Starting phenix.real_space_refine on Mon Aug 25 13:00:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ikj_60656/08_2025/9ikj_60656_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ikj_60656/08_2025/9ikj_60656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ikj_60656/08_2025/9ikj_60656_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ikj_60656/08_2025/9ikj_60656_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ikj_60656/08_2025/9ikj_60656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ikj_60656/08_2025/9ikj_60656.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.107 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 96 5.16 5 C 17792 2.51 5 N 4672 2.21 5 O 5904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 142 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28464 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "B" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "C" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "D" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "F" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "G" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "H" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "I" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "J" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "K" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "L" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "M" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "N" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "O" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "P" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1779 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Time building chain proxies: 6.87, per 1000 atoms: 0.24 Number of scatterers: 28464 At special positions: 0 Unit cell: (91.1257, 91.1257, 281.062, 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 96 16.00 O 5904 8.00 N 4672 7.00 C 17792 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: 2.34 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 82 sheets defined 13.0% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 94 through 98 removed outlier: 4.202A pdb=" N LEU A 98 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.570A pdb=" N GLY A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'B' and resid 34 through 41 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.862A pdb=" N LEU B 98 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.503A pdb=" N GLY B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'C' and resid 34 through 41 Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.649A pdb=" N LEU C 98 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 176 removed outlier: 3.748A pdb=" N GLY C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 216 removed outlier: 3.501A pdb=" N ARG C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 41 Processing helix chain 'D' and resid 66 through 71 Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.597A pdb=" N LEU D 98 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 removed outlier: 3.555A pdb=" N GLY D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 216 removed outlier: 3.623A pdb=" N ARG D 214 " --> pdb=" O ASP D 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 41 Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 94 through 98 removed outlier: 3.639A pdb=" N VAL E 97 " --> pdb=" O PRO E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 210 through 216 removed outlier: 3.535A pdb=" N ARG E 214 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 41 Processing helix chain 'F' and resid 66 through 71 Processing helix chain 'F' and resid 94 through 98 removed outlier: 3.648A pdb=" N VAL F 97 " --> pdb=" O PRO F 94 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 98 " --> pdb=" O ILE F 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 94 through 98' Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 210 through 216 Processing helix chain 'G' and resid 34 through 41 Processing helix chain 'G' and resid 66 through 71 Processing helix chain 'G' and resid 94 through 98 removed outlier: 3.602A pdb=" N LEU G 98 " --> pdb=" O ILE G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 176 removed outlier: 3.642A pdb=" N GLY G 176 " --> pdb=" O GLY G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 216 removed outlier: 3.555A pdb=" N ARG G 214 " --> pdb=" O ASP G 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 41 Processing helix chain 'H' and resid 66 through 71 Processing helix chain 'H' and resid 94 through 98 removed outlier: 3.734A pdb=" N LEU H 98 " --> pdb=" O ILE H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 176 removed outlier: 3.665A pdb=" N GLY H 176 " --> pdb=" O GLY H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 215 removed outlier: 3.576A pdb=" N ARG H 214 " --> pdb=" O ASP H 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 41 Processing helix chain 'I' and resid 66 through 71 Processing helix chain 'I' and resid 94 through 98 removed outlier: 3.680A pdb=" N LEU I 98 " --> pdb=" O ILE I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 176 Processing helix chain 'I' and resid 210 through 216 removed outlier: 3.591A pdb=" N ARG I 214 " --> pdb=" O ASP I 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 41 Processing helix chain 'J' and resid 66 through 71 Processing helix chain 'J' and resid 94 through 98 removed outlier: 3.571A pdb=" N LEU J 98 " --> pdb=" O ILE J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 176 Processing helix chain 'J' and resid 210 through 216 removed outlier: 3.588A pdb=" N ARG J 214 " --> pdb=" O ASP J 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 41 Processing helix chain 'K' and resid 66 through 71 Processing helix chain 'K' and resid 94 through 98 removed outlier: 3.558A pdb=" N LEU K 98 " --> pdb=" O ILE K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 176 removed outlier: 3.580A pdb=" N GLY K 176 " --> pdb=" O GLY K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 216 removed outlier: 3.563A pdb=" N ARG K 214 " --> pdb=" O ASP K 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 41 Processing helix chain 'L' and resid 66 through 71 Processing helix chain 'L' and resid 94 through 98 removed outlier: 3.528A pdb=" N LEU L 98 " --> pdb=" O ILE L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 176 Processing helix chain 'L' and resid 210 through 216 removed outlier: 3.653A pdb=" N ARG L 214 " --> pdb=" O ASP L 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 41 Processing helix chain 'M' and resid 66 through 71 Processing helix chain 'M' and resid 94 through 98 removed outlier: 3.608A pdb=" N LEU M 98 " --> pdb=" O ILE M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 176 Processing helix chain 'M' and resid 210 through 215 removed outlier: 3.668A pdb=" N ARG M 214 " --> pdb=" O ASP M 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 41 Processing helix chain 'N' and resid 66 through 71 Processing helix chain 'N' and resid 94 through 98 removed outlier: 3.518A pdb=" N VAL N 97 " --> pdb=" O PRO N 94 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU N 98 " --> pdb=" O ILE N 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 94 through 98' Processing helix chain 'N' and resid 172 through 176 Processing helix chain 'N' and resid 210 through 216 removed outlier: 3.617A pdb=" N ARG N 214 " --> pdb=" O ASP N 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 41 Processing helix chain 'O' and resid 66 through 71 Processing helix chain 'O' and resid 94 through 98 removed outlier: 3.691A pdb=" N VAL O 97 " --> pdb=" O PRO O 94 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU O 98 " --> pdb=" O ILE O 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 94 through 98' Processing helix chain 'O' and resid 172 through 176 Processing helix chain 'O' and resid 210 through 216 removed outlier: 3.637A pdb=" N ARG O 214 " --> pdb=" O ASP O 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 40 Processing helix chain 'P' and resid 66 through 71 Processing helix chain 'P' and resid 94 through 98 removed outlier: 3.553A pdb=" N LEU P 98 " --> pdb=" O ILE