Starting phenix.real_space_refine on Tue Jan 21 12:37:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fs5_50723/01_2025/9fs5_50723.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fs5_50723/01_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_50723/01_2025/9fs5_50723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fs5_50723/01_2025/9fs5_50723.map" model { file = "/net/cci-nas-00/data/ceres_data/9fs5_50723/01_2025/9fs5_50723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fs5_50723/01_2025/9fs5_50723.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 10.76, per 1000 atoms: 0.64 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: 3.97 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.71 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: 5.35 Time building geometry restraints manager: 4.62 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 37.700 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.090 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:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.930 ------------------------------------------------------------------------------- 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= 0.260 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 : 6.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (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 TRP 0.006 0.001 TRP C 92 HIS 0.001 0.000 HIS F 187 PHE 0.004 0.001 PHE D 34 TYR 0.005 0.001 TYR I 144 ARG 0.008 0.000 ARG J 169 *********************** 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 : 1.792 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: 1.0406 time to fit residues: 802.2099 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 : 1.780 ------------------------------------------------------------------------------- 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 185 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 12 ASN E 75 GLN F 36 GLN F 90 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN G 12 ASN G 77 ASN G 90 GLN ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 ASN ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN J 77 ASN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 GLN ** J 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.089762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.065309 restraints weight = 35675.310| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.02 r_work: 0.2820 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 1.0511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 16950 Z= 0.452 Angle : 0.824 10.836 22900 Z= 0.435 Chirality : 0.049 0.205 2690 Planarity : 0.005 0.056 2950 Dihedral : 5.935 58.937 2407 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 10.74 % Allowed : 26.17 % Favored : 63.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 2230 helix: 1.45 (0.20), residues: 770 sheet: 0.21 (0.19), residues: 820 loop : -0.46 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 24 HIS 0.012 0.004 HIS F 187 PHE 0.035 0.003 PHE B 34 TYR 0.021 0.002 TYR J 72 ARG 0.006 0.001 ARG B 11 *********************** 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 405 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 217 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8388 (ptp) cc_final: 0.8186 (ptp) REVERT: A 95 ARG cc_start: 0.8592 (mmp80) cc_final: 0.8183 (mmp80) REVERT: A 116 ASN cc_start: 0.5053 (OUTLIER) cc_final: 0.4229 (m110) REVERT: A 122 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7755 (tm) REVERT: A 126 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7934 (pp) REVERT: B 4 MET cc_start: 0.8860 (mmm) cc_final: 0.8636 (mmt) REVERT: B 29 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8458 (p) REVERT: B 95 ARG cc_start: 0.8380 (mmp80) cc_final: 0.8059 (mmp80) REVERT: B 116 ASN cc_start: 0.6231 (OUTLIER) cc_final: 0.5704 (m-40) REVERT: B 121 THR cc_start: 0.6741 (OUTLIER) cc_final: 0.6524 (t) REVERT: B 133 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7438 (ttp) REVERT: B 136 ASP cc_start: 0.8910 (t70) cc_final: 0.8367 (t0) REVERT: B 165 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8702 (m) REVERT: B 213 ASP cc_start: 0.8813 (m-30) cc_final: 0.8572 (m-30) REVERT: C 4 MET cc_start: 0.8785 (mmm) cc_final: 0.8469 (mmp) REVERT: C 95 ARG cc_start: 0.8270 (mmp80) cc_final: 0.8005 (tpp-160) REVERT: C 121 THR cc_start: 0.6254 (OUTLIER) cc_final: 0.6024 (t) REVERT: C 133 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7577 (ttp) REVERT: C 136 ASP cc_start: 0.8910 (t70) cc_final: 0.8082 (t0) REVERT: C 169 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8491 (ptp90) REVERT: D 4 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8143 (mmt) REVERT: D 86 LEU cc_start: 0.8875 (mt) cc_final: 0.8583 (mt) REVERT: D 136 ASP cc_start: 0.8546 (t70) cc_final: 0.8036 (t0) REVERT: D 213 ASP cc_start: 0.8919 (m-30) cc_final: 0.8564 (m-30) REVERT: E 84 