chirality : 0.043 0.120 2610 Planarity : 0.006 0.071 2960 Dihedral : 4.520 57.664 2318 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.33 % Allowed : 20.44 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.17), residues: 2160 helix: -0.11 (0.13), residues: 1340 sheet: -1.58 (0.24), residues: 300 loop : -1.29 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 126 TYR 0.014 0.002 TYR J 205 PHE 0.011 0.001 PHE A 103 TRP 0.006 0.001 TRP A 214 HIS 0.006 0.002 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00345 (16720) covalent geometry : angle 0.50738 (22850) hydrogen bonds : bond 0.04823 ( 840) hydrogen bonds : angle 4.94470 ( 2520) *********************** 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 322 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 0.684 Fit side-chains REVERT: A 130 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7304 (mmtm) REVERT: A 157 LYS cc_start: 0.8327 (mttm) cc_final: 0.7780 (mmtt) REVERT: A 174 LYS cc_start: 0.8144 (tttm) cc_final: 0.7800 (tmtt) REVERT: B 130 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7222 (mmtm) REVERT: C 199 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7848 (mt0) REVERT: E 157 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7798 (mmtt) REVERT: E 171 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7299 (mmt90) REVERT: F 49 GLU cc_start: 0.7700 (tp30) cc_final: 0.7338 (tt0) REVERT: F 130 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7345 (mmtm) REVERT: F 157 LYS cc_start: 0.8322 (mttm) cc_final: 0.7762 (mmtt) REVERT: H 33 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8250 (ttp) REVERT: H 199 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: J 157 LYS cc_start: 0.8329 (mtmm) cc_final: 0.7802 (mmtt) REVERT: J 171 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7304 (mmt90) outliers start: 37 outliers final: 1 residues processed: 308 average time/residue: 0.6814 time to fit residues: 231.5016 Evaluate side-chains 261 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 252 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain B 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 H residue 33 MET Chi-restraints excluded: chain H residue 199 GLN 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 75 optimal weight: 2.9990 chunk 65 optimal weight: 0.0870 chunk 122 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 177 optimal weight: 0.0470 chunk 67 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.124084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117125 restraints weight = 22200.126| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.16 r_work: 0.3285 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16720 Z= 0.115 Angle : 0.449 5.252 22850 Z= 0.245 Chirality : 0.042 0.122 2610 Planarity : 0.004 0.036 2960 Dihedral : 3.563 12.340 2310 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.39 % Allowed : 20.75 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.18), residues: 2160 helix: 1.23 (0.14), residues: 1350 sheet: -1.04 (0.27), residues: 300 loop : -0.55 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 126 TYR 0.019 0.001 TYR C 205 PHE 0.009 0.001 PHE E 103 TRP 0.008 0.001 TRP H 214 HIS 0.003 0.001 HIS J 200 Details of bonding type rmsd covalent geometry : bond 0.00263 (16720) covalent geometry : angle 0.44881 (22850) hydrogen bonds : bond 0.04180 ( 840) hydrogen bonds : angle 4.40014 ( 2520) *********************** 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 306 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 268 time to evaluate : 0.673 Fit side-chains REVERT: A 130 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7347 (mmtm) REVERT: A 157 LYS cc_start: 0.8427 (mttm) cc_final: 0.7854 (mmtt) REVERT: B 178 ASP cc_start: 0.8034 (m-30) cc_final: 0.7663 (m-30) REVERT: C 157 LYS cc_start: 0.8486 (mttm) cc_final: 0.7965 (mmtt) REVERT: C 174 LYS cc_start: 0.8225 (tmtm) cc_final: 0.7919 (tmtt) REVERT: C 199 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: D 130 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7320 (mmtm) REVERT: D 157 LYS cc_start: 0.8445 (mttm) cc_final: 0.7857 (mmtt) REVERT: E 157 LYS cc_start: 0.8395 (mtmm) cc_final: 0.7842 (mmtt) REVERT: E 171 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7320 (mmt90) REVERT: F 49 GLU cc_start: 0.7709 (tp30) cc_final: 