Starting phenix.real_space_refine on Thu Sep 18 12:42:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fs5_50723/09_2025/9fs5_50723.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fs5_50723/09_2025/9fs5_50723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fs5_50723/09_2025/9fs5_50723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fs5_50723/09_2025/9fs5_50723.map" model { file = "/net/cci-nas-00/data/ceres_data/9fs5_50723/09_2025/9fs5_50723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fs5_50723/09_2025/9fs5_50723.cif" } resolution = 2.66 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= 0.001 sd= 0.009 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 80 5.16 5 C 10390 2.51 5 N 2940 2.21 5 O 3360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16770 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1677 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "B" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1677 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "C" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1677 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "D" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1677 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "E" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1677 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "F" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1677 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "G" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1677 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "H" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1677 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "I" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1677 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "J" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1677 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Time building chain proxies: 4.34, per 1000 atoms: 0.26 Number of scatterers: 16770 At special positions: 0 Unit cell: (116.35, 120.25, 105.3, 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 80 16.00 O 3360 8.00 N 2940 7.00 C 10390 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: 1.58 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 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: 80 helices and 11 sheets defined 40.0% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.517A pdb=" N LYS A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 96 through 106 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 119 through 138 Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.590A pdb=" N ALA A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Proline residue: A 209 - end of helix removed outlier: 4.131A pdb=" N LEU A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 47 through 59 removed outlier: 3.502A pdb=" N LYS B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.507A pdb=" N LYS B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 96 through 106 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 119 through 138 Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.586A pdb=" N ALA B 207 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Proline residue: B 209 - end of helix removed outlier: 4.108A pdb=" N LEU B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 47 through 59 Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.504A pdb=" N LYS C 69 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 96 through 106 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 119 through 138 Processing helix chain 'C' and resid 203 through 224 removed outlier: 3.597A pdb=" N ALA C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Proline residue: C 209 - end of helix removed outlier: 4.148A pdb=" N LEU C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 47 through 59 Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.511A pdb=" N LYS D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 96 through 106 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 119 through 138 Processing helix chain 'D' and resid 203 through 224 removed outlier: 3.585A pdb=" N ALA D 207 " --> pdb=" O LYS D 203 " (cutoff:3.500A) Proline residue: D 209 - end of helix removed outlier: 4.132A pdb=" N LEU D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 47 through 59 removed outlier: 3.501A pdb=" N LYS E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 70 removed outlier: 3.518A pdb=" N LYS E 69 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 96 through 106 Processing helix chain 'E' and resid 107 through 112 Processing helix chain 'E' and resid 119 through 138 Processing helix chain 'E' and resid 203 through 224 removed outlier: 3.596A pdb=" N ALA E 207 " --> pdb=" O LYS E 203 " (cutoff:3.500A) Proline residue: E 209 - end of helix removed outlier: 4.135A pdb=" N LEU E 223 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY E 224 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 10 Processing helix chain 'F' and resid 47 through 59 Processing helix chain 'F' and resid 66 through 70 removed outlier: 3.517A pdb=" N LYS F 69 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 90 Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 107 through 112 Processing helix chain 'F' and resid 119 through 138 Processing helix chain 'F' and resid 203 through 224 removed outlier: 3.590A pdb=" N ALA F 207 " --> pdb=" O LYS F 203 " (cutoff:3.500A) Proline residue: F 209 - end of helix removed outlier: 4.131A pdb=" N LEU F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY F 224 " --> pdb=" O ALA F 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 10 Processing helix chain 'G' and resid 47 through 59 removed outlier: 3.502A pdb=" N LYS G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 70 removed outlier: 3.509A pdb=" N LYS G 69 " --> pdb=" O SER G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 90 Processing helix chain 'G' and resid 96 through 106 Processing helix chain 'G' and resid 107 through 112 Processing helix chain 'G' and resid 119 through 138 Processing helix chain 'G' and resid 203 through 224 removed outlier: 3.586A pdb=" N ALA G 207 " --> pdb=" O LYS G 203 " (cutoff:3.500A) Proline residue: G 209 - end of helix removed outlier: 4.108A pdb=" N LEU G 223 " --> pdb=" O ILE G 219 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY G 224 " --> pdb=" O ALA G 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 10 Processing helix chain 'H' and resid 47 through 59 Processing helix chain 'H' and resid 66 through 70 removed outlier: 3.503A pdb=" N LYS H 69 " --> pdb=" O SER H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 90 Processing helix chain 'H' and resid 96 through 106 Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 119 through 138 Processing helix chain 'H' and resid 203 through 224 removed outlier: 3.598A pdb=" N ALA H 207 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Proline residue: H 209 - end of helix removed outlier: 4.148A pdb=" N LEU H 223 " --> pdb=" O ILE H 219 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY H 224 " --> pdb=" O ALA H 220 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 10 Processing helix chain 'I' and resid 47 through 59 removed outlier: 3.500A pdb=" N LYS I 59 " --> pdb=" O ALA I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 70 removed outlier: 3.511A pdb=" N LYS I 69 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 90 Processing helix chain 'I' and resid 96 through 106 Processing helix chain 'I' and resid 107 through 112 