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7981 (ttp) REVERT: E 121 THR cc_start: 0.5148 (OUTLIER) cc_final: 0.4881 (t) REVERT: F 54 ASP cc_start: 0.8770 (m-30) cc_final: 0.8513 (m-30) REVERT: F 121 THR cc_start: 0.4955 (OUTLIER) cc_final: 0.4680 (t) REVERT: F 138 MET cc_start: 0.8249 (mtt) cc_final: 0.8013 (mmm) REVERT: F 213 ASP cc_start: 0.8599 (m-30) cc_final: 0.8294 (m-30) REVERT: G 192 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8502 (ttm170) REVERT: H 4 MET cc_start: 0.8603 (tpp) cc_final: 0.8381 (tpt) REVERT: H 138 MET cc_start: 0.8784 (mtp) cc_final: 0.8466 (mtt) REVERT: I 13 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8252 (tp) REVERT: I 133 MET cc_start: 0.8338 (ttp) cc_final: 0.7994 (tpp) REVERT: J 84 MET cc_start: 0.8638 (pmm) cc_final: 0.8353 (pmm) REVERT: J 92 TRP cc_start: 0.6470 (OUTLIER) cc_final: 0.6120 (t60) REVERT: J 190 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8208 (tt0) outliers start: 188 outliers final: 36 residues processed: 367 average time/residue: 1.0634 time to fit residues: 442.7779 Evaluate side-chains 175 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 120 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 ASN 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 130 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 121 THR 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 121 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain G residue 1 CYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 121 THR 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 142 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 225 SER Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 17 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 140 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN B 12 ASN B 143 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN D 77 ASN ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN F 75 GLN F 178 GLN ** F 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 ASN G 178 GLN G 187 HIS ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 196 ASN ** J 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.090078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.065908 restraints weight = 34401.628| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.95 r_work: 0.2782 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 1.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16950 Z= 0.181 Angle : 0.528 7.484 22900 Z= 0.278 Chirality : 0.042 0.137 2690 Planarity : 0.002 0.019 2950 Dihedral : 4.791 58.673 2391 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.03 % Allowed : 30.17 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.19), residues: 2230 helix: 1.97 (0.20), residues: 770 sheet: 0.57 (0.19), residues: 800 loop : -0.29 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 24 HIS 0.003 0.001 HIS G 187 PHE 0.018 0.001 PHE B 34 TYR 0.013 0.001 TYR J 72 ARG 0.002 0.000 ARG D 169 *********************** 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 230 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 142 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8571 (ptp) cc_final: 0.8312 (ptp) REVERT: A 95 ARG cc_start: 0.8568 (mmp80) cc_final: 0.8196 (mmp80) REVERT: B 4 MET cc_start: 0.8838 (mmm) cc_final: 0.8616 (mmt) REVERT: B 95 ARG cc_start: 0.8374 (mmp80) cc_final: 0.8119 (mmp80) REVERT: B 136 ASP cc_start: 0.8827 (t70) cc_final: 0.8302 (t0) REVERT: B 213 ASP cc_start: 0.8854 (m-30) cc_final: 0.8573 (m-30) REVERT: C 4 MET cc_start: 0.8831 (mmm) cc_final: 0.8550 (mmp) REVERT: C 95 ARG cc_start: 0.8249 (mmp80) cc_final: 0.7260 (mtm-85) REVERT: C 97 TYR cc_start: 0.8771 (m-10) cc_final: 0.8421 (m-10) REVERT: D 84 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7857 (ttp) REVERT: E 84 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7923 (ttp) REVERT: G 116 ASN cc_start: 0.5543 (OUTLIER) cc_final: 0.5201 (m110) REVERT: G 169 ARG cc_start: 0.8793 (ttp80) cc_final: 0.8585 (ttm-80) REVERT: G 192 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8550 (ttm170) REVERT: H 138 MET cc_start: 0.8782 (mtp) cc_final: 0.8508 (mtt) REVERT: J 94 ASN cc_start: 0.7242 (OUTLIER) cc_final: 0.6991 (p0) REVERT: J 169 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8429 (ptp90) REVERT: J 213 ASP cc_start: 0.8876 (m-30) cc_final: 0.8568 (m-30) outliers start: 88 outliers final: 27 residues processed: 203 average time/residue: 1.3687 time to fit residues: 309.2463 Evaluate side-chains 147 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 161 THR 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 161 THR Chi-restraints excluded: chain E residue 84 MET 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 1 CYS Chi-restraints excluded: chain F residue 84 MET 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 G residue 46 SER Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 192 ARG Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 142 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 94 ASN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 169 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 125 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 chunk 145 optimal weight: 0.0050 chunk 136 optimal weight: 7.