Starting phenix.real_space_refine on Mon May 26 10:39:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ikj_60656/05_2025/9ikj_60656_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ikj_60656/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ikj_60656/05_2025/9ikj_60656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ikj_60656/05_2025/9ikj_60656.map" model { file = "/net/cci-nas-00/data/ceres_data/9ikj_60656/05_2025/9ikj_60656_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ikj_60656/05_2025/9ikj_60656_neut.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.78, per 1000 atoms: 0.59 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: 7.94 Conformation dependent library (CDL) restraints added in 4.1 seconds 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: 4.79 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: 10.01 Time building geometry restraints manager: 9.09 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: 0.02 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 65.210 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.150 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.001 TRP M 76 PHE 0.018 0.001 PHE F 65 TYR 0.015 0.001 TYR K 179 ARG 0.011 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.18974 ( 767) hydrogen bonds : angle 9.39544 ( 2526) covalent geometry : bond 0.00363 (29088) covalent geometry : angle 0.64638 (39760) *********************** 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 : 3.472 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: 0.4315 time to fit residues: 291.9082 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 : 3.149 ------------------------------------------------------------------------------- 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 310 optimal weight: 9.9990 chunk 278 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 288 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 chunk 334 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN C 75 ASN C 175 ASN D 175 ASN E 175 ASN F 99 GLN G 1 ASN G 7 ASN H 1 ASN J 228 ASN K 175 ASN L 34 GLN L 175 ASN M 175 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.085239 restraints weight = 50168.038| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.21 r_work: 0.2966 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.117 29088 Z= 0.450 Angle : 0.841 11.355 39760 Z= 0.431 Chirality : 0.052 0.183 4464 Planarity : 0.007 0.081 5344 Dihedral : 7.568 75.853 4140 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 4.03 % Allowed : 15.05 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.12), residues: 3744 helix: -2.32 (0.22), residues: 416 sheet: -0.37 (0.17), residues: 832 loop : -3.07 (0.10), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP M 76 PHE 0.020 0.002 PHE O 65 TYR 0.021 0.002 TYR K 179 ARG 0.007 0.001 ARG C 126 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 767) hydrogen bonds : angle 7.58671 ( 2526) covalent geometry : bond 0.01086 (29088) covalent geometry : angle 0.84090 (39760) *********************** 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 491 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 366 time to evaluate : 2.974 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8503 (pt0) REVERT: B 196 ARG cc_start: 0.8915 (mmm-85) cc_final: 0.8409 (mmt90) REVERT: B 207 GLU cc_start: 0.8258 (pm20) cc_final: 0.7901 (pm20) REVERT: C 159 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7126 (pp20) REVERT: C 175 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7987 (m110) REVERT: C 200 GLU cc_start: 0.7632 (mp0) cc_final: 0.7377 (mp0) REVERT: D 131 GLU cc_start: 0.7966 (mp0) cc_final: 0.7758 (mp0) REVERT: D 138 ARG cc_start: 0.8619 (ptm-80) cc_final: 0.8171 (ptm-80) REVERT: D 200 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: F 131 GLU cc_start: 0.8264 (mp0) cc_final: 0.7859 (mp0) REVERT: F 159 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8403 (pp20) REVERT: F 194 TYR cc_start: 0.8610 (m-80) cc_final: 0.8213 (m-10) REVERT: G 131 GLU cc_start: 0.8206 (mp0) cc_final: 0.7750 (mp0) REVERT: G 149 ARG cc_start: 0.8816 (mtp180) cc_final: 0.8613 (mtp85) REVERT: G 209 ASP cc_start: 0.7877 (t0) cc_final: 0.6907 (t0) REVERT: G 218 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.8020 (mmt-90) REVERT: G 226 THR cc_start: 0.9191 (m) cc_final: 0.8958 (p) REVERT: G 233 MET cc_start: 0.8723 (ttp) cc_final: 0.8519 (ttp) REVERT: H 38 TYR