Processing helix chain 'I' and resid 119 through 138 Processing helix chain 'I' and resid 203 through 224 removed outlier: 3.585A pdb=" N ALA I 207 " --> pdb=" O LYS I 203 " (cutoff:3.500A) Proline residue: I 209 - end of helix removed outlier: 4.132A pdb=" N LEU I 223 " --> pdb=" O ILE I 219 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY I 224 " --> pdb=" O ALA I 220 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 10 Processing helix chain 'J' and resid 47 through 59 removed outlier: 3.501A pdb=" N LYS J 59 " --> pdb=" O ALA J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 70 removed outlier: 3.516A pdb=" N LYS J 69 " --> pdb=" O SER J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 90 Processing helix chain 'J' and resid 96 through 106 Processing helix chain 'J' and resid 107 through 112 Processing helix chain 'J' and resid 119 through 138 Processing helix chain 'J' and resid 203 through 224 removed outlier: 3.597A pdb=" N ALA J 207 " --> pdb=" O LYS J 203 " (cutoff:3.500A) Proline residue: J 209 - end of helix removed outlier: 4.134A pdb=" N LEU J 223 " --> pdb=" O ILE J 219 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY J 224 " --> pdb=" O ALA J 220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 19 removed outlier: 6.670A pdb=" N ASP A 141 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP A 85 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN A 143 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS A 83 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR A 145 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA A 81 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 147 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A 32 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE A 74 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE A 34 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA A 76 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN A 36 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL A 78 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS A 38 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N LYS A 80 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 170 Processing sheet with id=AA3, first strand: chain 'B' and resid 14 through 19 removed outlier: 6.674A pdb=" N ASP B 141 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP B 85 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN B 143 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS B 83 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B 145 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA B 81 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 147 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR B 32 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE B 74 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE B 34 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA B 76 " --> pdb=" O PHE B 34 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN B 36 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL B 78 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS B 38 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LYS B 80 " --> pdb=" O LYS B 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 14 through 19 removed outlier: 6.667A pdb=" N ASP C 141 " --> pdb=" O ASP C 85 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP C 85 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN C 143 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS C 83 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR C 145 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA C 81 " --> pdb=" O THR C 145 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 147 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 32 " --> pdb=" O TYR C 72 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE C 74 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE C 34 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA C 76 " --> pdb=" O PHE C 34 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN C 36 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL C 78 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LYS C 38 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LYS C 80 " --> pdb=" O LYS C 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 14 through 19 removed outlier: 6.670A pdb=" N ASP D 141 " --> pdb=" O ASP D 85 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASP D 85 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN D 143 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS D 83 " --> pdb=" O ASN D 143 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR D 145 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA D 81 " --> pdb=" O THR D 145 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE D 147 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR D 32 " --> pdb=" O TYR D 72 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE D 74 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE D 34 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ALA D 76 " --> pdb=" O PHE D 34 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN D 36 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL D 78 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS D 38 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LYS D 80 " --> pdb=" O LYS D 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 14 through 19 removed outlier: 6.665A pdb=" N ASP E 141 " --> pdb=" O ASP E 85 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP E 85 " --> pdb=" O ASP E 141 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN E 143 " --> pdb=" O LYS E 83 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS E 83 " --> pdb=" O ASN E 143 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR E 145 " --> pdb=" O ALA E 81 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA E 81 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE E 147 " --> pdb=" O LEU E 79 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR E 32 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE E 74 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE E 34 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ALA E 76 " --> pdb=" O PHE E 34 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN E 36 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL E 78 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS E 38 " --> pdb=" O VAL E 78 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LYS E 80 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 14 through 19 removed outlier: 6.671A pdb=" N ASP F 141 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP F 85 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN F 143 " --> pdb=" O LYS F 83 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS F 83 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR F 145 " --> pdb=" O ALA F 81 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA F 81 " --> pdb=" O THR F 145 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 147 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR F 32 " --> pdb=" O TYR F 72 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE F 74 " --> pdb=" O THR F 32 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE F 34 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA F 76 " --> pdb=" O PHE F 34 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN F 36 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL F 78 " --> pdb=" O GLN F 36 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS F 38 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N