0.7328 (tt0) REVERT: F 130 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7364 (mmtm) REVERT: F 157 LYS cc_start: 0.8348 (mttm) cc_final: 0.7804 (mmtt) REVERT: G 130 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7127 (mmtt) REVERT: H 157 LYS cc_start: 0.8531 (mtmm) cc_final: 0.7988 (mmtt) REVERT: H 174 LYS cc_start: 0.8259 (tmtm) cc_final: 0.7873 (tmtt) REVERT: H 199 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7884 (mt0) REVERT: I 130 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7303 (mmtm) REVERT: I 157 LYS cc_start: 0.8454 (mttm) cc_final: 0.7861 (mmtt) REVERT: J 49 GLU cc_start: 0.7872 (tp30) cc_final: 0.7246 (tt0) REVERT: J 157 LYS cc_start: 0.8379 (mtmm) cc_final: 0.7813 (mmtt) REVERT: J 171 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7297 (mmt90) outliers start: 38 outliers final: 10 residues processed: 292 average time/residue: 0.6770 time to fit residues: 218.7176 Evaluate side-chains 262 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain B residue 48 SER 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 84 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 B 158 ASN C 150 GLN D 150 GLN D 158 ASN E 150 GLN E 158 ASN E 162 ASN F 158 ASN F 162 ASN G 150 GLN G 158 ASN H 150 GLN I 150 GLN I 158 ASN J 150 GLN J 162 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113522 restraints weight = 22751.228| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.13 r_work: 0.3237 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16720 Z= 0.203 Angle : 0.521 5.219 22850 Z= 0.287 Chirality : 0.046 0.135 2610 Planarity : 0.005 0.041 2960 Dihedral : 3.992 14.709 2310 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.33 % Allowed : 18.36 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.18), residues: 2160 helix: 1.44 (0.14), residues: 1340 sheet: -0.79 (0.28), residues: 300 loop : -0.63 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 211 TYR 0.015 0.001 TYR C 205 PHE 0.015 0.002 PHE E 103 TRP 0.009 0.001 TRP C 214 HIS 0.006 0.002 HIS G 200 Details of bonding type rmsd covalent geometry : bond 0.00490 (16720) covalent geometry : angle 0.52067 (22850) hydrogen bonds : bond 0.05189 ( 840) hydrogen bonds : angle 4.60507 ( 2520) *********************** 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 299 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 0.673 Fit side-chains REVERT: A 130 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7394 (mmtm) REVERT: A 157 LYS cc_start: 0.8368 (mttm) cc_final: 0.7820 (mmtt) REVERT: B 178 ASP cc_start: 0.8012 (m-30) cc_final: 0.7587 (m-30) REVERT: C 130 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7318 (mmtm) REVERT: C 144 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8143 (m-30) REVERT: C 157 LYS cc_start: 0.8432 (mttm) cc_final: 0.7893 (mmtt) REVERT: C 174 LYS cc_start: 0.8389 (tmtm) cc_final: 0.8165 (tttm) REVERT: D 130 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7340 (mmtm) REVERT: D 157 LYS cc_start: 0.8462 (mttm) cc_final: 0.7920 (mmtt) REVERT: D 178 ASP cc_start: 0.7988 (m-30) cc_final: 0.7459 (m-30) REVERT: E 140 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8438 (mt-10) REVERT: E 150 GLN cc_start: 0.8476 (tp40) cc_final: 0.8225 (mm-40) REVERT: E 157 LYS cc_start: 0.8408 (mtmm) cc_final: 0.7867 (mmtt) REVERT: E 171 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8038 (mmt90) REVERT: E 174 LYS cc_start: 0.8338 (tptp) cc_final: 0.8120 (tptp) REVERT: F 49 GLU cc_start: 0.7837 (tp30) cc_final: 0.7278 (tt0) REVERT: F 130 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7430 (mmtm) REVERT: F 157 LYS cc_start: 0.8373 (mttm) cc_final: 0.7815 (mmtt) REVERT: G 140 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: H 130 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7319 (mmtm) REVERT: H 144 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8134 (m-30) REVERT: H 174 LYS cc_start: 0.8372 (tmtm) cc_final: 0.8161 (tttm) REVERT: I 130 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7345 (mmtm) REVERT: I 157 LYS cc_start: 0.8474 (mttm) cc_final: 0.7936 (mmtt) REVERT: I 178 ASP cc_start: 0.7968 (m-30) cc_final: 0.7436 (m-30) REVERT: J 140 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8507 (mt-10) REVERT: J 150 GLN cc_start: 0.8480 (tp40) cc_final: 0.8224 (mm-40) REVERT: J 157 LYS cc_start: 0.8394 (mtmm) cc_final: 