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN ** 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 75 GLN ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 GLN ** J 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.084474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.060366 restraints weight = 34591.890| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.88 r_work: 0.2638 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 1.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16950 Z= 0.402 Angle : 0.593 8.537 22900 Z= 0.314 Chirality : 0.044 0.144 2690 Planarity : 0.003 0.020 2950 Dihedral : 4.940 57.076 2387 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.66 % Allowed : 28.46 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.19), residues: 2230 helix: 1.73 (0.20), residues: 770 sheet: 0.48 (0.19), residues: 780 loop : -0.35 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 73 HIS 0.004 0.001 HIS B 187 PHE 0.021 0.002 PHE J 204 TYR 0.016 0.001 TYR C 61 ARG 0.004 0.000 ARG F 169 *********************** 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 221 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 122 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8312 (mmp80) cc_final: 0.8007 (mmp80) REVERT: B 95 ARG cc_start: 0.8231 (mmp80) cc_final: 0.7681 (mmp80) REVERT: B 110 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6410 (tp) REVERT: B 116 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.6761 (m-40) REVERT: B 165 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8686 (m) REVERT: B 169 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8285 (ptp90) REVERT: C 84 MET cc_start: 0.8519 (ptp) cc_final: 0.8317 (ptp) REVERT: C 95 ARG cc_start: 0.8286 (mmp80) cc_final: 0.7904 (tpp-160) REVERT: D 84 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7940 (ttp) REVERT: E 84 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7900 (ttp) REVERT: E 116 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.6952 (m-40) REVERT: E 133 MET cc_start: 0.8450 (ttp) cc_final: 0.8217 (ttm) REVERT: G 133 MET cc_start: 0.8218 (tpp) cc_final: 0.7945 (tpp) REVERT: H 84 MET cc_start: 0.8696 (ptp) cc_final: 0.8452 (ptp) REVERT: H 133 MET cc_start: 0.8159 (tpp) cc_final: 0.7930 (tpp) REVERT: I 45 MET cc_start: 0.9241 (mmm) cc_final: 0.8733 (mtm) REVERT: I 113 TYR cc_start: 0.5569 (m-80) cc_final: 0.5167 (t80) REVERT: I 169 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8203 (ptm160) REVERT: J 113 TYR cc_start: 0.5560 (m-80) cc_final: 0.5278 (t80) REVERT: J 169 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8320 (ptp90) outliers start: 99 outliers final: 37 residues processed: 196 average time/residue: 1.3773 time to fit residues: 299.3953 Evaluate side-chains 165 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 116 ASN 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 151 GLN Chi-restraints excluded: chain E residue 4 MET 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 150 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain F residue 1 CYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 192 ARG Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 169 ARG Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 169 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 0.0020 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 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** ** F 75 GLN ** 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 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 GLN J 190 GLN J 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.063473 restraints weight = 34610.045| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.91 r_work: 0.2698 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 1.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16950 Z= 0.194 Angle : 0.492 7.155 22900 Z= 0.261 Chirality : 0.041 0.129 2690 Planarity : 0.002 0.027 2950 Dihedral : 4.632 56.142 2387 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.40 % Allowed : 29.03 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.19), residues: 2230 helix: 1.97 (0.20), residues: 770 sheet: 0.46 (0.19), residues: 800 loop : -0.17 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 73 HIS 0.002 0.001 HIS I 187 PHE 0.013 0.001 PHE B 34 TYR 0.010 0.001 TYR J 72 ARG 0.006 0.000 ARG E 169 *********************** 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 194 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 117 time to evaluate : 2.172 Fit side-chains REVERT: A 116 ASN cc_start: 0.6425 (OUTLIER) cc_final: 0.5699 (m-40) REVERT: B 84 