LYS F 80 " --> pdb=" O LYS F 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 14 through 19 removed outlier: 6.676A pdb=" N ASP G 141 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP G 85 " --> pdb=" O ASP G 141 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN G 143 " --> pdb=" O LYS G 83 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS G 83 " --> pdb=" O ASN G 143 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR G 145 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA G 81 " --> pdb=" O THR G 145 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE G 147 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR G 32 " --> pdb=" O TYR G 72 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE G 74 " --> pdb=" O THR G 32 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE G 34 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA G 76 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN G 36 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL G 78 " --> pdb=" O GLN G 36 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS G 38 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LYS G 80 " --> pdb=" O LYS G 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 14 through 19 removed outlier: 6.666A pdb=" N ASP H 141 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP H 85 " --> pdb=" O ASP H 141 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN H 143 " --> pdb=" O LYS H 83 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS H 83 " --> pdb=" O ASN H 143 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR H 145 " --> pdb=" O ALA H 81 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA H 81 " --> pdb=" O THR H 145 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE H 147 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR H 32 " --> pdb=" O TYR H 72 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE H 74 " --> pdb=" O THR H 32 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE H 34 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA H 76 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN H 36 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL H 78 " --> pdb=" O GLN H 36 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LYS H 38 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N LYS H 80 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 14 through 19 removed outlier: 6.670A pdb=" N ASP I 141 " --> pdb=" O ASP I 85 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASP I 85 " --> pdb=" O ASP I 141 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN I 143 " --> pdb=" O LYS I 83 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS I 83 " --> pdb=" O ASN I 143 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR I 145 " --> pdb=" O ALA I 81 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA I 81 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE I 147 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR I 32 " --> pdb=" O TYR I 72 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE I 74 " --> pdb=" O THR I 32 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE I 34 " --> pdb=" O ILE I 74 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ALA I 76 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN I 36 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL I 78 " --> pdb=" O GLN I 36 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS I 38 " --> pdb=" O VAL I 78 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LYS I 80 " --> pdb=" O LYS I 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 14 through 19 removed outlier: 6.666A pdb=" N ASP J 141 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP J 85 " --> pdb=" O ASP J 141 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN J 143 " --> pdb=" O LYS J 83 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS J 83 " --> pdb=" O ASN J 143 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR J 145 " --> pdb=" O ALA J 81 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA J 81 " --> pdb=" O THR J 145 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE J 147 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR J 32 " --> pdb=" O TYR J 72 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE J 74 " --> pdb=" O THR J 32 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE J 34 " --> pdb=" O ILE J 74 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ALA J 76 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN J 36 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL J 78 " --> pdb=" O GLN J 36 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS J 38 " --> pdb=" O VAL J 78 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LYS J 80 " --> pdb=" O LYS J 38 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2778 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: 2.88 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5680 1.34 - 1.46: 3191 1.46 - 1.58: 7929 1.58 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 16950 Sorted by residual: bond pdb=" CG PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 1.503 1.476 0.027 3.40e-02 8.65e+02 6.18e-01 bond pdb=" CA GLY I 174 " pdb=" C GLY I 174 " ideal model delta sigma weight residual 1.511 1.496 0.015 1.97e-02 2.58e+03 6.02e-01 bond pdb=" CG PRO A 209 " pdb=" CD PRO A 209 " ideal model delta sigma weight residual 1.503 1.477 0.026 3.40e-02 8.65e+02 6.02e-01 bond pdb=" CG PRO F 209 " pdb=" CD PRO F 209 " ideal model delta sigma weight residual 1.503 1.477 0.026 3.40e-02 8.65e+02 6.02e-01 bond pdb=" CG PRO J 209 " pdb=" CD PRO J 209 " ideal model delta sigma weight residual 1.503 1.477 0.026 3.40e-02 8.65e+02 5.97e-01 ... (remaining 16945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 22642 1.63 - 3.25: 187 3.25 - 4.88: 61 4.88 - 6.50: 0 6.50 - 8.13: 10 Bond angle restraints: 22900 Sorted by residual: angle pdb=" C THR C 172 " pdb=" N SER C 173 " pdb=" CA SER C 173 " ideal model delta sigma weight residual 120.79 124.19 -3.40 1.39e+00 5.18e-01 5.98e+00 angle pdb=" C THR I 172 " pdb=" N SER I 173 " pdb=" CA SER I 173 " ideal model delta sigma weight residual 120.79 124.18 -3.39 1.39e+00 5.18e-01 5.96e+00 angle pdb=" C THR D 172 " pdb=" N SER D 173 " pdb=" CA SER D 173 " ideal model delta sigma weight residual 120.79 124.15 -3.36 1.39e+00 5.18e-01 5.85e+00 angle pdb=" C THR H 172 " pdb=" N SER H 173 " pdb=" CA SER H 173 " ideal model delta sigma weight residual 120.79 124.13 -3.34 1.39e+00 5.18e-01 5.77e+00 angle pdb=" C THR F 172 " pdb=" N SER F 173 " pdb=" CA SER F 173 " ideal model delta sigma weight residual 120.79 124.12 -3.33 1.39e+00 5.18e-01 5.72e+00 ... (remaining 22895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.62: 8404 11.62 - 23.23: 995 23.23 - 34.85: 569 34.85 - 46.47: 206 46.47 - 58.08: 126 Dihedral angle restraints: 10300 sinusoidal: 3890 harmonic: 6410 Sorted by residual: dihedral pdb=" N VAL A 142 " pdb=" CA VAL A 142 " pdb=" CB VAL A 142 " pdb=" CG1 VAL A 142 " ideal model delta sinusoidal sigma weight residual -60.00 -1.92 -58.08 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N VAL F 142 " pdb=" CA VAL F 142 " pdb=" CB VAL F 142 " pdb=" CG1 VAL F 142 " ideal model delta sinusoidal sigma weight residual -60.00 -1.92 -58.08 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N VAL J 142 " pdb=" CA VAL J 142 " pdb=" CB VAL J 142 " pdb=" CG1 VAL J 142 " ideal model delta sinusoidal sigma weight residual -60.00 -1.93 -58.07 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 10297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1391 0.024 - 0.048: 