0.7869 (mmtt) REVERT: J 171 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8032 (mmt90) REVERT: J 174 LYS cc_start: 0.8408 (tptp) cc_final: 0.8203 (tptp) outliers start: 53 outliers final: 14 residues processed: 281 average time/residue: 0.6641 time to fit residues: 206.8122 Evaluate side-chains 259 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 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 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 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 140 GLU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 130 LYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 140 GLU Chi-restraints excluded: chain J residue 171 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 196 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 B 158 ASN C 150 GLN C 158 ASN D 150 GLN D 158 ASN F 162 ASN G 150 GLN G 158 ASN H 150 GLN H 158 ASN I 150 GLN I 158 ASN J 162 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.115486 restraints weight = 22441.395| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.13 r_work: 0.3262 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3549 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= 0.133 Angle : 0.462 5.067 22850 Z= 0.254 Chirality : 0.043 0.123 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.710 13.190 2310 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.89 % Allowed : 18.74 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.18), residues: 2160 helix: 1.72 (0.14), residues: 1350 sheet: -0.59 (0.29), residues: 300 loop : -0.47 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 211 TYR 0.014 0.001 TYR C 205 PHE 0.010 0.001 PHE D 103 TRP 0.008 0.001 TRP F 214 HIS 0.003 0.001 HIS G 200 Details of bonding type rmsd covalent geometry : bond 0.00313 (16720) covalent geometry : angle 0.46248 (22850) hydrogen bonds : bond 0.04366 ( 840) hydrogen bonds : angle 4.32756 ( 2520) *********************** 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 288 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 0.484 Fit side-chains REVERT: A 30 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7924 (ttm170) REVERT: A 157 LYS cc_start: 0.8392 (mttm) cc_final: 0.7829 (mmtt) REVERT: A 174 LYS cc_start: 0.8332 (tttm) cc_final: 0.8046 (tmtt) REVERT: B 178 ASP cc_start: 0.7951 (m-30) cc_final: 0.7547 (m-30) REVERT: C 144 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8118 (m-30) REVERT: C 157 LYS cc_start: 0.8375 (mttm) cc_final: 0.7854 (mmtt) REVERT: C 174 LYS cc_start: 0.8361 (tmtm) cc_final: 0.8060 (tttm) REVERT: C 199 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: D 122 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8718 (mt) REVERT: D 130 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7379 (mmtm) REVERT: D 157 LYS cc_start: 0.8441 (mttm) cc_final: 0.7914 (mmtt) REVERT: D 178 ASP cc_start: 0.7914 (m-30) cc_final: 0.7395 (m-30) REVERT: E 150 GLN cc_start: 0.8481 (tp40) cc_final: 0.8180 (mm-40) REVERT: E 157 LYS cc_start: 0.8416 (mtmm) cc_final: 0.7874 (mmtt) REVERT: E 171 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7305 (mmt90) REVERT: F 30 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7907 (ttm170) REVERT: F 49 GLU cc_start: 0.7781 (tp30) cc_final: 0.7225 (tt0) REVERT: F 157 LYS cc_start: 0.8380 (mttm) cc_final: 0.7817 (mmtt) REVERT: G 130 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7204 (mmtt) REVERT: G 140 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: G 178 ASP cc_start: 0.8025 (m-30) cc_final: 0.7667 (m-30) REVERT: H 144 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: H 157 LYS cc_start: 0.8434 (mtmm) cc_final: 0.7887 (mmtt) REVERT: H 174 LYS cc_start: 0.8365 (tmtm) cc_final: 0.8064 (tttm) REVERT: H 199 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7934 (mt0) REVERT: I 122 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8696 (mt) REVERT: I 130 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7380 (mmtm) REVERT: I 157 LYS cc_start: 0.8456 (mttm) cc_final: 0.7919 (mmtt) REVERT: I 178 ASP cc_start: 0.7939 (m-30) cc_final: 0.7412 (m-30) REVERT: J 140 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8450 (mt-10) REVERT: J 150 GLN cc_start: 0.8479 (tp40) cc_final: 0.8177 (mm-40) REVERT: J 157 LYS cc_start: 0.8406 (mtmm) cc_final: 0.7869 (mmtt) REVERT: J 171 