cc_start: 0.9195 (m-80) cc_final: 0.8915 (m-80) REVERT: H 131 GLU cc_start: 0.8650 (mp0) cc_final: 0.8380 (mp0) REVERT: H 138 ARG cc_start: 0.8351 (ptm-80) cc_final: 0.8057 (ptm-80) REVERT: I 218 ARG cc_start: 0.8392 (mtp85) cc_final: 0.8071 (mtp85) REVERT: J 12 MET cc_start: 0.9248 (ttp) cc_final: 0.9048 (ttp) REVERT: J 34 GLN cc_start: 0.8599 (mm110) cc_final: 0.8326 (mm110) REVERT: J 149 ARG cc_start: 0.8977 (mtp180) cc_final: 0.8765 (mtt180) REVERT: J 169 ASP cc_start: 0.7354 (p0) cc_final: 0.6990 (p0) REVERT: K 131 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: M 79 MET cc_start: 0.8868 (mmt) cc_final: 0.8624 (mmt) REVERT: N 131 GLU cc_start: 0.8460 (mp0) cc_final: 0.8216 (mp0) REVERT: N 200 GLU cc_start: 0.7452 (mp0) cc_final: 0.7080 (mp0) REVERT: O 209 ASP cc_start: 0.7316 (t0) cc_final: 0.7094 (t0) REVERT: O 214 ARG cc_start: 0.4833 (mtp85) cc_final: 0.4533 (mtt90) outliers start: 125 outliers final: 90 residues processed: 460 average time/residue: 0.4330 time to fit residues: 306.2566 Evaluate side-chains 439 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 343 time to evaluate : 3.248 ------------------------------------------------------------------------------- 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 29 SER 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 95 ILE Chi-restraints excluded: chain C residue 159 GLU 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 145 SER Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 200 GLU 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 95 ILE Chi-restraints excluded: chain E residue 134 VAL 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 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 G residue 95 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 234 VAL 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 97 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 90 ILE 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 208 THR Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain L residue 22 MET 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 114 ASP 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 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 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 134 VAL 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 39 ILE Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 90 ILE Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 190 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 278 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 281 optimal weight: 0.9990 chunk 337 optimal weight: 2.9990 chunk 279 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 C 1 ASN D 44 GLN E 132 ASN I 23 GLN J 228 ASN K 1 ASN L 34 GLN O 132 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092116 restraints weight = 48790.254| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.25 r_work: 0.3067 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29088 Z= 0.138 Angle : 0.593 7.416 39760 Z= 0.307 Chirality : 0.043 0.150 4464 Planarity : 0.006 0.072 5344 Dihedral : 6.298 47.133 4120 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.87 % Allowed : 17.17 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.12), residues: 3744 helix: -2.07 (0.24), residues: 416 sheet: -0.40 (0.17), residues: 816 loop : -2.97 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 76 PHE 0.008 0.001 PHE M 30 TYR 0.012 0.001 TYR B 194 ARG 0.006 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03084 ( 767) hydrogen bonds : angle 6.73827 ( 2526) covalent geometry : bond 0.00339 (29088) covalent geometry : angle 0.59326 (39760) *********************** 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 494 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 405 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 ASP cc_start: 0.7580 (t0) cc_final: 0.7373 (t0) REVERT: B 207 GLU cc_start: 0.8003 (pm20) cc_final: 0.7701 (pm20) REVERT: C 22 MET cc_start: 0.9202 (ptm) cc_final: 0.8446 (ptp) REVERT: C 200 GLU cc_start: 0.7572 (mp0) cc_final: 0.7244 (mp0) REVERT: C 218 ARG cc_start: 0.7727 (ptp-110) cc_final: 0.7459 (ptp-110) REVERT: D 138 ARG cc_start: 0.8622 (ptm-80) cc_final: 0.8153 (ptm-80) REVERT: D 200 GLU cc_start: 0.7950 (mp0) cc_final: 0.7529 (mp0) REVERT: F 131 GLU cc_start: 0.8292 (mp0) cc_final: 0.7784 (mp0) REVERT: F 138 ARG cc_start: 0.8252 (ptt-90) cc_final: 0.7689 (ttp-110) REVERT: F 159 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7901 (pp20) REVERT: F 194 TYR cc_start: 0.8479 (m-80) cc_final: 0.8175 (m-10) REVERT: G 79 MET cc_start: 0.9055 (mmt) cc_final: 0.8483 (mmt) REVERT: G 131 GLU cc_start: 0.8254 (mp0) cc_final: 0.7637 (mp0) REVERT: G 209 ASP cc_start: 0.7787 (t0) cc_final: 0.6838 (t0) REVERT: G 218 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.7995 (mmt-90) REVERT: H 42 LEU cc_start: 0.8916 (mt) cc_final: 0.8694 (mt) REVERT: H 138 ARG cc_start: 0.8213 (ptm-80) cc_final: 0.7925 (ptm-80) REVERT: I 175 ASN cc_start: 0.8084 (m-40) cc_final: 0.7761 (m-40) REVERT: J 34 GLN cc_start: 0.8544 (mm110) cc_final: 0.8262 (mm110) REVERT: K 131 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8151 (mp0) REVERT: M 218 ARG cc_start: 0.8392 (mmt90) cc_final: 0.8151 (mmm-85) REVERT: O 209 ASP cc_start: 0.7163 (t0) cc_final: 0.6625 (t0) REVERT: O 214 ARG cc_start: 0.4525 (mtp85) cc_final: 0.4237 (mtt90) REVERT: P 159 GLU cc_start: 0.8203 (pm20) cc_final: 0.8000 (pm20) outliers start: 89 outliers final: 61 residues processed: 463 average time/residue: 0.4507 time to fit residues: 317.6418 Evaluate side-chains 431 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 368 time to evaluate : 3.425 ------------------------------------------------------------------------------- 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 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 97 VAL Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain F residue 114 ASP 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 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 90 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 J residue 95 ILE 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 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 22 MET Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 95 ILE 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 90 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 152 optimal weight: 3.9990 chunk 288 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 103 optimal weight: 0.0270 chunk 327 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 364 optimal weight: 0.4980 chunk 27 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 overall best weight: 3.1044 ------------------------------------------------------------------------------- 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 ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN L 34 GLN L 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.087847 restraints weight = 48974.921| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.04 r_work: 0.2994 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 29088 Z= 0.235 Angle : 0.655 9.162 39760 Z= 0.336 Chirality : 0.045 0.142 4464 Planarity : 0.006 0.074 5344 Dihedral : 6.389 51.029 4106 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 3.87 % Allowed : 17.53 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.12), residues: 3744 helix: -2.05 (0.24), residues: 416 sheet: -0.44 (0.17), residues: 816 loop : -2.94 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 76 PHE 0.011 0.001 PHE O 65 TYR 0.013 0.002 TYR K 179 ARG 0.007 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 767) hydrogen bonds : angle 6.81404 ( 2526) covalent geometry : bond 0.00569 (29088) covalent geometry : angle 0.65467 (39760) *********************** 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 483 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 363 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 207 GLU cc_start: 0.8026 (pm20) cc_final: 0.7761 (pm20) REVERT: C 22 MET cc_start: 0.9111 (ptm) cc_final: 0.8400 (ptp) REVERT: D 138 ARG cc_start: 0.8517 (ptm-80) cc_final: 0.8080 (ptm-80) REVERT: D 200 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: F 131 GLU cc_start: 0.8190 (mp0) cc_final: 0.7641 (mp0) REVERT: F 138 ARG cc_start: 0.8255 (ptt-90) cc_final: 0.7667 (ttp-110) REVERT: F 159 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8274 (pp20) REVERT: G 131 GLU cc_start: 0.8274 (mp0) cc_final: 0.7744 (mp0) REVERT: G 209 ASP cc_start: 0.7793 (t0) cc_final: 0.6894 (t0) REVERT: G 218 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.7978 (mmt-90) REVERT: H 42 LEU cc_start: 0.8975 (mt) cc_final: 0.8763 (mt) REVERT: H 138 ARG cc_start: 0.8247 (ptm-80) cc_final: 0.7989 (ptm-80) REVERT: J 169 ASP cc_start: 0.7093 (p0) cc_final: 0.6557 (p0) REVERT: K 131 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: N 131 GLU cc_start: 0.8231 (mp0) cc_final: 0.7770 (mp0) REVERT: N 200 GLU cc_start: 0.7331 (mp0) cc_final: 0.6945 (mp0) REVERT: N 206 ASP cc_start: 0.7879 (t0) cc_final: 0.7664 (t0) REVERT: O 5 GLU cc_start: 0.8750 (pt0) cc_final: 0.8525 (pt0) REVERT: O 206 ASP cc_start: 0.8624 (t0) cc_final: 0.8409 (t70) REVERT: O 209 ASP cc_start: 0.7126 (t0) cc_final: 0.6489 (t0) REVERT: O 214 ARG cc_start: 0.4610 (mtp85) cc_final: 0.4324 (mtt90) outliers start: 120 outliers final: 93 residues processed: 454 average time/residue: 0.4383 time to fit residues: 305.7945 Evaluate side-chains 443 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 347 time to evaluate : 3.208 ------------------------------------------------------------------------------- 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 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 95 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 200 GLU 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 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 114 ASP 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 210 ASP 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 49 ASP Chi-restraints excluded: chain H residue 95 ILE 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 67 SER 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 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 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 22 MET 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 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 O residue 208 THR 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 234 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 73 optimal weight: 8.9990 chunk 154 optimal weight: 0.0000 chunk 114 optimal weight: 2.9990 chunk 219 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 364 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 286 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.088383 restraints weight = 48458.583| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.04 r_work: 0.3005 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 29088 Z= 0.201 Angle : 0.630 8.473 39760 Z= 0.323 Chirality : 0.044 0.137 4464 Planarity : 0.006 0.071 5344 Dihedral : 6.295 53.493 4106 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 3.99 % Allowed : 17.75 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.12), residues: 3744 helix: -2.01 (0.24), residues: 416 sheet: -0.46 (0.17), residues: 816 loop : -2.91 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 76 PHE 0.010 0.001 PHE O 65 TYR 0.011 0.001 TYR K 179 ARG 0.007 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 767) hydrogen bonds : angle 6.67772 ( 2526) covalent geometry : bond 0.00489 (29088) covalent geometry : angle 0.63029 (39760) *********************** 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 493 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 369 time to evaluate : 3.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLU cc_start: 0.7864 (pm20) cc_final: 0.7660 (pm20) REVERT: C 22 MET cc_start: 0.9069 (ptm) cc_final: 0.8342 (ptp) REVERT: C 182 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8541 (mt) REVERT: C 200 GLU cc_start: 0.7615 (mp0) cc_final: 0.7353 (mp0) REVERT: D 37 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7928 (tt0) REVERT: D 131 GLU cc_start: 0.7935 (mp0) cc_final: 0.7484 (mp0) REVERT: D 200 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: F 131 GLU cc_start: 0.8228 (mp0) cc_final: 0.7675 (mp0) REVERT: F 138 ARG cc_start: 0.8298 (ptt-90) cc_final: 0.7733 (ttp-110) REVERT: F 159 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8295 (pp20) REVERT: G 79 MET cc_start: 0.8972 (mmt) cc_final: 0.8413 (mmt) REVERT: G 131 GLU cc_start: 0.8303 (mp0) cc_final: 0.7773 (mp0) REVERT: G 209 ASP cc_start: 0.7664 (t0) cc_final: 0.6748 (t0) REVERT: G 218 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7964 (mmt-90) REVERT: H 138 ARG cc_start: 0.8241 (ptm-80) cc_final: 0.7983 (ptm-80) REVERT: I 175 ASN cc_start: 0.8070 (m-40) cc_final: 0.7737 (m-40) REVERT: J 169 ASP cc_start: 0.7094 (p0) cc_final: 0.6602 (p0) REVERT: J 227 LEU cc_start: 0.9135 (tp) cc_final: 0.8852 (tp) REVERT: K 131 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: M 194 TYR cc_start: 0.8279 (m-80) cc_final: 0.7850 (m-80) REVERT: M 218 ARG cc_start: 0.8482 (mmt90) cc_final: 