848 0.048 - 0.072: 244 0.072 - 0.097: 73 0.097 - 0.121: 134 Chirality restraints: 2690 Sorted by residual: chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA ILE I 152 " pdb=" N ILE I 152 " pdb=" C ILE I 152 " pdb=" CB ILE I 152 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA ILE H 23 " pdb=" N ILE H 23 " pdb=" C ILE H 23 " pdb=" CB ILE H 23 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 2687 not shown) Planarity restraints: 2950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 169 " 0.073 9.50e-02 1.11e+02 3.30e-02 8.66e-01 pdb=" NE ARG J 169 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG J 169 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG J 169 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG J 169 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 169 " 0.073 9.50e-02 1.11e+02 3.28e-02 8.30e-01 pdb=" NE ARG E 169 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG E 169 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG E 169 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 169 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN J 170 " -0.004 2.00e-02 2.50e+03 8.98e-03 8.06e-01 pdb=" C GLN J 170 " 0.016 2.00e-02 2.50e+03 pdb=" O GLN J 170 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY J 171 " -0.005 2.00e-02 2.50e+03 ... (remaining 2947 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2268 2.76 - 3.29: 15279 3.29 - 3.83: 27327 3.83 - 4.36: 32004 4.36 - 4.90: 55994 Nonbonded interactions: 132872 Sorted by model distance: nonbonded pdb=" O GLY F 171 " pdb=" N SER F 173 " model vdw 2.222 3.120 nonbonded pdb=" O GLY A 171 " pdb=" N SER A 173 " model vdw 2.222 3.120 nonbonded pdb=" O GLY D 171 " pdb=" N SER D 173 " model vdw 2.226 3.120 nonbonded pdb=" O GLY I 171 " pdb=" N SER I 173 " model vdw 2.227 3.120 nonbonded pdb=" O GLY H 171 " pdb=" N SER H 173 " model vdw 2.228 3.120 ... (remaining 132867 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: 8.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.600 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 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 : 0.004 0.034 16950 Z= 0.175 Angle : 0.500 8.129 22900 Z= 0.273 Chirality : 0.040 0.121 2690 Planarity : 0.002 0.033 2950 Dihedral : 15.592 58.082 6200 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.60 % Allowed : 22.51 % Favored : 73.89 % 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: 0.97 (0.19), residues: 2230 helix: 1.98 (0.20), residues: 810 sheet: 0.26 (0.19), residues: 850 loop : -0.58 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 169 TYR 0.005 0.001 TYR I 144 PHE 0.004 0.001 PHE D 34 TRP 0.006 0.001 TRP C 92 HIS 0.001 0.000 HIS F 187 Details of bonding type rmsd covalent geometry : bond 0.00393 (16950) covalent geometry : angle 0.49977 (22900) hydrogen bonds : bond 0.13556 ( 986) hydrogen bonds : angle 5.89663 ( 2778) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 633 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 SER cc_start: 0.7799 (t) cc_final: 0.7425 (m) REVERT: A 21 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6348 (mm-30) REVERT: A 40 THR cc_start: 0.8380 (p) cc_final: 0.7423 (m) REVERT: A 79 LEU cc_start: 0.7488 (tp) cc_final: 0.7162 (tm) REVERT: A 84 MET cc_start: 0.7153 (ptp) cc_final: 0.6525 (pmm) REVERT: A 94 ASN cc_start: 0.6705 (OUTLIER) cc_final: 0.6347 (p0) REVERT: A 95 ARG cc_start: 0.8566 (mmp80) cc_final: 0.8059 (mmp80) REVERT: A 97 TYR cc_start: 0.8137 (m-80) cc_final: 0.7906 (m-10) REVERT: B 72 TYR cc_start: 0.6587 (m-80) cc_final: 0.6334 (m-80) REVERT: B 84 MET cc_start: 0.6123 (ptp) cc_final: 0.5261 (pmm) REVERT: B 95 ARG cc_start: 0.8403 (mmp80) cc_final: 0.8192 (mmp80) REVERT: B 97 TYR cc_start: 0.7859 (m-80) cc_final: 0.7539 (m-10) REVERT: B 98 GLU cc_start: 0.7953 (tt0) cc_final: 0.7658 (tm-30) REVERT: B 143 ASN cc_start: 0.7308 (t0) cc_final: 0.6055 (t0) REVERT: D 64 VAL cc_start: 0.6942 (m) cc_final: 0.6606 (p) REVERT: D 86 LEU cc_start: 0.8815 (mt) cc_final: 0.8450 (mp) REVERT: D 121 THR cc_start: 0.5065 (OUTLIER) cc_final: 0.4856 (t) REVERT: D 141 ASP cc_start: 0.6108 (t0) cc_final: 0.5740 (t0) REVERT: E 64 VAL cc_start: 0.5729 (m) cc_final: 0.5080 (p) REVERT: E 86 LEU cc_start: 0.8191 (mt) cc_final: 0.7899 (mm) REVERT: E 98 GLU cc_start: 0.5765 (tt0) cc_final: 0.5444 (tm-30) REVERT: F 191 THR cc_start: 0.4451 (t) cc_final: 0.4103 (m) REVERT: H 138 MET cc_start: 0.7057 (mtp) cc_final: 0.6748 (pp-130) REVERT: I 30 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7220 (mp0) REVERT: I 36 GLN cc_start: 0.6780 (tt0) cc_final: 0.6503 (tt0) REVERT: I 86 LEU cc_start: 0.6557 (mt) cc_final: 0.5619 (mt) REVERT: J 56 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8475 (m) REVERT: J 94 ASN cc_start: 0.6664 (OUTLIER) cc_final: 0.6017 (p0) REVERT: J 95 ARG cc_start: 0.8431 (mmp80) cc_final: 0.7902 (mmp80) REVERT: J 113 TYR cc_start: 0.4662 (m-80) cc_final: 0.4277 (t80) outliers start: 63 outliers final: 16 residues processed: 678 average time/residue: 0.4781 time to fit residues: 367.8804 Evaluate side-chains 390 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 370 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain F residue 1 CYS Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain G residue 1 CYS Chi-restraints excluded: chain H residue 1 CYS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 1 CYS Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 94 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0060 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 ASN B 151 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN C 151 GLN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN D 178 GLN ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 GLN F 178 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN G 178 GLN H 143 ASN ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 GLN J 196 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.096476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.074458 restraints weight = 34730.856| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.99 r_work: 0.2972 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.7419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16950 Z= 0.197 Angle : 0.721 9.312 22900 Z= 0.384 Chirality : 0.046 0.177 2690 Planarity : 0.004 0.047 2950 Dihedral : 5.777 59.121 2407 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 10.11 % Allowed : 27.26 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.19), residues: 2230 helix: 1.69 (0.20), residues: 770 sheet: 0.38 (0.19), residues: 840 loop : -0.34 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 155 TYR 0.021 0.002 TYR G 189 PHE 0.033 0.002 PHE B 34 TRP 0.014 0.002 TRP G 73 HIS 0.010 0.002 HIS F 187 Details of bonding type rmsd covalent geometry : bond 0.00427 (16950) covalent geometry : angle 0.72113 (22900) hydrogen bonds : bond 0.04117 ( 986) hydrogen bonds : angle 5.15160 ( 2778) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 300 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8003 (ptp) cc_final: 0.7220 (pmm) REVERT: A 95 ARG cc_start: 0.8569 (mmp80) cc_final: 0.8183 (mmp80) REVERT: A 110 ILE cc_start: 0.6762 (tp) cc_final: 0.6545 (tp) REVERT: A 116 ASN cc_start: 0.4498 (OUTLIER) cc_final: 0.3660 (m110) REVERT: A 122 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7648 (tm) REVERT: A 126 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7872 (pp) REVERT: A 176 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7799 (mttm) REVERT: B 10 LYS cc_start: 0.8741 (mttm) cc_final: 0.8536 (ptpt) REVERT: B 