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8369 (ptp) REVERT: B 165 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8765 (m) REVERT: C 95 ARG cc_start: 0.8199 (mmp80) cc_final: 0.7977 (mmp80) REVERT: C 116 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7183 (m-40) REVERT: E 84 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7816 (ttp) REVERT: E 116 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7362 (m-40) REVERT: E 133 MET cc_start: 0.8442 (ttp) cc_final: 0.8175 (ttm) REVERT: F 14 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: F 84 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7854 (ptp) REVERT: F 88 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8595 (tp30) REVERT: G 84 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8113 (ptp) REVERT: G 116 ASN cc_start: 0.5798 (OUTLIER) cc_final: 0.5387 (m110) REVERT: G 192 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8593 (ttm170) REVERT: G 203 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8501 (mmtt) REVERT: H 84 MET cc_start: 0.8740 (ptp) cc_final: 0.8513 (ptp) REVERT: H 133 MET cc_start: 0.8052 (tpp) cc_final: 0.7789 (tpp) REVERT: I 45 MET cc_start: 0.9251 (mmm) cc_final: 0.8595 (mtm) REVERT: J 94 ASN cc_start: 0.7464 (OUTLIER) cc_final: 0.7067 (p0) REVERT: J 169 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8334 (ptp90) REVERT: J 203 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8386 (mtpp) outliers start: 77 outliers final: 31 residues processed: 177 average time/residue: 1.4403 time to fit residues: 282.3595 Evaluate side-chains 164 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE 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 146 MET Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain E residue 4 MET 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 159 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 192 ARG Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 80 LYS Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 169 ARG Chi-restraints excluded: chain J residue 203 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 208 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 176 optimal weight: 10.0000 chunk 116 optimal weight: 0.0870 chunk 7 optimal weight: 5.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 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 ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 ASN J 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.084771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.060697 restraints weight = 34991.424| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.92 r_work: 0.2640 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 1.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16950 Z= 0.346 Angle : 0.552 10.727 22900 Z= 0.287 Chirality : 0.043 0.130 2690 Planarity : 0.002 0.017 2950 Dihedral : 4.798 56.779 2387 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.37 % Allowed : 27.89 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 2230 helix: 1.90 (0.20), residues: 770 sheet: 0.37 (0.19), residues: 800 loop : -0.18 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 73 HIS 0.003 0.001 HIS I 187 PHE 0.016 0.002 PHE J 204 TYR 0.017 0.001 TYR C 61 ARG 0.004 0.000 ARG F 169 *********************** 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 205 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 111 time to evaluate : 1.764 Fit side-chains REVERT: A 110 ILE cc_start: 0.6861 (OUTLIER) cc_final: 0.6554 (tp) REVERT: A 116 ASN cc_start: 0.6586 (OUTLIER) cc_final: 0.5933 (m-40) REVERT: A 169 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8294 (ptp90) REVERT: B 45 MET cc_start: 0.9324 (mmm) cc_final: 0.8622 (mtm) REVERT: B 165 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8725 (m) REVERT: B 169 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8298 (ptp90) REVERT: C 116 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7189 (m-40) REVERT: C 157 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.9246 (mtpp) REVERT: D 169 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7928 (ttp80) REVERT: E 84 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7852 (ttp) REVERT: E 116 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7362 (m-40) REVERT: E 133 MET cc_start: 0.8437 (ttp) cc_final: 0.8185 (ttm) REVERT: F 14 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8559 (tt0) REVERT: F 84 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7697 (ptp) REVERT: F 169 ARG cc_start: 0.8767 (ttm-80) cc_final: 0.8501 (ttp80) REVERT: G 84 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8114 (ptp) REVERT: G 116 ASN cc_start: 0.5556 (OUTLIER) cc_final: 0.4992 (m110) REVERT: H 84 MET cc_start: 0.8699 (ptp) cc_final: 0.8493 (ptp) REVERT: J 157 LYS cc_start: 0.9582 (OUTLIER) cc_final: 0.9328 (mtpp) REVERT: J 169 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8295 (ptp90) REVERT: J 203 