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7300 (mmt90) outliers start: 46 outliers final: 13 residues processed: 274 average time/residue: 0.6541 time to fit residues: 197.8983 Evaluate side-chains 258 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain 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 171 ARG Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain 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 I residue 144 ASP 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 139 optimal weight: 0.0770 chunk 42 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- 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 B 158 ASN C 150 GLN D 158 ASN E 162 ASN F 162 ASN G 150 GLN G 158 ASN H 150 GLN I 158 ASN J 162 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115824 restraints weight = 22499.039| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.12 r_work: 0.3256 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3629 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= 0.127 Angle : 0.453 5.832 22850 Z= 0.248 Chirality : 0.043 0.122 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.656 12.628 2310 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.70 % Allowed : 18.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.18), residues: 2160 helix: 1.90 (0.14), residues: 1350 sheet: -0.46 (0.29), residues: 300 loop : -0.36 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 211 TYR 0.014 0.001 TYR C 205 PHE 0.009 0.001 PHE C 103 TRP 0.008 0.001 TRP A 214 HIS 0.002 0.001 HIS G 200 Details of bonding type rmsd covalent geometry : bond 0.00298 (16720) covalent geometry : angle 0.45278 (22850) hydrogen bonds : bond 0.04216 ( 840) hydrogen bonds : angle 4.22446 ( 2520) *********************** 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 285 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 0.688 Fit side-chains REVERT: A 30 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7923 (ttm170) REVERT: A 157 LYS cc_start: 0.8389 (mttm) cc_final: 0.7837 (mmtt) REVERT: A 174 LYS cc_start: 0.8193 (tttm) cc_final: 0.7870 (tptp) REVERT: B 140 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: B 178 ASP cc_start: 0.7956 (m-30) cc_final: 0.7511 (m-30) REVERT: C 144 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8125 (m-30) REVERT: C 157 LYS cc_start: 0.8384 (mttm) cc_final: 0.7876 (mmtt) REVERT: C 174 LYS cc_start: 0.8397 (tmtm) cc_final: 0.8064 (tttm) REVERT: C 199 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7933 (mt0) REVERT: D 122 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8731 (mt) REVERT: D 130 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7334 (mmtm) REVERT: D 157 LYS cc_start: 0.8447 (mttm) cc_final: 0.7936 (mmtt) REVERT: D 178 ASP cc_start: 0.7872 (m-30) cc_final: 0.7356 (m-30) REVERT: E 49 GLU cc_start: 0.7902 (tp30) cc_final: 0.7336 (tt0) REVERT: E 140 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8392 (mt-10) REVERT: E 150 GLN cc_start: 0.8476 (tp40) cc_final: 0.8197 (mm-40) REVERT: E 157 LYS cc_start: 0.8421 (mtmm) cc_final: 0.7888 (mmtt) REVERT: E 171 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7256 (mmt90) REVERT: F 30 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7905 (ttm170) REVERT: F 49 GLU cc_start: 0.7758 (tp30) cc_final: 0.7210 (tt0) REVERT: F 157 LYS cc_start: 0.8384 (mttm) cc_final: 0.7837 (mmtt) REVERT: G 130 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7137 (mmtt) REVERT: G 140 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: H 157 LYS cc_start: 0.8442 (mtmm) cc_final: 0.7900 (mmtt) REVERT: H 174 LYS cc_start: 0.8387 (tmtm) cc_final: 0.8062 (tttm) REVERT: H 199 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: I 122 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8667 (mt) REVERT: I 130 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7378 (mmtm) REVERT: I 157 LYS cc_start: 0.8488 (mttm) cc_final: 0.7956 (mmtt) REVERT: I 178 ASP cc_start: 0.7840 (m-30) cc_final: 0.7296 (m-30) REVERT: J 140 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8459 (mt-10) REVERT: J 150 GLN cc_start: 0.8468 (tp40) cc_final: 0.8188 (mm-40) REVERT: J 157 LYS cc_start: 0.8432 (mtmm) cc_final: 0.7890 (mmtt) REVERT: J 171 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8187 (mmt90) outliers start: 43 outliers final: 12 residues processed: 269 average