P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 176 Processing helix chain 'P' and resid 210 through 216 removed outlier: 3.584A pdb=" N ARG P 214 " --> pdb=" O ASP P 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 27 through 32 removed outlier: 3.561A pdb=" N SER A 4 " --> pdb=" O MET E 233 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET E 233 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR E 135 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 77 through 81 removed outlier: 6.512A pdb=" N VAL E 224 " --> pdb=" O MET E 79 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU E 60 " --> pdb=" O ILE E 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 22 removed outlier: 3.594A pdb=" N GLY A 46 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE A 182 " --> pdb=" O GLY A 46 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 48 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE A 180 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 136 removed outlier: 4.038A pdb=" N TYR A 135 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 77 through 81 removed outlier: 6.631A pdb=" N VAL A 224 " --> pdb=" O MET A 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 89 through 90 removed outlier: 3.585A pdb=" N ILE A 90 " --> pdb=" O TYR A 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 27 through 32 removed outlier: 6.531A pdb=" N VAL F 224 " --> pdb=" O MET F 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 27 through 32 removed outlier: 4.195A pdb=" N TYR F 135 " --> pdb=" O ALA F 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.919A pdb=" N GLY B 46 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE B 182 " --> pdb=" O GLY B 46 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B 48 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE B 180 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 18 through 22 Processing sheet with id=AB2, first strand: chain 'B' and resid 135 through 136 removed outlier: 4.055A pdb=" N TYR B 135 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 60 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 135 through 136 removed outlier: 4.055A pdb=" N TYR B 135 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 77 through 81 removed outlier: 6.530A pdb=" N VAL B 224 " --> pdb=" O MET B 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 89 through 90 removed outlier: 3.558A pdb=" N ILE B 90 " --> pdb=" O TYR B 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 27 through 32 removed outlier: 4.090A pdb=" N TYR G 135 " --> pdb=" O ALA G 62 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 77 through 81 removed outlier: 6.566A pdb=" N VAL G 224 " --> pdb=" O MET G 79 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU G 60 " --> pdb=" O ILE G 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 18 through 22 removed outlier: 3.722A pdb=" N GLY C 46 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE C 182 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 48 " --> pdb=" O PHE C 180 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE C 180 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 18 through 22 Processing sheet with id=AC1, first strand: chain 'C' and resid 135 through 136 removed outlier: 4.107A pdb=" N TYR C 135 " --> pdb=" O ALA C 62 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU C 60 " --> pdb=" O ILE C 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 135 through 136 removed outlier: 4.107A pdb=" N TYR C 135 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 77 through 81 removed outlier: 6.614A pdb=" N VAL C 224 " --> pdb=" O MET C 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 89 through 90 removed outlier: 3.586A pdb=" N ILE C 90 " --> pdb=" O TYR C 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'H' and resid 27 through 32 removed outlier: 8.065A pdb=" N VAL H 28 " --> pdb=" O ASN D 7 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR D 9 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE H 30 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR D 11 " --> pdb=" O PHE H 30 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE H 32 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASP D 13 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR H 135 " --> pdb=" O ALA H 62 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 77 through 81 removed outlier: 6.566A pdb=" N VAL H 224 " --> pdb=" O MET H 79 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU H 60 " --> pdb=" O ILE H 151 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 18 through 22 removed outlier: 7.866A pdb=" N GLN D 44 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL D 186 " --> pdb=" O GLN D 44 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLY D 46 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE D 184 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 48 " --> pdb=" O ILE D 182 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 18 through 22 Processing sheet with id=AC9, first strand: chain 'D' and resid 135 through 136 removed outlier: 4.071A pdb=" N TYR D 135 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU D 60 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 135 through 136 removed outlier: 4.071A pdb=" N TYR D 135 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 77 through 81 removed outlier: 6.569A pdb=" N VAL D 224 " --> pdb=" O MET D 79 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 89 through 90 Processing sheet with id=AD4, first strand: chain 'I' and resid 27 through 32 removed outlier: 4.298A pdb=" N TYR I 135 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 77 through 81 removed outlier: 6.510A pdb=" N VAL I 224 " --> pdb=" O MET I 79 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU I 60 " --> pdb=" O ILE I 151 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 18 through 22 removed outlier: 7.866A pdb=" N GLN E 44 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL E 186 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY E 46 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE E 184 " --> pdb=" O GLY E 46 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL E 48 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 18 through 22 Processing sheet with id=AD8, first strand: chain 'E' and resid 89 through 90 Processing sheet with id=AD9, first strand: chain 'J' and resid 27 through 32 removed outlier: 6.538A pdb=" N VAL J 224 " --> pdb=" O MET J 79 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 27 through 32 removed outlier: 4.165A pdb=" N TYR J 135 " --> pdb=" O ALA J 62 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 18 through 22 removed outlier: 7.864A pdb=" N GLN F 44 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL F 186 " --> pdb=" O GLN F 44 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY F 46 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE F 184 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL F 48 " --> pdb=" O ILE F 182 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 18 through 22 Processing sheet with id=AE4, first strand: chain 'F' and resid 89 through 90 Processing sheet with id=AE5, first strand: chain 'K' and resid 27 through 32 removed outlier: 6.507A pdb=" N VAL K 224 " --> pdb=" O MET K 79 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 27 through 32 removed outlier: 4.220A pdb=" N TYR K 135 " --> pdb=" O ALA K 62 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 18 through 22 removed outlier: 7.895A pdb=" N GLN G 44 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL G 186 " --> pdb=" O GLN G 44 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY G 46 " --> pdb=" O PHE G 184 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N PHE G 184 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL G 48 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 18 through 22 Processing sheet with id=AE9, first strand: chain 'G' and resid 89 through 90 Processing sheet with id=AF1, first strand: chain 'L' and resid 27 through 32 removed outlier: 8.123A pdb=" N VAL L 28 " --> pdb=" O ASN H 7 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR H 9 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE L 30 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR H 11 " --> pdb=" O PHE L 30 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE L 32 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP H 13 " --> pdb=" O PHE L 32 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR L 135 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 77 through 81 removed outlier: 6.544A pdb=" N VAL L 224 " --> pdb=" O MET L 79 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU L 60 " --> pdb=" O ILE L 151 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.703A pdb=" N GLY H 46 " --> pdb=" O ILE H 182 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE H 182 " --> pdb=" O GLY H 46 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL H 48 " --> pdb=" O PHE H 180 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE H 180 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 18 through 22 Processing sheet with id=AF5, first strand: chain 'H' and resid 89 through 90 Processing sheet with id=AF6, first strand: chain 'M' and resid 27 through 32 removed outlier: 4.176A pdb=" N TYR M 135 " --> pdb=" O ALA M 62 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 77 through 81 removed outlier: 6.559A pdb=" N VAL M 224 " --> pdb=" O MET M 79 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU M 60 " --> pdb=" O ILE M 151 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 18 through 22 removed outlier: 7.809A pdb=" N GLN I 44 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL I 186 " --> pdb=" O GLN I 44 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY I 46 " --> pdb=" O PHE I 184 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE I 184 " --> pdb=" O GLY I 46 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL I 48 " --> pdb=" O ILE I 182 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 18 through 22 Processing sheet with id=AG1, first strand: chain 'I' and resid 89 through 90 Processing sheet with id=AG2, first strand: chain 'N' and resid 27 through 32 removed outlier: 4.224A pdb=" N TYR N 135 " --> pdb=" O ALA N 62 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 77 through 81 removed outlier: 6.597A pdb=" N VAL N 224 " --> pdb=" O MET N 79 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU N 60 " --> pdb=" O ILE N 151 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 18 through 22 removed outlier: 3.757A pdb=" N GLY J 46 " --> pdb=" O ILE J 182 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE J 182 " --> pdb=" O GLY J 46 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL J 48 " --> pdb=" O PHE J 180 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE J 180 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 18 through 22 Processing sheet with id=AG6, first strand: chain 'J' and resid 89 through 90 Processing sheet with id=AG7, first strand: chain 'O' and resid 27 through 32 removed outlier: 7.884A pdb=" N VAL O 28 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N THR K 9 " --> pdb=" O VAL O 28 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE O 30 " --> pdb=" O THR K 9 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N THR K 11 " --> pdb=" O PHE O 30 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE O 32 " --> pdb=" O THR K 11 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP K 13 " --> pdb=" O PHE O 32 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR O 135 " --> pdb=" O ALA O 62 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 77 through 81 removed outlier: 6.558A pdb=" N VAL O 224 " --> pdb=" O MET O 79 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU O 60 " --> pdb=" O ILE O 151 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 18 through 22 removed outlier: 7.825A pdb=" N GLN K 44 " --> pdb=" O VAL K 186 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL K 186 " --> pdb=" O GLN K 44 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLY K 46 " --> pdb=" O PHE K 184 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE K 184 " --> pdb=" O GLY K 46 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL K 48 " --> pdb=" O ILE K 182 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 18 through 22 Processing sheet with id=AH2, first strand: chain 'K' and resid 89 through 90 Processing sheet with id=AH3, first strand: chain 'P' and resid 27 through 32 removed outlier: 6.620A pdb=" N VAL P 224 " --> pdb=" O MET P 79 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 27 through 32 removed outlier: 4.328A pdb=" N TYR P 135 " --> pdb=" O ALA P 62 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 18 through 22 removed outlier: 7.855A pdb=" N GLN L 44 " --> pdb=" O VAL L 186 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL L 186 " --> pdb=" O GLN L 44 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY L 46 " --> pdb=" O PHE L 184 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE L 184 " --> pdb=" O GLY L 46 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL L 48 " --> pdb=" O ILE L 182 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AH7, first strand: chain 'L' and resid 89 through 90 Processing sheet with id=AH8, first strand: chain 'M' and resid 18 through 22 removed outlier: 3.789A pdb=" N GLY M 46 " --> pdb=" O ILE M 182 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE M 182 " --> pdb=" O GLY M 46 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL M 48 " --> pdb=" O PHE M 180 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE M 180 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'M' and resid 18 through 22 Processing sheet with id=AI1, first strand: chain 'M' and resid 89 through 90 Processing sheet with id=AI2, first strand: chain 'N' and resid 18 through 22 removed outlier: 7.834A pdb=" N GLN N 44 " --> pdb=" O VAL N 186 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL N 186 " --> pdb=" O GLN N 44 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY N 46 " --> pdb=" O PHE N 184 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE N 184 " --> pdb=" O GLY N 46 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL N 48 " --> pdb=" O ILE N 182 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'N' and resid 18 through 22 Processing sheet with id=AI4, first strand: chain 'N' and resid 89 through 90 Processing sheet with id=AI5, first strand: chain 'O' and resid 18 through 22 removed outlier: 7.860A pdb=" N GLN O 44 " --> pdb=" O VAL O 186 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL O 186 " --> pdb=" O GLN O 44 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY O 46 " --> pdb=" O PHE O 184 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE O 184 " --> pdb=" O GLY O 46 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'O' and resid 18 through 22 Processing sheet with id=AI7, first strand: chain 'O' and resid 89 through 90 Processing sheet with id=AI8, first strand: chain 'P' and resid 18 through 22 removed outlier: 7.911A pdb=" N GLN P 44 " --> pdb=" O VAL P 186 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL P 186 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY P 46 " --> pdb=" O PHE P 184 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N PHE P 184 " --> pdb=" O GLY P 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL P 48 " --> pdb=" O ILE P 182 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'P' and resid 18 through 22 Processing sheet with id=AJ1, first strand: chain 'P' and resid 89 through 90 958 hydrogen bonds defined for protein. 