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8432 (mtpp) outliers start: 94 outliers final: 40 residues processed: 187 average time/residue: 1.4013 time to fit residues: 290.2743 Evaluate side-chains 173 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 116 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 110 ILE 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 146 MET Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 202 LEU 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 202 LEU Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain E residue 4 MET 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 142 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 80 LYS Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 157 LYS Chi-restraints excluded: chain J residue 169 ARG Chi-restraints excluded: chain J residue 203 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** 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 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.063105 restraints weight = 34302.699| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.94 r_work: 0.2693 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 1.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16950 Z= 0.190 Angle : 0.520 11.129 22900 Z= 0.260 Chirality : 0.041 0.125 2690 Planarity : 0.002 0.015 2950 Dihedral : 4.603 57.769 2387 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.66 % Allowed : 29.43 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 2230 helix: 2.05 (0.20), residues: 770 sheet: 0.45 (0.19), residues: 800 loop : -0.13 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 92 HIS 0.002 0.001 HIS I 187 PHE 0.011 0.001 PHE B 34 TYR 0.010 0.001 TYR C 61 ARG 0.004 0.000 ARG H 169 *********************** 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 176 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 112 time to evaluate : 1.758 Fit side-chains REVERT: A 116 ASN cc_start: 0.6653 (OUTLIER) cc_final: 0.5999 (m-40) REVERT: A 169 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8220 (ptp90) REVERT: B 45 MET cc_start: 0.9307 (mmm) cc_final: 0.8619 (mtm) REVERT: B 116 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.6965 (m-40) REVERT: C 116 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7180 (m-40) REVERT: E 46 SER cc_start: 0.9524 (OUTLIER) cc_final: 0.9313 (p) REVERT: E 84 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7806 (ttp) REVERT: E 116 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7468 (m-40) REVERT: E 133 MET cc_start: 0.8438 (ttp) cc_final: 0.8195 (ttm) REVERT: F 14 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8548 (tt0) REVERT: F 84 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7746 (ptp) REVERT: G 84 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8097 (ptp) REVERT: J 94 ASN cc_start: 0.7472 (OUTLIER) cc_final: 0.7144 (p0) REVERT: J 169 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8324 (ptp90) outliers start: 64 outliers final: 30 residues processed: 161 average time/residue: 1.3905 time to fit residues: 248.9875 Evaluate side-chains 160 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 23 ILE 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 146 MET Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 151 GLN 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 142 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 80 LYS Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 169 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 69 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** 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 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.085060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.060996 restraints weight = 34579.634| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.91 r_work: 0.2645 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 1.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16950 Z= 0.314 Angle : 0.557 11.300 22900 Z= 0.282 Chirality : 0.042 0.128 2690 Planarity : 0.002 0.018 2950 Dihedral : 4.785 57.407 2387 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.94 % Allowed : 28.91 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.19), residues: 2230 helix: 1.97 (0.20), residues: 770 sheet: 0.44 (0.19), residues: 780 loop : -0.25 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.003 0.001 HIS I 187 PHE 0.012 0.002 PHE J 204 TYR 0.016 0.001 TYR C 61 ARG 0.005 0.000 ARG F 169 *********************** 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 176 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 107 time to evaluate : 1.872 Fit side-chains REVERT: A 116 ASN cc_start: 0.6810 (OUTLIER) cc_final: 0.6228 (m-40) REVERT: A 169 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8274 (ptp90) REVERT: B 84 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8352 (ptp) REVERT: B 116 ASN cc_start: 0.7459 (OUTLIER) cc_final: 