29 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8427 (p) REVERT: B 84 MET cc_start: 0.7517 (ptp) cc_final: 0.6663 (pmm) REVERT: B 116 ASN cc_start: 0.5794 (OUTLIER) cc_final: 0.5024 (m-40) REVERT: B 165 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8635 (m) REVERT: C 20 SER cc_start: 0.8481 (t) cc_final: 0.8201 (m) REVERT: C 61 TYR cc_start: 0.6999 (m-10) cc_final: 0.6752 (m-10) REVERT: C 95 ARG cc_start: 0.7911 (mmp80) cc_final: 0.7648 (tpp-160) REVERT: C 98 GLU cc_start: 0.7866 (tt0) cc_final: 0.7388 (pp20) REVERT: C 169 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7711 (ptp90) REVERT: D 4 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7628 (mmt) REVERT: D 86 LEU cc_start: 0.8753 (mt) cc_final: 0.8430 (mt) REVERT: D 136 ASP cc_start: 0.7935 (t70) cc_final: 0.7538 (t0) REVERT: E 11 ARG cc_start: 0.8603 (ptt-90) cc_final: 0.8222 (ptt-90) REVERT: E 84 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7683 (ttp) REVERT: E 98 GLU cc_start: 0.6888 (tt0) cc_final: 0.6638 (tt0) REVERT: E 182 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8365 (mp0) REVERT: F 68 ASP cc_start: 0.7880 (m-30) cc_final: 0.7619 (m-30) REVERT: F 138 MET cc_start: 0.7997 (mtt) cc_final: 0.7667 (mmm) REVERT: G 68 ASP cc_start: 0.8283 (m-30) cc_final: 0.7695 (p0) REVERT: G 69 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8507 (pptt) REVERT: G 192 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8090 (ttm170) REVERT: H 68 ASP cc_start: 0.8674 (m-30) cc_final: 0.8203 (p0) REVERT: H 85 ASP cc_start: 0.9009 (t0) cc_final: 0.8794 (t0) REVERT: H 97 TYR cc_start: 0.7466 (m-10) cc_final: 0.7221 (m-80) REVERT: H 122 LEU cc_start: 0.6885 (tp) cc_final: 0.6678 (tm) REVERT: H 138 MET cc_start: 0.8511 (mtp) cc_final: 0.8154 (mtt) REVERT: H 164 ASN cc_start: 0.8403 (t0) cc_final: 0.8167 (t0) REVERT: H 213 ASP cc_start: 0.7636 (m-30) cc_final: 0.7422 (m-30) REVERT: I 97 TYR cc_start: 0.7612 (m-80) cc_final: 0.7297 (m-10) REVERT: I 133 MET cc_start: 0.8125 (ttp) cc_final: 0.7863 (tpp) REVERT: J 20 SER cc_start: 0.8516 (t) cc_final: 0.8173 (m) REVERT: J 23 ILE cc_start: 0.8482 (pp) cc_final: 0.8144 (mt) REVERT: J 30 GLU cc_start: 0.8875 (mm-30) cc_final: 0.7940 (mp0) REVERT: J 84 MET cc_start: 0.8131 (pmm) cc_final: 0.7871 (pmm) REVERT: J 92 TRP cc_start: 0.6197 (OUTLIER) cc_final: 0.5979 (t60) REVERT: J 94 ASN cc_start: 0.6965 (OUTLIER) cc_final: 0.6744 (p0) REVERT: J 98 GLU cc_start: 0.8484 (tt0) cc_final: 0.8250 (tm-30) REVERT: J 102 VAL cc_start: 0.6649 (t) cc_final: 0.6351 (t) REVERT: J 190 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8728 (tt0) REVERT: J 198 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8456 (t0) outliers start: 177 outliers final: 31 residues processed: 438 average time/residue: 0.5309 time to fit residues: 260.5610 Evaluate side-chains 221 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 192 ARG Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain I residue 113 TYR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 92 TRP Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 190 GLN Chi-restraints excluded: chain J residue 198 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 5 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 chunk 212 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 143 ASN B 151 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN ** F 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN G 151 GLN ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN J 143 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.091068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.067226 restraints weight = 35468.292| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.02 r_work: 0.2806 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.9774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16950 Z= 0.157 Angle : 0.603 13.083 22900 Z= 0.312 Chirality : 0.043 0.180 2690 Planarity : 0.003 0.026 2950 Dihedral : 4.316 55.630 2387 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.77 % Allowed : 30.40 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.19), residues: 2230 helix: 1.90 (0.20), residues: 780 sheet: 0.58 (0.19), residues: 820 loop : -0.20 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 95 TYR 0.018 0.001 TYR J 72 PHE 0.025 0.002 PHE F 34 TRP 0.012 0.001 TRP A 24 HIS 0.003 0.001 HIS I 187 Details of bonding type rmsd covalent geometry : bond 0.00349 (16950) covalent geometry : angle 0.60254 (22900) hydrogen bonds : bond 0.03572 ( 986) hydrogen bonds : angle 4.79431 ( 2778) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 184 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8509 (ptp) cc_final: 0.7803 (pmm) REVERT: A 95 ARG cc_start: 0.8595 (mmp80) cc_final: 0.7384 (mpp80) REVERT: B 84 MET cc_start: 0.8412 (ptp) cc_final: 0.7592 (pmm) REVERT: B 95 ARG cc_start: 0.8500 (mmt180) cc_final: 0.7171 (mtm-85) REVERT: C 95 ARG cc_start: 0.8119 (mmp80) cc_final: 0.7203 (mtm-85) REVERT: C 136 ASP cc_start: 0.8164 (t70) cc_final: 0.7549 (t0) REVERT: C 213 ASP cc_start: 0.8878 (m-30) cc_final: 0.8674 (m-30) REVERT: D 84 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7547 (ttp) REVERT: D 86 LEU cc_start: 0.8815 (mt) cc_final: 0.8612 (mt) REVERT: D 138 MET cc_start: 0.8535 (mmm) cc_final: 0.8331 (mmm) REVERT: E 4 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.7126 (mmp) REVERT: E 65 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9061 (p) REVERT: E 68 ASP cc_start: 0.8867 (m-30) cc_final: 0.8514 (m-30) REVERT: E 84 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7823 (ttp) REVERT: E 86 LEU cc_start: 0.9026 (mt) cc_final: 0.8820 (mt) REVERT: E 116 ASN cc_start: 0.7180 (OUTLIER) cc_final: 0.6549 (m-40) REVERT: E 213 ASP cc_start: 0.8671 (m-30) cc_final: 0.8373 (m-30) REVERT: F 116 ASN cc_start: 0.6287 (OUTLIER) cc_final: 0.5815 (m110) REVERT: G 68 ASP cc_start: 0.8792 (m-30) cc_final: 0.8283 (p0) REVERT: G 192 ARG cc_start: 0.8767 (ptm160) cc_final: 0.8561 (ttm170) REVERT: H 68 ASP cc_start: 0.9145 (m-30) cc_final: 0.8675 (p0) REVERT: H 138 MET cc_start: 0.8790 (mtp) cc_final: 0.8478 (mtt) REVERT: H 192 ARG cc_start: 0.8995 (ttm170) cc_final: 0.8637 (ttm170) REVERT: I 14 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7706 (tt0) REVERT: I 19 MET cc_start: 0.9221 (mtm) cc_final: 0.8939 (mtt) REVERT: I 80 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8150 (ptpp) REVERT: I 110 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6815 (tp) REVERT: J 94 ASN cc_start: 0.6992 (OUTLIER) cc_final: 0.6733 (p0) outliers start: 101 outliers final: 35 residues processed: 262 average time/residue: 0.5176 time to fit residues: 151.9110 Evaluate side-chains 166 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 1 CYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain I residue 80 LYS Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 116 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 101 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 198 ASN B 77 ASN B 143 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 ASN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN H 75 GLN ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN I 75 GLN ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.085130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.060604 restraints weight = 35352.294| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.90 r_work: 0.2663 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 1.