2526 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: 5.95 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5817 1.33 - 1.45: 7314 1.45 - 1.57: 15797 1.57 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 29088 Sorted by residual: bond pdb=" C LYS G 104 " pdb=" N PRO G 105 " ideal model delta sigma weight residual 1.328 1.363 -0.034 1.26e-02 6.30e+03 7.47e+00 bond pdb=" C LYS G 104 " pdb=" O LYS G 104 " ideal model delta sigma weight residual 1.235 1.207 0.028 1.12e-02 7.97e+03 6.28e+00 bond pdb=" N LYS G 104 " pdb=" CA LYS G 104 " ideal model delta sigma weight residual 1.453 1.415 0.037 1.51e-02 4.39e+03 6.05e+00 bond pdb=" C ASN O 92 " pdb=" N LEU O 93 " ideal model delta sigma weight residual 1.331 1.301 0.030 2.07e-02 2.33e+03 2.15e+00 bond pdb=" C ASN F 92 " pdb=" N LEU F 93 " ideal model delta sigma weight residual 1.331 1.302 0.029 2.07e-02 2.33e+03 1.93e+00 ... (remaining 29083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 38523 1.61 - 3.22: 1089 3.22 - 4.83: 109 4.83 - 6.44: 34 6.44 - 8.06: 5 Bond angle restraints: 39760 Sorted by residual: angle pdb=" C ASP I 114 " pdb=" CA ASP I 114 " pdb=" CB ASP I 114 " ideal model delta sigma weight residual 116.54 109.64 6.90 1.15e+00 7.56e-01 3.60e+01 angle pdb=" N ASP I 114 " pdb=" CA ASP I 114 " pdb=" C ASP I 114 " ideal model delta sigma weight residual 108.31 114.05 -5.74 1.52e+00 4.33e-01 1.43e+01 angle pdb=" CA ASP I 114 " pdb=" C ASP I 114 " pdb=" N SER I 115 " ideal model delta sigma weight residual 119.52 116.69 2.83 7.90e-01 1.60e+00 1.28e+01 angle pdb=" CA LYS G 104 " pdb=" C LYS G 104 " pdb=" O LYS G 104 " ideal model delta sigma weight residual 120.97 117.86 3.11 1.05e+00 9.07e-01 8.78e+00 angle pdb=" CA ARG B 126 " pdb=" CB ARG B 126 " pdb=" CG ARG B 126 " ideal model delta sigma weight residual 114.10 120.00 -5.90 2.00e+00 2.50e-01 8.71e+00 ... (remaining 39755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 15182 18.07 - 36.14: 1582 36.14 - 54.21: 257 54.21 - 72.28: 41 72.28 - 90.35: 42 Dihedral angle restraints: 17104 sinusoidal: 6256 harmonic: 10848 Sorted by residual: dihedral pdb=" CA ASP L 201 " pdb=" C ASP L 201 " pdb=" N GLN L 202 " pdb=" CA GLN L 202 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ASP K 201 " pdb=" C ASP K 201 " pdb=" N GLN K 202 " pdb=" CA GLN K 202 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA GLU L 200 " pdb=" C GLU L 200 " pdb=" N ASP L 201 " pdb=" CA ASP L 201 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 17101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2465 0.028 - 0.055: 1197 0.055 - 0.083: 458 0.083 - 0.111: 283 0.111 - 0.139: 61 Chirality restraints: 4464 Sorted by residual: chirality pdb=" CA VAL E 80 " pdb=" N VAL E 80 " pdb=" C VAL E 80 " pdb=" CB VAL E 80 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA VAL A 80 " pdb=" N VAL A 80 " pdb=" C VAL A 80 " pdb=" CB VAL A 80 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA VAL M 80 " pdb=" N VAL M 80 " pdb=" C VAL M 80 " pdb=" CB VAL M 80 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 4461 not shown) Planarity restraints: 5344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 201 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C ASP B 201 " -0.066 2.00e-02 2.50e+03 pdb=" O ASP B 201 " 0.025 2.00e-02 2.50e+03 pdb=" N GLN B 202 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 104 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C LYS G 104 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS G 104 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO G 105 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA J 156 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO J 157 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO J 157 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 157 " 0.034 5.00e-02 4.00e+02 ... (remaining 5341 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 153 2.49 - 3.09: 20191 3.09 - 3.70: 42517 3.70 - 4.30: 63277 4.30 - 4.90: 109047 Nonbonded interactions: 235185 Sorted by model distance: nonbonded pdb=" O ASN O 110 " pdb=" OD1 ASN O 110 " model vdw 1.891 3.040 nonbonded pdb=" O ASN D 88 " pdb=" OD1 ASN D 88 " model vdw 2.184 3.040 nonbonded pdb=" NE2 GLN M 102 " pdb=" O LYS M 104 " model vdw 2.199 3.120 nonbonded pdb=" NE2 GLN K 102 " pdb=" O LYS K 104 " model vdw 2.202 3.120 nonbonded pdb=" NE2 GLN J 102 " pdb=" O LYS J 104 " model vdw 2.218 3.120 ... (remaining 235180 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 26.870 Find NCS groups from input model: 0.510 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: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 0.037 29088 Z= 0.170 Angle : 0.646 8.056 39760 Z= 0.363 Chirality : 0.042 0.139 4464 Planarity : 0.006 0.061 5344 Dihedral : 15.331 90.347 10192 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 1.29 % Allowed : 13.56 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.12), residues: 3744 helix: -2.14 (0.23), residues: 416 sheet: 0.10 (0.17), residues: 832 loop : -3.04 (0.10), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 113 TYR 0.015 0.001 TYR K 179 PHE 0.018 0.001 PHE F 65 TRP 0.011 0.001 TRP M 76 Details of bonding type rmsd covalent geometry : bond 0.00363 (29088) covalent geometry : angle 0.64638 (39760) hydrogen bonds : bond 0.18974 ( 767) hydrogen bonds : angle 9.39544 ( 2526) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 413 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7754 (pt0) cc_final: 0.6986 (mp0) REVERT: B 34 GLN cc_start: 0.7828 (mp10) cc_final: 0.7545 (mp10) REVERT: B 73 GLU cc_start: 0.7387 (tp30) cc_final: 0.7040 (tm-30) REVERT: C 22 MET cc_start: 0.9207 (ptm) cc_final: 0.8358 (ptp) REVERT: C 113 ARG cc_start: 0.6754 (tpp80) cc_final: 0.6444 (tpp80) REVERT: C 126 ARG cc_start: 0.8420 (ptt90) cc_final: 0.7900 (ttp80) REVERT: D 138 ARG cc_start: 0.8479 (ptm-80) cc_final: 0.8123 (ptm-80) REVERT: E 37 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8092 (mt-10) REVERT: F 15 GLN cc_start: 0.8930 (mt0) cc_final: 0.8676 (mt0) REVERT: F 131 GLU cc_start: 0.8234 (mp0) cc_final: 0.7827 (mp0) REVERT: G 79 MET cc_start: 0.9025 (mmt) cc_final: 0.8345 (mmt) REVERT: G 209 ASP cc_start: 0.7667 (t0) cc_final: 0.6870 (t0) REVERT: G 218 ARG cc_start: 0.8354 (mmm-85) cc_final: 0.7892 (mmt-90) REVERT: G 226 THR cc_start: 0.9003 (m) cc_final: 0.8573 (p) REVERT: H 131 GLU cc_start: 0.8360 (mp0) cc_final: 0.7917 (mp0) REVERT: I 175 ASN cc_start: 0.8220 (m-40) cc_final: 0.7883 (m-40) REVERT: J 34 GLN cc_start: 0.8586 (mm110) cc_final: 0.8347 (mm110) REVERT: J 149 ARG cc_start: 0.8709 (mtp180) cc_final: 0.8355 (mtt180) REVERT: K 209 ASP cc_start: 0.7952 (t0) cc_final: 0.7044 (t0) REVERT: L 202 GLN cc_start: 0.7351 (pm20) cc_final: 0.7091 (pm20) REVERT: M 131 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8651 (mt-10) REVERT: N 131 GLU cc_start: 0.8244 (mp0) cc_final: 0.7843 (mp0) REVERT: O 208 THR cc_start: 0.8989 (p) cc_final: 0.8703 (t) REVERT: O 214 ARG cc_start: 0.4691 (mtp85) cc_final: 0.4258 (mtt90) outliers start: 40 outliers final: 35 residues processed: 440 average time/residue: 0.1976 time to fit residues: 133.6197 Evaluate side-chains 398 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 363 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain H residue 12 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 182 ILE Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain N residue 22 MET Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 7 ASN A 99 GLN A 155 ASN B 1 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN C 1 ASN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN D 175 ASN F 99 GLN G 1 ASN G 7 ASN H 1 ASN L 34 GLN L 175 ASN M 175 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.090318 restraints weight = 49320.579| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.27 r_work: 0.3040 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29088 Z= 0.203 Angle : 0.636 7.530 39760 Z= 0.329 Chirality : 0.045 0.147 4464 Planarity : 0.006 0.070 5344 Dihedral : 6.546 73.771 4140 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.06 % Allowed : 13.66 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.12), residues: 3744 helix: -2.05 (0.23), residues: 416 sheet: -0.12 (0.17), residues: 832 loop : -2.95 (0.10), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 126 TYR 0.015 0.001 TYR K 179 PHE 0.013 0.001 PHE O 65 TRP 0.011 0.001 TRP M 76 Details of bonding type rmsd covalent geometry : bond 0.00493 (29088) covalent geometry : angle 0.63592 (39760) hydrogen bonds : bond 0.03595 ( 767) hydrogen bonds : angle 7.18105 ( 2526) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 394 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 ASN cc_start: 0.6893 (m110) cc_final: 0.6477 (t0) REVERT: A 207 GLU cc_start: 0.7773 (pt0) cc_final: 0.7089 (mp0) REVERT: B 207 GLU cc_start: 0.7916 (pm20) cc_final: 0.7642 (pm20) REVERT: C 22 MET cc_start: 0.9251 (ptm) cc_final: 0.8462 (ptp) REVERT: C 113 ARG cc_start: 0.6855 (tpp80) cc_final: 0.6620 (tpp80) REVERT: C 175 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7877 (m110) REVERT: C 200 GLU cc_start: 0.7461 (mp0) cc_final: 0.7195 (mp0) REVERT: D 131 GLU cc_start: 0.7901 (mp0) cc_final: 0.7684 (mp0) REVERT: D 138 ARG cc_start: 0.8541 (ptm-80) cc_final: 0.8019 (ptm-80) REVERT: F 15 GLN cc_start: 0.8926 (mt0) cc_final: 0.8648 (mt0) REVERT: F 131 GLU cc_start: 0.8257 (mp0) cc_final: 0.7777 (mp0) REVERT: F 159 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7830 (pp20) REVERT: F 194 TYR cc_start: 0.8406 (m-80) cc_final: 0.8130 (m-10) REVERT: G 131 GLU cc_start: 0.8075 (mp0) cc_final: 0.7740 (mp0) REVERT: G 209 ASP cc_start: 0.7636 (t0) cc_final: 0.6694 (t0) REVERT: G 218 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.7967 (mmt-90) REVERT: H 38 TYR cc_start: 0.9089 (m-80) cc_final: 0.8795 (m-80) REVERT: H 138 ARG cc_start: 0.8197 (ptm-80) cc_final: 0.7958 (ptm-80) REVERT: J 34 GLN cc_start: 0.8542 (mm110) cc_final: 0.8294 (mm110) REVERT: J 169 ASP cc_start: 0.7207 (p0) cc_final: 0.6954 (p0) REVERT: K 131 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: O 208 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8602 (t) REVERT: O 209 ASP cc_start: 0.7193 (t0) cc_final: 0.6928 (t0) REVERT: O 214 ARG cc_start: 0.4550 (mtp85) cc_final: 0.4250 (mtt90) outliers start: 95 outliers final: 61 residues processed: 465 average time/residue: 0.1867 time to fit residues: 133.1361 Evaluate side-chains 427 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 362 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain H residue 12 MET Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 22 MET Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain K residue 49 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 94 optimal weight: 10.0000 chunk 333 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 306 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 310 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 7 ASN B 23 GLN C 7 ASN C 15 GLN C 228 ASN E 175 ASN G 228 ASN J 228 ASN K 1 ASN K 175 ASN L 34 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.087153 restraints weight = 48767.708| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.05 r_work: 0.2982 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 29088 Z= 0.277 Angle : 0.697 10.030 39760 Z= 0.356 Chirality : 0.046 0.147 4464 Planarity : 0.007 0.072 5344 Dihedral : 6.601 52.490 4112 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 3.38 % Allowed : 15.11 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.18 (0.12), residues: 3744 helix: -2.13 (0.23), residues: 416 sheet: -0.34 (0.17), residues: 816 loop : -2.95 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 113 TYR 0.017 0.002 TYR K 179 PHE 0.014 0.001 PHE O 65 TRP 0.011 0.002 TRP M 76 Details of bonding type rmsd covalent geometry : bond 0.00669 (29088) covalent geometry : angle 0.69734 (39760) hydrogen bonds : bond 0.03572 ( 767) hydrogen bonds : angle 7.04817 ( 2526) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 368 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 ASN cc_start: 0.6858 (m110) cc_final: 0.6255 (t0) REVERT: A 207 GLU cc_start: 0.7772 (pt0) cc_final: 0.7232 (mp0) REVERT: B 207 GLU cc_start: 0.8108 (pm20) cc_final: 0.7817 (pm20) REVERT: C 200 GLU cc_start: 0.7614 (mp0) cc_final: 0.7293 (mp0) REVERT: D 138 ARG cc_start: 0.8537 (ptm-80) cc_final: 0.8103 (ptm-80) REVERT: F 102 GLN cc_start: 0.8246 (tt0) cc_final: 0.8035 (tt0) REVERT: F 131 GLU cc_start: 0.8218 (mp0) cc_final: 0.7683 (mp0) REVERT: F 159 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8305 (pp20) REVERT: F 194 TYR cc_start: 0.8480 (m-80) cc_final: 0.8193 (m-10) REVERT: G 79 MET cc_start: 0.9030 (mmt) cc_final: 0.8206 (mmt) REVERT: G 131 GLU cc_start: 0.8238 (mp0) cc_final: 0.7479 (mp0) REVERT: G 209 ASP cc_start: 0.7798 (t0) cc_final: 0.6929 (t0) REVERT: G 218 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.8040 (mmt-90) REVERT: G 226 THR cc_start: 0.9062 (m) cc_final: 0.8812 (p) REVERT: H 138 ARG cc_start: 0.8309 (ptm-80) cc_final: 0.8074 (ptm-80) REVERT: I 131 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8470 (mm-30) REVERT: I 218 ARG cc_start: 0.8367 (mtp85) cc_final: 0.8123 (mtp85) REVERT: J 34 GLN cc_start: 0.8596 (mm110) cc_final: 0.8299 (mm110) REVERT: J 90 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8686 (tt) REVERT: K 131 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: K 206 ASP cc_start: 0.8025 (t0) cc_final: 0.7755 (t0) REVERT: M 79 MET cc_start: 0.8824 (mmt) cc_final: 0.8601 (mmt) REVERT: M 131 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8634 (mt-10) REVERT: N 131 GLU cc_start: 0.8289 (mp0) cc_final: 0.7826 (mp0) REVERT: O 209 ASP cc_start: 0.7149 (t0) cc_final: 0.6623 (t0) REVERT: O 214 ARG cc_start: 0.4880 (mtp85) cc_final: 0.4506 (mtt90) outliers start: 105 outliers final: 82 residues processed: 442 average time/residue: 0.2081 time to fit residues: 140.7424 Evaluate side-chains 435 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 350 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 22 MET Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain K residue 49 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 110 ASN Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 1 ASN Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 190 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 243 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 305 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 213 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 351 optimal weight: 6.9990 chunk 360 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN E 228 ASN I 23 GLN L 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.089953 restraints weight = 48150.831| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.05 r_work: 0.3031 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29088 Z= 0.166 Angle : 0.605 8.265 39760 Z= 0.311 Chirality : 0.044 0.135 4464 Planarity : 0.006 0.071 5344 Dihedral : 6.124 40.804 4107 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.35 % Allowed : 16.43 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.12), residues: 3744 helix: -1.97 (0.24), residues: 416 sheet: -0.33 (0.17), residues: 816 loop : -2.89 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 113 TYR 0.014 0.001 TYR K 179 PHE 0.009 0.001 PHE O 65 TRP 0.008 0.001 TRP H 76 Details of bonding type rmsd covalent geometry : bond 0.00407 (29088) covalent geometry : angle 0.60468 (39760) hydrogen bonds : bond 0.03008 ( 767) hydrogen bonds : angle 6.64156 ( 2526) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 377 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6672 (mt-10) REVERT: A 110 ASN cc_start: 0.6887 (m110) cc_final: 0.6261 (t0) REVERT: A 207 GLU cc_start: 0.7656 (pt0) cc_final: 0.7157 (mp0) REVERT: B 207 GLU cc_start: 0.7945 (pm20) cc_final: 0.7725 (pm20) REVERT: C 22 MET cc_start: 0.9082 (ptm) cc_final: 0.8398 (ptp) REVERT: C 218 ARG cc_start: 0.7973 (ptp-110) cc_final: 0.7746 (ptp-110) REVERT: D 131 GLU cc_start: 0.7965 (mp0) cc_final: 0.7515 (mp0) REVERT: D 138 ARG cc_start: 0.8519 (ptm-80) cc_final: 0.8085 (ptm-80) REVERT: F 102 GLN cc_start: 0.8051 (tt0) cc_final: 0.7841 (tt0) REVERT: F 131 GLU cc_start: 0.8203 (mp0) cc_final: 0.7681 (mp0) REVERT: F 138 ARG cc_start: 0.8241 (ptt-90) cc_final: 0.7661 (ttp-110) REVERT: F 159 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8043 (pp20) REVERT: F 194 TYR cc_start: 0.8398 (m-80) cc_final: 0.8088 (m-10) REVERT: G 79 MET cc_start: 0.8960 (mmt) cc_final: 0.7960 (mmt) REVERT: G 131 GLU cc_start: 0.8058 (mp0) cc_final: 0.7537 (mp0) REVERT: G 209 ASP cc_start: 0.7720 (t0) cc_final: 0.6853 (t0) REVERT: G 218 ARG cc_start: 0.8232 (mmm-85) cc_final: 0.7979 (mmt-90) REVERT: H 138 ARG cc_start: 0.8237 (ptm-80) cc_final: 0.7976 (ptm-80) REVERT: I 175 ASN cc_start: 0.8047 (m-40) cc_final: 0.7711 (m-40) REVERT: J 149 ARG cc_start: 0.8560 (mtp180) cc_final: 0.8310 (mtt180) REVERT: J 169 ASP cc_start: 0.7033 (p0) cc_final: 0.6545 (p0) REVERT: K 131 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8198 (mp0) REVERT: M 79 MET