time/residue: 0.6376 time to fit residues: 188.9498 Evaluate side-chains 256 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 140 GLU 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 140 GLU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain H residue 48 SER 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 I residue 144 ASP Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 140 GLU Chi-restraints excluded: chain J residue 171 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 186 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 150 GLN B 158 ASN C 150 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN F 162 ASN G 150 GLN G 158 ASN H 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 = 0.122799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115927 restraints weight = 22381.691| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.11 r_work: 0.3269 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3677 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= 0.128 Angle : 0.454 5.674 22850 Z= 0.248 Chirality : 0.043 0.122 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.644 12.612 2310 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.39 % Allowed : 18.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.18), residues: 2160 helix: 1.98 (0.14), residues: 1350 sheet: -0.38 (0.29), residues: 300 loop : -0.33 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 211 TYR 0.013 0.001 TYR C 205 PHE 0.009 0.001 PHE H 103 TRP 0.008 0.001 TRP F 214 HIS 0.002 0.001 HIS G 200 Details of bonding type rmsd covalent geometry : bond 0.00299 (16720) covalent geometry : angle 0.45356 (22850) hydrogen bonds : bond 0.04185 ( 840) hydrogen bonds : angle 4.18473 ( 2520) *********************** 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 275 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.609 Fit side-chains REVERT: A 30 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7918 (ttm170) REVERT: A 157 LYS cc_start: 0.8366 (mttm) cc_final: 0.7824 (mmtt) REVERT: B 140 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: B 178 ASP cc_start: 0.7874 (m-30) cc_final: 0.7432 (m-30) REVERT: C 144 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8106 (m-30) REVERT: C 157 LYS cc_start: 0.8386 (mttm) cc_final: 0.7879 (mmtt) REVERT: C 174 LYS cc_start: 0.8402 (tmtm) cc_final: 0.8173 (tttm) REVERT: C 199 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7935 (mt0) REVERT: D 122 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8663 (mt) REVERT: D 130 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7319 (mmtm) REVERT: D 157 LYS cc_start: 0.8444 (mttm) cc_final: 0.7932 (mmtt) REVERT: D 178 ASP cc_start: 0.7835 (m-30) cc_final: 0.7295 (m-30) REVERT: E 49 GLU cc_start: 0.7896 (tp30) cc_final: 0.7336 (tt0) REVERT: E 150 GLN cc_start: 0.8464 (tp40) cc_final: 0.8182 (mm-40) REVERT: E 157 LYS cc_start: 0.8429 (mtmm) cc_final: 0.7888 (mmtt) REVERT: E 171 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8200 (mmt90) REVERT: F 30 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7910 (ttm170) REVERT: F 49 GLU cc_start: 0.7733 (tp30) cc_final: 0.7176 (tt0) REVERT: F 157 LYS cc_start: 0.8378 (mttm) cc_final: 0.7831 (mmtt) REVERT: G 130 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7156 (mmtt) REVERT: G 140 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: G 174 LYS cc_start: 0.8388 (tttm) cc_final: 0.7942 (tmtt) REVERT: G 178 ASP cc_start: 0.8004 (m-30) cc_final: 0.7640 (m-30) REVERT: H 144 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8093 (m-30) REVERT: H 157 LYS cc_start: 0.8425 (mtmm) cc_final: 0.7893 (mmtt) REVERT: H 174 LYS cc_start: 0.8386 (tmtm) cc_final: 0.8165 (tttm) REVERT: H 199 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7940 (mt0) REVERT: I 122 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8651 (mt) REVERT: I 130 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7356 (mmtm) REVERT: I 157 LYS cc_start: 0.8476 (mttm) cc_final: 0.7941 (mmtt) REVERT: I 178 ASP cc_start: 0.7846 (m-30) cc_final: 0.7312 (m-30) REVERT: J 49 GLU cc_start: 0.7894 (tp30) cc_final: 0.7342 (tt0) REVERT: J 140 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8463 (mt-10) REVERT: J 150 GLN cc_start: 0.8465 (tp40) cc_final: 0.8183 (mm-40) REVERT: J 157 LYS cc_start: 0.8438 (mtmm) cc_final: 0.7898 (mmtt) REVERT: J 171 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7235 (mmt90) outliers start: 38 outliers final: 16 residues processed: 265 average time/residue: 0.5817 time to fit residues: 170.7700 Evaluate side-chains 261 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 158 ASN 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 130 LYS Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain G residue 158 ASN 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 I residue 130 LYS Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 140 GLU Chi-restraints excluded: chain J residue 171 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 116 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 150 GLN C 150 GLN D 158 ASN E 162 ASN F 162 ASN G 150 GLN H 150 GLN I 158 ASN J 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.115363 restraints weight = 22565.825| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.12 r_work: 0.3260 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3678 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= 0.141 Angle : 0.471 7.372 22850 Z= 0.257 Chirality : 0.044 0.123 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.701 13.076 2310 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.33 % Allowed : 18.99 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.18), residues: 2160 helix: 1.97 (0.14), residues: 1350 sheet: -0.38 (0.29), residues: 300 loop : -0.37 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 211 TYR 0.013 0.001 TYR C 205 PHE 0.010 0.001 PHE C 103 TRP 0.007 0.001 TRP F 214 HIS 0.003 0.001 HIS G 200 Details of bonding type rmsd covalent geometry : bond 0.00335 (16720) covalent geometry : angle 0.47137 (22850) hydrogen bonds : bond 0.04341 ( 840) hydrogen bonds : angle 4.21376 ( 2520) *********************** 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: 37 poor density : 234 time to evaluate : 0.651 Fit side-chains REVERT: A 157 LYS cc_start: 0.8372 (mttm) cc_final: 0.7814 (mmtt) REVERT: A 174 LYS cc_start: 0.8247 (tttm) cc_final: 0.7868 (tptp) REVERT: B 140 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: C 144 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: C 157 LYS cc_start: 0.8392 (mttm) cc_final: 0.7883 (mmtt) REVERT: C 174 LYS cc_start: 0.8422 (tmtm) cc_final: 0.8165 (tttm) REVERT: C 199 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: D 122 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8676 (mt) REVERT: D 130 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7321 (mmtm) REVERT: D 157 LYS cc_start: 0.8443 (mttm) cc_final: 0.7921 (mmtt) REVERT: D 178 ASP cc_start: 0.7832 (m-30) cc_final: 0.7311 (m-30) REVERT: E 150 GLN cc_start: 0.8453 (tp40) cc_final: 0.8173 (mm-40) REVERT: E 157 LYS cc_start: 0.8433 (mtmm) cc_final: 0.7896 (mmtt) REVERT: E 171 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7228 (mmt90) REVERT: F 49 GLU cc_start: 0.7775 (tp30) cc_final: 0.7211 (tt0) REVERT: F 157 LYS cc_start: 0.8354 (mttm) cc_final: 0.7810 (mmtt) REVERT: G 130 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7236 (mmtt) REVERT: G 174 LYS cc_start: 0.8385 (tttm) cc_final: 0.7924 (tmtt) REVERT: G 178 ASP cc_start: 0.8046 (m-30) cc_final: 0.7646 (m-30) REVERT: H 144 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: H 157 LYS cc_start: 0.8427 (mtmm) cc_final: 0.7892 (mmtt) REVERT: H 174 LYS cc_start: 0.8409 (tmtm) cc_final: 0.8156 (tttm) REVERT: H 199 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7934 (mt0) REVERT: I 122 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8672 (mt) REVERT: I 130 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7373 (mmtm) REVERT: I 157 LYS cc_start: 0.8478 (mttm) cc_final: 0.7948 (mmtt) REVERT: I 178 ASP cc_start: 0.7865 (m-30) cc_final: 0.7344 (m-30) REVERT: J 140 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: J 150 GLN cc_start: 0.8442 (tp40) cc_final: 0.8159 (mm-40) REVERT: J 157 LYS cc_start: 0.8442 (mtmm) cc_final: 0.7897 (mmtt) REVERT: J 171 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7212 (mmt90) outliers start: 37 outliers final: 18 residues processed: 262 average time/residue: 0.6584 time to fit residues: 190.6423 Evaluate side-chains 259 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 140 GLU 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 130 LYS Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain H residue 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 I residue 130 LYS Chi-restraints excluded: chain I residue 144 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 209 optimal weight: 4.9990 chunk 131 optimal weight: 0.0040 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 180 optimal weight: 0.4980 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 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 = 0.3448 r_free = 0.3448 target = 0.123764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116848 restraints weight = 22369.213| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.12 r_work: 0.3284 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3731 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= 0.115 Angle : 0.447 6.802 22850 Z= 0.244 Chirality : 0.043 0.121 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.560 12.053 2310 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.14 % Allowed : 18.81 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.18), residues: 2160 helix: 2.07 (0.14), residues: 1350 sheet: -0.32 (0.29), residues: 300 loop : -0.29 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.013 0.001 TYR C 205 PHE 0.008 0.001 PHE H 103 TRP 0.008 0.001 TRP I 214 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00266 (16720) covalent geometry : angle 0.44650 (22850) hydrogen bonds : bond 0.03935 ( 840) hydrogen bonds : angle 4.07731 ( 2520) *********************** 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 267 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.724 Fit side-chains REVERT: A 30 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7910 (ttm170) REVERT: A 157 LYS cc_start: 0.8382 (mttm) cc_final: 0.7842 (mmtt) REVERT: A 174 LYS cc_start: 0.8224 (tttm) cc_final: 0.7865 (tptp) REVERT: B 140 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7982 (mt-10) REVERT: B 178 ASP cc_start: 0.7809 (m-30) cc_final: 0.7353 (m-30) REVERT: C 144 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: C 157 LYS cc_start: 0.8397 (mttm) cc_final: 0.7894 (mmtt) REVERT: C 174 LYS cc_start: 0.8421 (tmtm) cc_final: 0.8191 (tttm) REVERT: D 122 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8656 (mt) REVERT: D 157 LYS cc_start: 0.8453 (mttm) cc_final: 0.7952 (mmtt) REVERT: D 178 ASP cc_start: 0.7809 (m-30) cc_final: 0.7292 (m-30) REVERT: E 49 GLU cc_start: 0.7884 (tp30) cc_final: 0.7314 (tt0) REVERT: E 150 GLN cc_start: 0.8450 (tp40) cc_final: 0.8178 (mm-40) REVERT: E 157 LYS cc_start: 0.8459 (mtmm) cc_final: 0.7912 (mmtt) REVERT: E 171 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8280 (mmt90) REVERT: F 30 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7898 (ttm170) REVERT: F 49 GLU cc_start: 0.7716 (tp30) cc_final: 0.7168 (tt0) REVERT: F 157 LYS cc_start: 0.8376 (mttm) cc_final: 0.7835 (mmtt) REVERT: G 130 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7133 (mmtt) REVERT: G 174 LYS cc_start: 0.8381 (tttm) cc_final: 0.7839 (tmtt) REVERT: G 178 ASP cc_start: 0.7980 (m-30) cc_final: 0.7566 (m-30) REVERT: H 157 LYS cc_start: 0.8424 (mtmm) cc_final: 0.7896 (mmtt) REVERT: H 174 LYS cc_start: 0.8420 (tmtm) cc_final: 0.8196 (tttm) REVERT: I 122 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8644 (mt) REVERT: I 157 LYS cc_start: 0.8482 (mttm) cc_final: 0.7951 (mmtt) REVERT: I 178 ASP cc_start: 0.7806 (m-30) cc_final: 0.7288 (m-30) REVERT: J 49 GLU cc_start: 0.7894 (tp30) cc_final: 0.7344 (tt0) REVERT: J 140 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8466 (mt-10) REVERT: J 150 GLN cc_start: 0.8446 (tp40) cc_final: 0.8172 (mm-40) REVERT: J 157 LYS cc_start: 0.8440 (mtmm) cc_final: 0.7904 (mmtt) REVERT: J 171 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8270 (mmt90) outliers start: 34 outliers final: 15 residues processed: 260 average time/residue: 0.7202 time to fit residues: 206.3147 Evaluate side-chains 253 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 144 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 120 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 45 optimal weight: 0.0070 chunk 72 optimal weight: 0.6980 chunk 76 optimal weight: 0.0970 chunk 111 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.124269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117325 restraints weight = 22243.872| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.12 