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16950 Z= 0.273 Angle : 0.629 7.646 22900 Z= 0.332 Chirality : 0.044 0.184 2690 Planarity : 0.003 0.021 2950 Dihedral : 4.798 56.246 2384 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 6.06 % Allowed : 28.46 % Favored : 65.49 % 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: 0.93 (0.19), residues: 2230 helix: 1.67 (0.20), residues: 780 sheet: 0.39 (0.19), residues: 820 loop : -0.25 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 192 TYR 0.018 0.001 TYR D 61 PHE 0.018 0.002 PHE B 34 TRP 0.011 0.001 TRP A 24 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00627 (16950) covalent geometry : angle 0.62865 (22900) hydrogen bonds : bond 0.04015 ( 986) hydrogen bonds : angle 5.09378 ( 2778) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 125 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8713 (ptp) cc_final: 0.8454 (ptp) REVERT: A 95 ARG cc_start: 0.8419 (mmp80) cc_final: 0.8196 (mmp80) REVERT: B 14 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: B 165 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8621 (m) REVERT: C 4 MET cc_start: 0.8836 (mmm) cc_final: 0.8613 (mmt) REVERT: C 95 ARG cc_start: 0.8291 (mmp80) cc_final: 0.7944 (tpp-160) REVERT: C 165 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8656 (m) REVERT: E 84 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7975 (ttp) REVERT: E 116 ASN cc_start: 0.7493 (OUTLIER) cc_final: 0.7003 (m-40) REVERT: F 84 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7866 (ptp) REVERT: F 116 ASN cc_start: 0.6771 (OUTLIER) cc_final: 0.6351 (m110) REVERT: G 133 MET cc_start: 0.8237 (tpp) cc_final: 0.8023 (tpp) REVERT: H 84 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8034 (ptp) REVERT: H 122 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6667 (tm) REVERT: I 113 TYR cc_start: 0.5458 (m-80) cc_final: 0.5089 (t80) REVERT: J 169 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8346 (ptp90) outliers start: 106 outliers final: 34 residues processed: 206 average time/residue: 0.6245 time to fit residues: 142.3213 Evaluate side-chains 161 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain F residue 1 CYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 192 ARG Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 169 ARG Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 169 ARG Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 169 ARG Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 190 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 61 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN B 143 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.086301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.062934 restraints weight = 34501.128| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.89 r_work: 0.2709 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 1.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16950 Z= 0.155 Angle : 0.517 8.904 22900 Z= 0.273 Chirality : 0.042 0.149 2690 Planarity : 0.002 0.022 2950 Dihedral : 4.459 56.074 2384 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.57 % Allowed : 29.83 % Favored : 65.60 % 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: 1.11 (0.19), residues: 2230 helix: 1.84 (0.20), residues: 780 sheet: 0.49 (0.19), residues: 800 loop : -0.15 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 169 TYR 0.012 0.001 TYR J 72 PHE 0.014 0.001 PHE B 34 TRP 0.006 0.001 TRP E 73 HIS 0.002 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00345 (16950) covalent geometry : angle 0.51688 (22900) hydrogen bonds : bond 0.03260 ( 986) hydrogen bonds : angle 4.84477 ( 2778) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 119 time to evaluate : 0.587 Fit side-chains REVERT: A 84 MET cc_start: 0.8777 (ptp) cc_final: 0.8531 (ptp) REVERT: A 113 TYR cc_start: 0.5432 (m-80) cc_final: 0.5201 (t80) REVERT: A 177 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8745 (mm) REVERT: B 14 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: B 116 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.6768 (m-40) REVERT: C 4 MET cc_start: 0.8821 (mmm) cc_final: 0.8553 (mmt) REVERT: C 165 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8671 (m) REVERT: E 84 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7893 (ttp) REVERT: E 116 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7346 (m-40) REVERT: F 84 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7755 (ptp) REVERT: F 116 ASN cc_start: 0.6921 (OUTLIER) cc_final: 0.6709 (m110) REVERT: F 121 THR cc_start: 0.6187 (p) cc_final: 0.5985 (t) REVERT: F 169 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7966 (ttp80) REVERT: G 133 MET cc_start: 0.8237 (tpp) cc_final: 0.8001 (tpp) REVERT: G 192 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8484 (ttm170) REVERT: H 84 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8139 (ptp) REVERT: H 122 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6705 (tm) REVERT: H 133 MET cc_start: 0.8085 (tpp) cc_final: 0.7877 (tpp) REVERT: I 133 MET cc_start: 0.8285 (ttm) cc_final: 0.7573 (tpp) REVERT: J 169 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8335 (ptp90) outliers start: 80 outliers final: 28 residues processed: 178 average time/residue: 0.6117 time to fit residues: 120.7510 Evaluate side-chains 162 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 192 ARG Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 169 ARG Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 169 ARG Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 169 ARG Chi-restraints excluded: chain J residue 183 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 130 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN B 143 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.083918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.060376 restraints weight = 35018.405| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.88 r_work: 0.2606 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 1.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16950 Z= 0.260 Angle : 0.576 10.469 22900 Z= 0.303 Chirality : 0.044 0.178 2690 Planarity : 0.003 0.019 2950 Dihedral : 4.746 57.251 2384 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.14 % Allowed : 28.80 % Favored : 66.06 % 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: 0.96 (0.19), residues: 2230 helix: 1.72 (0.20), residues: 780 sheet: 0.47 (0.19), residues: 780 loop : -0.31 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 169 TYR 0.021 0.001 TYR C 61 PHE 0.014 0.002 PHE B 34 TRP 0.010 0.001 TRP J 92 HIS 0.004 0.001 HIS I 187 Details of bonding type rmsd covalent geometry : bond 0.00595 (16950) covalent geometry : angle 0.57558 (22900) hydrogen bonds : bond 0.03874 ( 986) hydrogen bonds : angle 5.07819 ( 2778) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 112 time to evaluate : 0.671 Fit side-chains REVERT: A 116 ASN cc_start: 0.6489 (OUTLIER) cc_final: 0.5784 (m-40) REVERT: A 177 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8772 (mm) REVERT: B 14 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: B 45 MET cc_start: 0.9306 (mmm) cc_final: 0.8768 (mtm) REVERT: B 116 ASN cc_start: 0.7408 (OUTLIER) cc_final: 0.6867 (m-40) REVERT: B 157 LYS cc_start: 0.9617 (OUTLIER) cc_final: 0.9399 (mtpp) REVERT: C 4 MET cc_start: 0.8827 (mmm) cc_final: 0.8601 (mmt) REVERT: D 84 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7409 (ptp) REVERT: E 84 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7868 (ttp) REVERT: E 116 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7351 (m-40) REVERT: F 84 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7791 (ptp) REVERT: F 116 ASN cc_start: 0.7029 (OUTLIER) cc_final: 0.6776 (m110) REVERT: F 169 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8004 (ttp80) REVERT: G 133 MET cc_start: 0.8153 (tpp) cc_final: 0.7830 (tpp) REVERT: G 192 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8510 (ttm170) REVERT: H 84 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8048 (ptp) REVERT: I 19 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.9007 (ttm) REVERT: J 169 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8304 (ptp90) outliers start: 90 outliers final: 36 residues processed: 181 average time/residue: 0.6287 time to fit residues: 126.6871 Evaluate side-chains 159 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 108 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 1 CYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 192 ARG Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 169 ARG Chi-restraints excluded: chain I residue 19 MET Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 169 ARG Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 169 ARG Chi-restraints excluded: chain J residue 183 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 GLN J 151 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.083636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.059890 restraints weight = 35024.439| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.86 r_work: 0.2622 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 1.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16950 Z= 0.277 Angle : 0.617 11.981 22900 Z= 0.313 Chirality : 0.044 0.174 2690 Planarity : 0.003 0.021 2950 Dihedral : 4.836 57.842 2384 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.46 % Allowed : 29.03 % Favored : 66.51 % 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 (0.19), residues: 2230 helix: 1.69 (0.20), residues: 780 sheet: 0.37 (0.19), residues: 780 loop : -0.34 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 169 TYR 0.025 0.001 TYR C 61 PHE 0.013 0.002 PHE B 34 TRP 0.009 0.001 TRP D 73 HIS 0.004 0.001 HIS I 187 Details of bonding type rmsd covalent geometry : bond 0.00637 (16950) covalent geometry : angle 0.61715 (22900) hydrogen bonds : bond 0.03909 ( 986) hydrogen bonds : angle 5.11006 ( 2778) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 110 time to evaluate : 0.698 Fit side-chains REVERT: A 116 ASN cc_start: 0.6805 (OUTLIER) cc_final: 0.6189 (m-40) REVERT: A 177 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8793 (mm) REVERT: B 14 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: B 116 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7059 (m-40) REVERT: C 4 MET cc_start: 0.8860 (mmm) cc_final: 0.8605 (mmt) REVERT: C 45 MET cc_start: 0.9225 (mmm) cc_final: 0.8631 (mtm) REVERT: C 116 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.7381 (m-40) REVERT: C 157 LYS cc_start: 0.9565 (OUTLIER) cc_final: 0.9045 (mtpp) REVERT: D 84 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7530 (ptp) REVERT: D 169 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8027 (ttp80) REVERT: E 84 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8010 (ttp) REVERT: E 116 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7411 (m-40) REVERT: F 84 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7881 (ptp) REVERT: F 169 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8028 (ttp80) REVERT: G 84 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8170 (ptp) REVERT: G 133 MET cc_start: 0.8044 (tpp) cc_final: 0.7806 (tpp) REVERT: G 192 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8572 (ttm170) REVERT: H 84 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8110 (ptp) REVERT: I 133 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8048 (ttp) REVERT: J 169 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8292 (ptp90) outliers start: 78 outliers final: 34 residues processed: 169 average time/residue: 0.5936 time to fit residues: 111.4340 Evaluate side-chains 160 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 1 CYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 192 ARG Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 169 ARG Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 169 ARG Chi-restraints excluded: chain J residue 183 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 159 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 GLN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.085091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.061511 restraints weight = 34719.713| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.88 r_work: 0.2667 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 1.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16950 Z= 0.180 Angle : 0.548 10.918 22900 Z= 0.278 Chirality : 0.042 0.150 2690 Planarity : 0.002 0.021 2950 Dihedral : 4.633 58.308 2384 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.66 % Allowed : 29.71 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.19), residues: 2230 helix: 1.85 (0.20), residues: 780 sheet: 0.40 (0.19), residues: 780 loop : -0.26 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 169 TYR 0.016 0.001 TYR C 61 PHE 0.012 0.002 PHE B 34 TRP 0.011 0.001 TRP A 92 HIS 0.002 0.001 HIS I 187 Details of bonding type rmsd covalent geometry : bond 0.00405 (16950) covalent geometry : angle 0.54820 (22900) hydrogen bonds : bond 0.03387 ( 986) hydrogen bonds : angle 4.93616 ( 2778) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 110 time to evaluate : 0.505 Fit side-chains REVERT: A 116 ASN cc_start: 0.6971 (OUTLIER) cc_final: 0.6384 (m-40) REVERT: A 177 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8769 (mm) REVERT: B 14 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: B 45 MET cc_start: 0.9287 (mmm) cc_final: 0.8629 (mtm) REVERT: B 116 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7109 (m-40) REVERT: B 169 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8259 (ptp90) REVERT: C 4 MET cc_start: 0.8819 (mmm) cc_final: 0.8592 (mmt) REVERT: C 45 MET cc_start: 0.9175 (mmm) cc_final: 0.8601 (mtm) REVERT: C 116 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7335 (m-40) REVERT: D 84 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7482 (ptp) REVERT: E 84 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7967 (ttp) REVERT: E 116 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7419 (m-40) REVERT: F 84 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7888 (ptp) REVERT: F 116 ASN cc_start: 0.6896 (OUTLIER) cc_final: 0.6457 (m110) REVERT: F 169 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7955 (ttp80) REVERT: G 84 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8103 (ptp) REVERT: G 133 MET cc_start: 0.8016 (tpp) cc_final: 0.7728 (tpp) REVERT: H 84 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8137 (ptp) REVERT: I 133 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8041 (ttp) REVERT: J 94 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7253 (p0) REVERT: J 113 TYR cc_start: 0.6233 (OUTLIER) cc_final: 0.6033 (m-80) REVERT: J 116 ASN cc_start: 0.6387 (OUTLIER) cc_final: 0.5971 (m-40) REVERT: J 169 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8274 (ptp90) outliers start: 64 outliers final: 32 residues processed: 159 average time/residue: 0.6664 time to fit residues: 116.7899 Evaluate side-chains 160 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 1 CYS Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 169 ARG Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 113 TYR Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 169 ARG Chi-restraints excluded: chain J residue 183 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 152 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.084249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.059838 restraints weight = 35250.421| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.89 r_work: 0.2624 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 1.