cc_start: 0.8738 (mmt) cc_final: 0.8477 (mmt) REVERT: M 218 ARG cc_start: 0.8429 (mmt90) cc_final: 0.8168 (mmm-85) REVERT: N 200 GLU cc_start: 0.7324 (mp0) cc_final: 0.6935 (mp0) REVERT: O 209 ASP cc_start: 0.7068 (t0) cc_final: 0.6472 (t0) REVERT: O 214 ARG cc_start: 0.4695 (mtp85) cc_final: 0.4301 (mtt90) outliers start: 104 outliers final: 75 residues processed: 446 average time/residue: 0.2049 time to fit residues: 139.3617 Evaluate side-chains 435 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 358 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 38 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 22 MET Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain K residue 49 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 110 ASN Chi-restraints excluded: chain O residue 131 GLU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 190 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 212 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 196 optimal weight: 10.0000 chunk 302 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 310 optimal weight: 9.9990 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 202 GLN B 23 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN L 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088597 restraints weight = 48543.192| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.04 r_work: 0.3009 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29088 Z= 0.214 Angle : 0.637 9.572 39760 Z= 0.326 Chirality : 0.045 0.139 4464 Planarity : 0.006 0.070 5344 Dihedral : 6.188 41.984 4101 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 3.70 % Allowed : 17.40 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.12), residues: 3744 helix: -1.95 (0.24), residues: 416 sheet: -0.37 (0.18), residues: 816 loop : -2.87 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 113 TYR 0.016 0.001 TYR K 179 PHE 0.011 0.001 PHE O 65 TRP 0.008 0.001 TRP M 76 Details of bonding type rmsd covalent geometry : bond 0.00520 (29088) covalent geometry : angle 0.63747 (39760) hydrogen bonds : bond 0.03157 ( 767) hydrogen bonds : angle 6.69130 ( 2526) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 368 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7601 (pt0) cc_final: 0.7162 (mp0) REVERT: B 37 GLU cc_start: 0.7855 (tt0) cc_final: 0.7556 (tt0) REVERT: B 73 GLU cc_start: 0.7493 (tp30) cc_final: 0.7010 (tm-30) REVERT: B 207 GLU cc_start: 0.7845 (pm20) cc_final: 0.7624 (pm20) REVERT: C 22 MET cc_start: 0.9056 (ptm) cc_final: 0.8343 (ptp) REVERT: C 131 GLU cc_start: 0.8254 (mp0) cc_final: 0.7962 (mp0) REVERT: D 37 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7916 (tt0) REVERT: D 138 ARG cc_start: 0.8489 (ptm-80) cc_final: 0.8064 (ptm-80) REVERT: F 102 GLN cc_start: 0.8137 (tt0) cc_final: 0.7898 (tt0) REVERT: F 131 GLU cc_start: 0.8230 (mp0) cc_final: 0.7667 (mp0) REVERT: F 138 ARG cc_start: 0.8260 (ptt-90) cc_final: 0.7692 (ttp-110) REVERT: G 131 GLU cc_start: 0.8117 (mp0) cc_final: 0.7634 (mp0) REVERT: G 209 ASP cc_start: 0.7776 (t0) cc_final: 0.6873 (t0) REVERT: G 218 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.8023 (mmt-90) REVERT: H 38 TYR cc_start: 0.9132 (m-80) cc_final: 0.8890 (m-80) REVERT: H 138 ARG cc_start: 0.8231 (ptm-80) cc_final: 0.7949 (ptm-80) REVERT: J 149 ARG cc_start: 0.8584 (mtp180) cc_final: 0.8079 (mtt180) REVERT: J 169 ASP cc_start: 0.7069 (p0) cc_final: 0.6546 (p0) REVERT: K 131 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8210 (mp0) REVERT: M 79 MET cc_start: 0.8770 (mmt) cc_final: 0.8524 (mmt) REVERT: N 131 GLU cc_start: 0.8202 (mp0) cc_final: 0.7688 (mp0) REVERT: O 206 ASP cc_start: 0.8643 (t0) cc_final: 0.8405 (t70) REVERT: O 209 ASP cc_start: 0.7274 (t0) cc_final: 0.6544 (t0) REVERT: O 214 ARG cc_start: 0.4892 (mtp85) cc_final: 0.4451 (mtt90) outliers start: 115 outliers final: 92 residues processed: 455 average time/residue: 0.2029 time to fit residues: 142.4455 Evaluate side-chains 440 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 347 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 22 MET Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain K residue 49 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 110 ASN Chi-restraints excluded: chain O residue 131 GLU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 1 ASN Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 234 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 166 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 286 optimal weight: 7.9990 chunk 346 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 300 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 23 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN L 34 GLN N 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.105866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.088013 restraints weight = 48586.964| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.04 r_work: 0.2980 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 29088 Z= 0.238 Angle : 0.655 9.911 39760 Z= 0.335 Chirality : 0.045 0.139 4464 Planarity : 0.006 0.072 5344 Dihedral : 6.280 43.538 4101 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 4.25 % Allowed : 17.85 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.12 (0.12), residues: 3744 helix: -2.01 (0.24), residues: 416 sheet: -0.41 (0.18), residues: 816 loop : -2.87 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 113 TYR 0.017 0.001 TYR K 179 PHE 0.011 0.001 PHE O 65 TRP 0.011 0.001 TRP D 76 Details of bonding type rmsd covalent geometry : bond 0.00576 (29088) covalent geometry : angle 0.65489 (39760) hydrogen bonds : bond 0.03209 ( 767) hydrogen bonds : angle 6.72680 ( 2526) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 355 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7241 (mt-10) REVERT: A 202 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: A 207 GLU cc_start: 0.7640 (pt0) cc_final: 0.7170 (mp0) REVERT: B 73 GLU cc_start: 0.7500 (tp30) cc_final: 0.6936 (tm-30) REVERT: B 207 GLU cc_start: 0.7855 (pm20) cc_final: 0.7639 (pm20) REVERT: C 22 MET cc_start: 0.9088 (ptm) cc_final: 0.8357 (ptp) REVERT: C 182 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8499 (mt) REVERT: D 37 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7898 (mt-10) REVERT: D 131 GLU cc_start: 0.7995 (mp0) cc_final: 0.7551 (mp0) REVERT: E 218 ARG cc_start: 0.8009 (ptp-110) cc_final: 0.7797 (ptp-110) REVERT: F 37 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8405 (tt0) REVERT: F 102 GLN cc_start: 0.8193 (tt0) cc_final: 0.7969 (tt0) REVERT: F 131 GLU cc_start: 0.8293 (mp0) cc_final: 0.7665 (mp0) REVERT: F 138 ARG cc_start: 0.8288 (ptt-90) cc_final: 0.7705 (ttp-110) REVERT: F 159 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8335 (pp20) REVERT: G 79 MET cc_start: 0.8993 (mmt) cc_final: 0.8536 (mmt) REVERT: G 131 GLU cc_start: 0.8156 (mp0) cc_final: 0.7635 (mp0) REVERT: G 209 ASP cc_start: 0.7794 (t0) cc_final: 0.6861 (t0) REVERT: G 218 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.7991 (mmt-90) REVERT: H 38 TYR cc_start: 0.9129 (m-80) cc_final: 0.8862 (m-80) REVERT: H 138 ARG cc_start: 0.8284 (ptm-80) cc_final: 0.7984 (ptm-80) REVERT: J 90 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8781 (tp) REVERT: J 149 ARG cc_start: 0.8557 (mtp180) cc_final: 0.8052 (mtt180) REVERT: J 169 ASP cc_start: 0.7138 (p0) cc_final: 0.6636 (p0) REVERT: K 131 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: M 79 MET cc_start: 0.8782 (mmt) cc_final: 0.8512 (mmt) REVERT: N 200 GLU cc_start: 0.7259 (mp0) cc_final: 0.6832 (mp0) REVERT: O 206 ASP cc_start: 0.8687 (t0) cc_final: 0.8462 (t70) REVERT: O 209 ASP cc_start: 0.7329 (t0) cc_final: 0.6588 (t0) REVERT: O 214 ARG cc_start: 0.4822 (mtp85) cc_final: 0.4423 (mtt90) outliers start: 132 outliers final: 108 residues processed: 454 average time/residue: 0.1986 time to fit residues: 138.7822 Evaluate side-chains 459 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 346 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 49 ASP Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 22 MET Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain K residue 49 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 