0.6963 (m-40) REVERT: C 116 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.7099 (m-40) REVERT: E 116 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7405 (m-40) REVERT: E 133 MET cc_start: 0.8408 (ttp) cc_final: 0.8114 (ttm) REVERT: F 84 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7721 (ptp) REVERT: F 169 ARG cc_start: 0.8781 (ttm-80) cc_final: 0.8502 (ttp80) REVERT: G 84 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8129 (ptp) REVERT: G 157 LYS cc_start: 0.9565 (OUTLIER) cc_final: 0.9339 (mtpp) REVERT: H 157 LYS cc_start: 0.9531 (OUTLIER) cc_final: 0.9322 (mtpp) REVERT: J 94 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.7198 (p0) REVERT: J 157 LYS cc_start: 0.9584 (OUTLIER) cc_final: 0.9337 (mtpp) REVERT: J 169 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8288 (ptp90) outliers start: 69 outliers final: 36 residues processed: 162 average time/residue: 1.3885 time to fit residues: 250.2170 Evaluate side-chains 162 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 113 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 23 ILE 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 146 MET Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 142 VAL 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 142 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 157 LYS Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 157 LYS Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 80 LYS Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 157 LYS Chi-restraints excluded: chain J residue 169 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 106 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 182 optimal weight: 0.5980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** 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 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.085439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.061659 restraints weight = 34625.381| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.91 r_work: 0.2657 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 1.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16950 Z= 0.292 Angle : 0.545 11.488 22900 Z= 0.275 Chirality : 0.042 0.128 2690 Planarity : 0.002 0.031 2950 Dihedral : 4.777 58.213 2387 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.60 % Allowed : 29.14 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.19), residues: 2230 helix: 1.99 (0.20), residues: 770 sheet: 0.32 (0.19), residues: 800 loop : -0.13 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 92 HIS 0.003 0.001 HIS I 187 PHE 0.012 0.002 PHE J 204 TYR 0.015 0.001 TYR C 61 ARG 0.008 0.000 ARG D 169 *********************** 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 172 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 109 time to evaluate : 1.862 Fit side-chains REVERT: A 116 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6428 (m-40) REVERT: A 169 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8258 (ptp90) REVERT: A 203 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8479 (mtpp) REVERT: B 45 MET cc_start: 0.9296 (mmm) cc_final: 0.8600 (mtm) REVERT: B 84 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8403 (ptp) REVERT: B 116 ASN cc_start: 0.7540 (OUTLIER) cc_final: 0.7053 (m-40) REVERT: C 116 ASN cc_start: 0.7566 (OUTLIER) cc_final: 0.7138 (m-40) REVERT: C 157 LYS cc_start: 0.9514 (OUTLIER) cc_final: 0.9205 (mtpp) REVERT: D 84 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7888 (ttp) REVERT: E 116 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7432 (m-40) REVERT: E 169 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7879 (ttp80) REVERT: F 14 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8564 (tt0) REVERT: F 84 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7748 (ptp) REVERT: F 169 ARG cc_start: 0.8775 (ttm-80) cc_final: 0.8499 (ttp80) REVERT: G 84 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8124 (ptp) REVERT: G 157 LYS cc_start: 0.9559 (OUTLIER) cc_final: 0.9331 (mtpp) REVERT: H 157 LYS cc_start: 0.9520 (OUTLIER) cc_final: 0.9310 (mtpp) REVERT: J 94 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.7236 (p0) REVERT: J 157 LYS cc_start: 0.9580 (OUTLIER) cc_final: 0.9337 (mtpp) REVERT: J 169 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8264 (ptp90) outliers start: 63 outliers final: 38 residues processed: 162 average time/residue: 1.3460 time to fit residues: 242.3445 Evaluate side-chains 172 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 116 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 23 ILE 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 146 MET Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 202 LEU 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 202 LEU Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 84 MET 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 G residue 20 SER Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 