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16950 Z= 0.264 Angle : 0.591 10.801 22900 Z= 0.302 Chirality : 0.044 0.169 2690 Planarity : 0.002 0.034 2950 Dihedral : 4.780 58.020 2384 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.83 % Allowed : 28.97 % Favored : 67.20 % 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: 0.90 (0.19), residues: 2230 helix: 1.76 (0.20), residues: 780 sheet: 0.30 (0.19), residues: 780 loop : -0.28 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 169 TYR 0.022 0.001 TYR C 61 PHE 0.012 0.002 PHE B 34 TRP 0.009 0.001 TRP D 73 HIS 0.004 0.001 HIS I 187 Details of bonding type rmsd covalent geometry : bond 0.00607 (16950) covalent geometry : angle 0.59107 (22900) hydrogen bonds : bond 0.03777 ( 986) hydrogen bonds : angle 5.04520 ( 2778) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 109 time to evaluate : 0.490 Fit side-chains REVERT: A 116 ASN cc_start: 0.7050 (OUTLIER) cc_final: 0.6513 (m-40) REVERT: A 169 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8075 (ptp90) REVERT: A 177 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8799 (mm) REVERT: B 14 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: B 45 MET cc_start: 0.9346 (mmm) cc_final: 0.8801 (mtm) REVERT: B 116 ASN cc_start: 0.7619 (OUTLIER) cc_final: 0.7180 (m-40) REVERT: B 169 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8276 (ptp90) REVERT: C 4 MET cc_start: 0.8833 (mmm) cc_final: 0.8605 (mmt) REVERT: C 116 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7319 (m-40) REVERT: D 84 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7508 (ptp) REVERT: E 116 ASN cc_start: 0.7635 (OUTLIER) cc_final: 0.7354 (m-40) REVERT: F 84 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7895 (ptp) REVERT: F 116 ASN cc_start: 0.6838 (OUTLIER) cc_final: 0.6346 (m110) REVERT: F 169 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8019 (ttp80) REVERT: G 84 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8142 (ptp) REVERT: H 84 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8123 (ptp) REVERT: I 133 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8048 (ttp) REVERT: J 94 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7280 (p0) REVERT: J 116 ASN cc_start: 0.6444 (OUTLIER) cc_final: 0.6047 (m-40) REVERT: J 169 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8324 (ptp90) outliers start: 67 outliers final: 35 residues processed: 164 average time/residue: 0.6105 time to fit residues: 111.1757 Evaluate side-chains 162 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 1 CYS Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 169 ARG Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 169 ARG Chi-restraints excluded: chain J residue 183 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 54 optimal weight: 6.9990 chunk 219 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 141 optimal weight: 0.0670 chunk 83 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN D 77 ASN ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.086312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.062883 restraints weight = 34495.021| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.88 r_work: 0.2688 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 1.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16950 Z= 0.138 Angle : 0.521 11.480 22900 Z= 0.264 Chirality : 0.041 0.147 2690 Planarity : 0.002 0.019 2950 Dihedral : 4.505 58.474 2384 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.97 % Allowed : 29.71 % Favored : 67.31 % 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: 1.12 (0.19), residues: 2230 helix: 2.04 (0.20), residues: 770 sheet: 0.29 (0.19), residues: 800 loop : -0.10 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 11 TYR 0.014 0.001 TYR C 61 PHE 0.012 0.001 PHE B 34 TRP 0.007 0.001 TRP A 92 HIS 0.002 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00300 (16950) covalent geometry : angle 0.52081 (22900) hydrogen bonds : bond 0.03099 ( 986) hydrogen bonds : angle 4.80444 ( 2778) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 112 time to evaluate : 0.457 Fit side-chains REVERT: A 116 ASN cc_start: 0.7133 (OUTLIER) cc_final: 0.6584 (m-40) REVERT: A 169 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7987 (ptp90) REVERT: B 14 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: B 45 MET cc_start: 0.9292 (mmm) cc_final: 0.8678 (mtm) REVERT: B 116 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7344 (m-40) REVERT: B 169 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8287 (ptp90) REVERT: C 116 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7303 (m-40) REVERT: D 84 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7534 (ptp) REVERT: E 84 MET cc_start: 0.8265 (ttm) cc_final: 0.7893 (ttp) REVERT: E 116 ASN cc_start: 0.7624 (OUTLIER) cc_final: 0.7400 (m-40) REVERT: F 84 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7882 (ptp) REVERT: F 116 ASN cc_start: 0.6875 (OUTLIER) cc_final: 0.6414 (m110) REVERT: F 169 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7911 (ttp80) REVERT: G 84 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8101 (ptp) REVERT: H 84 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8155 (ptp) REVERT: I 133 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7762 (tpp) REVERT: J 94 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7271 (p0) REVERT: J 116 ASN cc_start: 0.6526 (OUTLIER) cc_final: 0.6135 (m-40) REVERT: J 169 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8308 (ptp90) outliers start: 52 outliers final: 30 residues processed: 153 average time/residue: 0.6396 time to fit residues: 108.4654 Evaluate side-chains 155 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 169 ARG Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 138 MET Chi-restraints excluded: chain J residue 169 ARG Chi-restraints excluded: chain J residue 183 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 184 optimal weight: 0.0970 chunk 128 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.087084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.063524 restraints weight = 34413.512| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.91 r_work: 0.2703 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 1.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16950 Z= 0.125 Angle : 0.506 11.224 22900 Z= 0.256 Chirality : 0.041 0.146 2690 Planarity : 0.002 0.020 2950 Dihedral : 4.335 58.619 2384 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.69 % Allowed : 30.11 % Favored : 67.20 % 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: 1.24 (0.19), residues: 2230 helix: 2.16 (0.20), residues: 770 sheet: 0.36 (0.19), residues: 800 loop : -0.05 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 169 TYR 0.013 0.001 TYR C 61 PHE 0.011 0.001 PHE B 34 TRP 0.007 0.001 TRP A 92 HIS 0.002 0.001 HIS I 187 Details of bonding type rmsd covalent geometry : bond 0.00271 (16950) covalent geometry : angle 0.50603 (22900) hydrogen bonds : bond 0.02920 ( 986) hydrogen bonds : angle 4.66506 ( 2778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4815.48 seconds wall clock time: 83 minutes 14.39 seconds (4994.39 seconds total)