110 ASN Chi-restraints excluded: chain O residue 131 GLU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 1 ASN Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 234 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 154 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 312 optimal weight: 7.9990 chunk 288 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 349 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 296 optimal weight: 8.9990 chunk 281 optimal weight: 5.9990 chunk 329 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 23 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN H 102 GLN L 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.103371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.085607 restraints weight = 49085.571| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.03 r_work: 0.2958 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 29088 Z= 0.336 Angle : 0.737 11.264 39760 Z= 0.376 Chirality : 0.048 0.155 4464 Planarity : 0.007 0.074 5344 Dihedral : 6.660 50.694 4101 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 4.09 % Allowed : 18.30 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.23 (0.12), residues: 3744 helix: -2.13 (0.23), residues: 416 sheet: -0.53 (0.17), residues: 816 loop : -2.92 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 113 TYR 0.018 0.002 TYR K 179 PHE 0.013 0.002 PHE O 65 TRP 0.011 0.002 TRP D 76 Details of bonding type rmsd covalent geometry : bond 0.00809 (29088) covalent geometry : angle 0.73731 (39760) hydrogen bonds : bond 0.03547 ( 767) hydrogen bonds : angle 6.94878 ( 2526) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 364 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7505 (mt-10) cc_final: 0.6897 (mt-10) REVERT: A 202 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: B 73 GLU cc_start: 0.7574 (tp30) cc_final: 0.7060 (tm-30) REVERT: B 207 GLU cc_start: 0.7898 (pm20) cc_final: 0.7695 (pm20) REVERT: C 159 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7179 (pp20) REVERT: C 182 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8556 (mt) REVERT: D 37 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7887 (mt-10) REVERT: F 102 GLN cc_start: 0.8393 (tt0) cc_final: 0.8167 (tt0) REVERT: F 131 GLU cc_start: 0.8242 (mp0) cc_final: 0.7570 (mp0) REVERT: F 138 ARG cc_start: 0.8283 (ptt-90) cc_final: 0.7961 (ptt90) REVERT: F 159 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8430 (pp20) REVERT: G 131 GLU cc_start: 0.8195 (mp0) cc_final: 0.7706 (mp0) REVERT: G 209 ASP cc_start: 0.7750 (t0) cc_final: 0.6818 (t0) REVERT: G 218 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.8022 (mmt-90) REVERT: H 38 TYR cc_start: 0.9206 (m-80) cc_final: 0.8982 (m-80) REVERT: H 138 ARG cc_start: 0.8305 (ptm-80) cc_final: 0.7996 (ptm-80) REVERT: I 131 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8396 (mm-30) REVERT: J 90 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8765 (tp) REVERT: K 131 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: N 131 GLU cc_start: 0.8272 (mp0) cc_final: 0.7757 (mp0) REVERT: O 209 ASP cc_start: 0.7390 (t0) cc_final: 0.6603 (t0) REVERT: O 214 ARG cc_start: 0.5011 (mtp85) cc_final: 0.4665 (mtt90) REVERT: P 209 ASP cc_start: 0.7596 (t0) cc_final: 0.6622 (t0) outliers start: 127 outliers final: 103 residues processed: 460 average time/residue: 0.1878 time to fit residues: 134.2379 Evaluate side-chains 459 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 350 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 49 ASP Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 102 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 22 MET Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain K residue 49 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 110 ASN Chi-restraints excluded: chain O residue 131 GLU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 1 ASN Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 234 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 334 optimal weight: 0.0030 chunk 329 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 359 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN C 15 GLN C 34 GLN E 132 ASN G 23 GLN G 132 ASN G 228 ASN J 228 ASN L 34 GLN N 132 ASN N 228 ASN O 132 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092866 restraints weight = 47994.912| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.05 r_work: 0.3073 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29088 Z= 0.110 Angle : 0.567 6.726 39760 Z= 0.294 Chirality : 0.043 0.140 4464 Planarity : 0.006 0.073 5344 Dihedral : 5.847 47.625 4101 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.58 % Allowed : 19.88 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.05 (0.12), residues: 3744 helix: -1.85 (0.25), residues: 416 sheet: -0.39 (0.18), residues: 816 loop : -2.83 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 113 TYR 0.017 0.001 TYR F 194 PHE 0.007 0.001 PHE O 184 TRP 0.006 0.001 TRP D 76 Details of bonding type rmsd covalent geometry : bond 0.00274 (29088) covalent geometry : angle 0.56665 (39760) hydrogen bonds : bond 0.02688 ( 767) hydrogen bonds : angle 6.30443 ( 2526) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 402 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 202 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7460 (pm20) REVERT: B 73 GLU cc_start: 0.7588 (tp30) cc_final: 0.7114 (tm-30) REVERT: C 22 MET cc_start: 0.9011 (ptm) cc_final: 0.8333 (ptp) REVERT: C 34 GLN cc_start: 0.7971 (mp-120) cc_final: 0.7726 (mp10) REVERT: C 45 TYR cc_start: 0.8775 (m-80) cc_final: 0.8538 (m-80) REVERT: C 95 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8675 (tt) REVERT: D 37 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7848 (mt-10) REVERT: D 126 ARG cc_start: 0.6569 (ptt90) cc_final: 0.5933 (ttp80) REVERT: E 37 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8470 (tt0) REVERT: F 37 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8195 (tt0) REVERT: F 131 GLU cc_start: 0.8249 (mp0) cc_final: 0.7688 (mp0) REVERT: F 138 ARG cc_start: 0.8271 (ptt-90) cc_final: 0.7788 (ttp-110) REVERT: F 207 GLU cc_start: 0.7221 (mp0) cc_final: 0.6983 (mp0) REVERT: G 131 GLU cc_start: 0.8114 (mp0) cc_final: 0.7727 (mp0) REVERT: G 202 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6505 (pm20) REVERT: G 209 ASP cc_start: 0.7635 (t0) cc_final: 0.6759 (t0) REVERT: G 218 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.7996 (mmt-90) REVERT: H 138 ARG cc_start: 0.8222 (ptm-80) cc_final: 0.7983 (ptm-80) REVERT: I 65 PHE cc_start: 0.9066 (t80) cc_final: 0.8591 (t80) REVERT: I 175 ASN cc_start: 0.7942 (m-40) cc_final: 0.7620 (m-40) REVERT: J 169 ASP cc_start: 0.7013 (p0) cc_final: 0.6523 (p0) REVERT: M 79 MET cc_start: 0.8529 (mmt) cc_final: 0.8236 (mtt) REVERT: M 218 ARG cc_start: 0.8263 (mmt90) cc_final: 0.8006 (mmm-85) REVERT: N 131 GLU cc_start: 0.8059 (mp0) cc_final: 0.7602 (mp0) REVERT: N 200 GLU cc_start: 0.7219 (mp0) cc_final: 0.6768 (mp0) REVERT: O 209 ASP cc_start: 0.7160 (t0) cc_final: 0.6494 (t0) REVERT: O 214 ARG cc_start: 0.4881 (mtp85) cc_final: 0.4511 (mtt90) outliers start: 80 outliers final: 54 residues processed: 461 average time/residue: 0.1882 time to fit residues: 133.6438 Evaluate side-chains 429 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 372 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 38 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 22 MET Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 131 GLU Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 167 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 303 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN G 228 ASN H 102 GLN J 228 ASN L 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.089458 restraints weight = 48419.141| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.04 r_work: 0.3021 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 29088 Z= 0.189 Angle : 0.623 8.282 39760 Z= 0.320 Chirality : 0.044 0.154 4464 Planarity : 0.006 0.075 5344 Dihedral : 6.019 44.951 4101 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 2.51 % Allowed : 19.81 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.01 (0.12), residues: 3744 