157 LYS Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 157 LYS Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 169 ARG Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 157 LYS Chi-restraints excluded: chain J residue 169 ARG Chi-restraints excluded: chain J residue 190 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 75 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 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 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.084218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.060396 restraints weight = 34827.295| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.90 r_work: 0.2625 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 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 0.045 16950 Z= 0.390 Angle : 0.580 11.251 22900 Z= 0.295 Chirality : 0.043 0.130 2690 Planarity : 0.002 0.032 2950 Dihedral : 4.926 57.917 2387 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.43 % Allowed : 29.20 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 2230 helix: 1.91 (0.20), residues: 770 sheet: 0.30 (0.19), residues: 780 loop : -0.25 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 73 HIS 0.004 0.001 HIS I 187 PHE 0.015 0.002 PHE J 204 TYR 0.019 0.001 TYR C 61 ARG 0.008 0.000 ARG D 169 ********************** 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 169 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 109 time to evaluate : 1.793 Fit side-chains REVERT: A 116 ASN cc_start: 0.6998 (OUTLIER) cc_final: 0.6476 (m-40) REVERT: A 169 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8327 (ptp90) REVERT: A 203 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8527 (mtpp) REVERT: B 45 MET cc_start: 0.9357 (mmm) cc_final: 0.8706 (mtm) REVERT: B 84 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8382 (ptp) REVERT: B 116 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.7091 (m-40) REVERT: C 116 ASN cc_start: 0.7549 (OUTLIER) cc_final: 0.7126 (m-40) REVERT: C 157 LYS cc_start: 0.9514 (OUTLIER) cc_final: 0.9163 (mtpp) REVERT: D 84 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7943 (ttp) REVERT: E 116 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7300 (m-40) REVERT: E 169 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7874 (ttp80) REVERT: F 14 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8570 (tt0) REVERT: F 84 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7754 (ptp) REVERT: F 169 ARG cc_start: 0.8784 (ttm-80) cc_final: 0.8498 (ttp80) REVERT: G 84 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8124 (ptp) REVERT: G 157 LYS cc_start: 0.9563 (OUTLIER) cc_final: 0.9293 (mtpp) REVERT: H 157 LYS cc_start: 0.9532 (OUTLIER) cc_final: 0.9331 (mtpp) REVERT: J 94 ASN cc_start: 0.7559 (OUTLIER) cc_final: 0.7240 (p0) REVERT: J 157 LYS cc_start: 0.9583 (OUTLIER) cc_final: 0.9326 (mtpp) REVERT: J 169 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8284 (ptp90) outliers start: 60 outliers final: 34 residues processed: 159 average time/residue: 1.3875 time to fit residues: 244.6599 Evaluate side-chains 162 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 110 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 23 ILE 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 A residue 203 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 202 LEU 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 D residue 10 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 84 MET 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 G residue 20 SER Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 157 LYS Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 157 LYS Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 157 LYS Chi-restraints excluded: chain J residue 169 ARG Chi-restraints excluded: chain J residue 190 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 90 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** 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 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.061688 restraints weight = 34601.129| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.89 r_work: 0.2652 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 1.2269 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= 0.268 Angle : 0.534 11.412 22900 Z= 0.271 Chirality : 0.042 0.129 2690 Planarity : 0.002 0.031 2950 Dihedral : 4.794 58.211 2387 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.37 % Allowed : 29.20 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.19), residues: 2230 helix: 2.00 (0.20), residues: 770 sheet: 0.26 (0.19), residues: 800 loop : -0.13 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 73 HIS 0.003 0.001 HIS I 187 PHE 0.011 0.002 PHE J 204 TYR 0.014 0.001 TYR C 61 ARG 0.008 0.000 ARG D 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9767.20 seconds wall clock time: 174 minutes 25.63 seconds (10465.63 seconds total)