r_work: 0.3291 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16720 Z= 0.110 Angle : 0.445 7.351 22850 Z= 0.243 Chirality : 0.042 0.120 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.518 12.135 2310 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.70 % Allowed : 18.99 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.18), residues: 2160 helix: 2.14 (0.14), residues: 1350 sheet: -0.26 (0.30), residues: 300 loop : -0.26 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 211 TYR 0.013 0.001 TYR C 205 PHE 0.008 0.001 PHE C 103 TRP 0.008 0.001 TRP I 214 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00252 (16720) covalent geometry : angle 0.44517 (22850) hydrogen bonds : bond 0.03832 ( 840) hydrogen bonds : angle 4.01927 ( 2520) ********************** 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: 27 poor density : 234 time to evaluate : 0.678 Fit side-chains REVERT: A 30 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7902 (ttm170) REVERT: A 157 LYS cc_start: 0.8379 (mttm) cc_final: 0.7834 (mmtt) REVERT: C 144 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8065 (m-30) REVERT: C 157 LYS cc_start: 0.8403 (mttm) cc_final: 0.7897 (mmtt) REVERT: C 174 LYS cc_start: 0.8457 (tmtm) cc_final: 0.8205 (tttm) REVERT: D 122 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8652 (mt) REVERT: D 157 LYS cc_start: 0.8458 (mttm) cc_final: 0.7956 (mmtt) REVERT: D 178 ASP cc_start: 0.7727 (m-30) cc_final: 0.7265 (m-30) REVERT: E 49 GLU cc_start: 0.7882 (tp30) cc_final: 0.7325 (tt0) REVERT: E 150 GLN cc_start: 0.8447 (tp40) cc_final: 0.8186 (mm-40) REVERT: E 157 LYS cc_start: 0.8425 (mtmm) cc_final: 0.7867 (mmtt) REVERT: F 30 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7908 (ttm170) REVERT: F 49 GLU cc_start: 0.7748 (tp30) cc_final: 0.7218 (tt0) REVERT: F 157 LYS cc_start: 0.8374 (mttm) cc_final: 0.7831 (mmtt) REVERT: G 130 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7127 (mmtt) REVERT: G 174 LYS cc_start: 0.8361 (tttm) cc_final: 0.7853 (tmtt) REVERT: G 178 ASP cc_start: 0.7899 (m-30) cc_final: 0.7481 (m-30) REVERT: H 157 LYS cc_start: 0.8427 (mtmm) cc_final: 0.7900 (mmtt) REVERT: H 174 LYS cc_start: 0.8421 (tmtm) cc_final: 0.8179 (tttm) REVERT: I 122 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8637 (mt) REVERT: I 157 LYS cc_start: 0.8480 (mttm) cc_final: 0.7954 (mmtt) REVERT: I 178 ASP cc_start: 0.7762 (m-30) cc_final: 0.7253 (m-30) REVERT: J 49 GLU cc_start: 0.7881 (tp30) cc_final: 0.7323 (tt0) REVERT: J 140 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8448 (mt-10) REVERT: J 150 GLN cc_start: 0.8451 (tp40) cc_final: 0.8183 (mm-40) REVERT: J 157 LYS cc_start: 0.8402 (mtmm) cc_final: 0.7855 (mmtt) outliers start: 27 outliers final: 15 residues processed: 258 average time/residue: 0.7224 time to fit residues: 205.1830 Evaluate side-chains 248 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 144 ASP Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J 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 189 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN D 150 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN F 162 ASN G 150 GLN ** G 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3388 r_free = 0.3388 target = 0.119159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112199 restraints weight = 22475.884| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.13 r_work: 0.3233 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16720 Z= 0.215 Angle : 0.537 7.986 22850 Z= 0.295 Chirality : 0.047 0.135 2610 Planarity : 0.005 0.038 2960 Dihedral : 4.017 14.884 2310 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.51 % Allowed : 19.12 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.18), residues: 2160 helix: 1.87 (0.14), residues: 1350 sheet: -0.47 (0.29), residues: 300 loop : -0.48 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 211 TYR 0.011 0.001 TYR C 205 PHE 0.013 0.002 PHE C 103 TRP 0.007 0.001 TRP I 214 HIS 0.005 0.002 HIS G 200 Details of bonding type rmsd covalent geometry : bond 0.00522 (16720) covalent geometry : angle 0.53745 (22850) hydrogen bonds : bond 0.05123 ( 840) hydrogen bonds : angle 4.42725 ( 2520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5188.77 seconds wall clock time: 89 minutes 35.51 seconds (5375.51 seconds total)