helix: -1.88 (0.24), residues: 416 sheet: -0.37 (0.18), residues: 816 loop : -2.79 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 113 TYR 0.019 0.001 TYR F 194 PHE 0.009 0.001 PHE J 65 TRP 0.009 0.001 TRP D 76 Details of bonding type rmsd covalent geometry : bond 0.00459 (29088) covalent geometry : angle 0.62297 (39760) hydrogen bonds : bond 0.02954 ( 767) hydrogen bonds : angle 6.47759 ( 2526) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 370 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: B 73 GLU cc_start: 0.7564 (tp30) cc_final: 0.7096 (tm-30) REVERT: C 22 MET cc_start: 0.9071 (ptm) cc_final: 0.8398 (ptp) REVERT: C 200 GLU cc_start: 0.7596 (mp0) cc_final: 0.7031 (mp0) REVERT: D 37 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7900 (mt-10) REVERT: D 126 ARG cc_start: 0.6613 (ptt90) cc_final: 0.5946 (ttp80) REVERT: D 200 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: E 37 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8402 (tt0) REVERT: F 131 GLU cc_start: 0.8265 (mp0) cc_final: 0.7638 (mp0) REVERT: F 138 ARG cc_start: 0.8267 (ptt-90) cc_final: 0.7767 (ttp-110) REVERT: F 207 GLU cc_start: 0.7199 (mp0) cc_final: 0.6882 (mp0) REVERT: G 131 GLU cc_start: 0.8122 (mp0) cc_final: 0.7659 (mp0) REVERT: G 209 ASP cc_start: 0.7739 (t0) cc_final: 0.6853 (t0) REVERT: G 218 ARG cc_start: 0.8224 (mmm-85) cc_final: 0.7969 (mmt-90) REVERT: H 38 TYR cc_start: 0.9067 (m-80) cc_final: 0.8830 (m-80) REVERT: H 131 GLU cc_start: 0.7983 (mp0) cc_final: 0.7781 (mp0) REVERT: H 138 ARG cc_start: 0.8203 (ptm-80) cc_final: 0.7923 (ptm-80) REVERT: I 175 ASN cc_start: 0.8003 (m-40) cc_final: 0.7653 (m-40) REVERT: J 169 ASP cc_start: 0.7044 (p0) cc_final: 0.6534 (p0) REVERT: K 131 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: L 79 MET cc_start: 0.8997 (mmt) cc_final: 0.8777 (mmt) REVERT: M 79 MET cc_start: 0.8661 (mmt) cc_final: 0.8187 (mtt) REVERT: M 218 ARG cc_start: 0.8407 (mmt90) cc_final: 0.8148 (mmm-85) REVERT: N 34 GLN cc_start: 0.8553 (mt0) cc_final: 0.8342 (mt0) REVERT: N 131 GLU cc_start: 0.8157 (mp0) cc_final: 0.7734 (mp0) REVERT: N 200 GLU cc_start: 0.7271 (mp0) cc_final: 0.6832 (mp0) REVERT: O 209 ASP cc_start: 0.7271 (t0) cc_final: 0.6541 (t0) REVERT: O 214 ARG cc_start: 0.4876 (mtp85) cc_final: 0.4398 (mtt90) REVERT: P 209 ASP cc_start: 0.7450 (t0) cc_final: 0.6639 (t0) outliers start: 78 outliers final: 67 residues processed: 425 average time/residue: 0.1947 time to fit residues: 128.2775 Evaluate side-chains 432 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 362 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 38 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 49 ASP Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 102 GLN Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 22 MET Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 131 GLU Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 238 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 218 optimal weight: 0.2980 chunk 122 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 202 optimal weight: 0.8980 chunk 214 optimal weight: 4.9990 chunk 359 optimal weight: 0.2980 chunk 47 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN C 34 GLN G 228 ASN L 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092808 restraints weight = 47847.265| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.06 r_work: 0.3072 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29088 Z= 0.122 Angle : 0.574 8.680 39760 Z= 0.297 Chirality : 0.043 0.156 4464 Planarity : 0.006 0.071 5344 Dihedral : 5.712 43.854 4101 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.09 % Allowed : 20.26 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.93 (0.12), residues: 3744 helix: -1.81 (0.25), residues: 416 sheet: -0.30 (0.18), residues: 816 loop : -2.74 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 113 TYR 0.017 0.001 TYR O 179 PHE 0.007 0.001 PHE H 101 TRP 0.007 0.001 TRP I 76 Details of bonding type rmsd covalent geometry : bond 0.00301 (29088) covalent geometry : angle 0.57388 (39760) hydrogen bonds : bond 0.02652 ( 767) hydrogen bonds : angle 6.22150 ( 2526) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 389 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7264 (mt-10) REVERT: A 202 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: A 207 GLU cc_start: 0.7476 (pt0) cc_final: 0.6975 (mp0) REVERT: B 73 GLU cc_start: 0.7562 (tp30) cc_final: 0.7230 (tm-30) REVERT: C 22 MET cc_start: 0.9008 (ptm) cc_final: 0.8364 (ptp) REVERT: C 45 TYR cc_start: 0.8805 (m-80) cc_final: 0.8598 (m-80) REVERT: C 95 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8644 (tt) REVERT: C 200 GLU cc_start: 0.7605 (mp0) cc_final: 0.7048 (mp0) REVERT: D 37 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7749 (mt-10) REVERT: D 38 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.7080 (t80) REVERT: D 200 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: E 37 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8464 (tt0) REVERT: E 218 ARG cc_start: 0.7640 (ptp-110) cc_final: 0.7354 (ptp90) REVERT: F 15 GLN cc_start: 0.8935 (mt0) cc_final: 0.8618 (mt0) REVERT: F 131 GLU cc_start: 0.8221 (mp0) cc_final: 0.7658 (mp0) REVERT: F 138 ARG cc_start: 0.8234 (ptt-90) cc_final: 0.7773 (ttp-110) REVERT: F 207 GLU cc_start: 0.7174 (mp0) cc_final: 0.6919 (mp0) REVERT: G 131 GLU cc_start: 0.8059 (mp0) cc_final: 0.7643 (mp0) REVERT: G 202 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6490 (pm20) REVERT: G 209 ASP cc_start: 0.7625 (t0) cc_final: 0.6727 (t0) REVERT: G 218 ARG cc_start: 0.8152 (mmm-85) cc_final: 0.7934 (mmt-90) REVERT: H 138 ARG cc_start: 0.8177 (ptm-80) cc_final: 0.7935 (ptm-80) REVERT: I 65 PHE cc_start: 0.9059 (t80) cc_final: 0.8625 (t80) REVERT: I 175 ASN cc_start: 0.7912 (m-40) cc_final: 0.7552 (m-40) REVERT: J 169 ASP cc_start: 0.6920 (p0) cc_final: 0.6455 (p0) REVERT: K 131 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: M 79 MET cc_start: 0.8546 (mmt) cc_final: 0.8198 (mtt) REVERT: M 218 ARG cc_start: 0.8218 (mmt90) cc_final: 0.7960 (mmm-85) REVERT: N 34 GLN cc_start: 0.8460 (mt0) cc_final: 0.8259 (mt0) REVERT: N 131 GLU cc_start: 0.8065 (mp0) cc_final: 0.7568 (mp0) REVERT: N 200 GLU cc_start: 0.7280 (mp0) cc_final: 0.6884 (mp0) REVERT: O 209 ASP cc_start: 0.7070 (t0) cc_final: 0.6407 (t0) REVERT: O 214 ARG cc_start: 0.4918 (mtp85) cc_final: 0.4422 (mtt90) REVERT: P 209 ASP cc_start: 0.7309 (t0) cc_final: 0.6547 (t0) outliers start: 65 outliers final: 54 residues processed: 436 average time/residue: 0.2082 time to fit residues: 139.5329 Evaluate side-chains 431 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 371 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 38 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 49 ASP Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 22 MET Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 131 GLU Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 79 optimal weight: 9.9990 chunk 264 optimal weight: 0.3980 chunk 236 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 249 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 92 ASN C 34 GLN H 15 GLN J 102 GLN L 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092424 restraints weight = 47845.672| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.06 r_work: 0.3070 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29088 Z= 0.129 Angle : 0.582 8.445 39760 Z= 0.301 Chirality : 0.043 0.172 4464 Planarity : 0.006 0.072 5344 Dihedral : 5.628 44.179 4098 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.16 % Allowed : 20.52 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.88 (0.12), residues: 3744 helix: -1.77 (0.25), residues: 416 sheet: -0.25 (0.18), residues: 816 loop : -2.72 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 113 TYR 0.014 0.001 TYR K 179 PHE 0.014 0.001 PHE D 65 TRP 0.007 0.001 TRP D 76 Details of bonding type rmsd covalent geometry : bond 0.00319 (29088) covalent geometry : angle 0.58184 (39760) hydrogen bonds : bond 0.02676 ( 767) hydrogen bonds : angle 6.21039 ( 2526) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6271.24 seconds wall clock time: 108 minutes 21.38 seconds (6501.38 seconds total)