0.8220 (mmm-85) REVERT: O 5 GLU cc_start: 0.8748 (pt0) cc_final: 0.8513 (pt0) REVERT: O 206 ASP cc_start: 0.8659 (t0) cc_final: 0.8412 (t70) REVERT: O 209 ASP cc_start: 0.7276 (t0) cc_final: 0.6533 (t0) REVERT: O 214 ARG cc_start: 0.4779 (mtp85) cc_final: 0.4467 (mtt90) outliers start: 124 outliers final: 96 residues processed: 465 average time/residue: 0.4331 time to fit residues: 310.4751 Evaluate side-chains 449 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 349 time to evaluate : 3.375 ------------------------------------------------------------------------------- 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 25 SER Chi-restraints excluded: chain B residue 29 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 169 ASP Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 200 GLU 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 187 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 210 ASP 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 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 67 SER 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 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 L residue 227 LEU Chi-restraints excluded: chain M residue 22 MET 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 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 187 VAL Chi-restraints excluded: chain O residue 208 THR 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 212 VAL 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 109 optimal weight: 6.9990 chunk 325 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 316 optimal weight: 7.9990 chunk 257 optimal weight: 7.9990 chunk 282 optimal weight: 4.9990 chunk 319 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 182 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- 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 C 228 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 ASN L 34 GLN N 228 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.104578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.086822 restraints weight = 48880.133| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.03 r_work: 0.2974 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 29088 Z= 0.268 Angle : 0.681 9.537 39760 Z= 0.348 Chirality : 0.046 0.144 4464 Planarity : 0.006 0.073 5344 Dihedral : 6.518 58.124 4106 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 4.48 % Allowed : 18.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.12), residues: 3744 helix: -2.10 (0.23), residues: 416 sheet: -0.53 (0.17), residues: 816 loop : -2.93 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 76 PHE 0.012 0.001 PHE O 65 TYR 0.012 0.002 TYR C 194 ARG 0.011 0.000 ARG J 149 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 767) hydrogen bonds : angle 6.81630 ( 2526) covalent geometry : bond 0.00648 (29088) covalent geometry : angle 0.68094 (39760) *********************** 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 502 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 363 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 GLU cc_start: 0.7573 (tp30) cc_final: 0.7090 (tm-30) REVERT: C 182 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8537 (mt) REVERT: D 37 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7915 (mt-10) REVERT: D 200 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: F 131 GLU cc_start: 0.8282 (mp0) cc_final: 0.7661 (mp0) REVERT: F 138 ARG cc_start: 0.8289 (ptt-90) cc_final: 0.7724 (ttp-110) REVERT: F 159 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8460 (pp20) REVERT: G 79 MET cc_start: 0.9019 (mmt) cc_final: 0.8403 (mmt) REVERT: G 131 GLU cc_start: 0.8318 (mp0) cc_final: 0.7734 (mp0) REVERT: G 209 ASP cc_start: 0.7768 (t0) cc_final: 0.6838 (t0) REVERT: G 218 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8035 (mmt-90) REVERT: H 38 TYR cc_start: 0.9186 (m-80) cc_final: 0.8953 (m-80) REVERT: H 138 ARG cc_start: 0.8296 (ptm-80) cc_final: 0.7997 (ptm-80) REVERT: J 169 ASP cc_start: 0.7115 (p0) cc_final: 0.6617 (p0) REVERT: K 131 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: M 79 MET cc_start: 0.8770 (mmt) cc_final: 0.8555 (mmt) REVERT: M 194 TYR cc_start: 0.8276 (m-80) cc_final: 0.7858 (m-80) REVERT: N 131 GLU cc_start: 0.8216 (mp0) cc_final: 0.7812 (mp0) REVERT: N 200 GLU cc_start: 0.7266 (mp0) cc_final: 0.6850 (mp0) REVERT: O 5 GLU cc_start: 0.8808 (pt0) cc_final: 0.8593 (pt0) REVERT: O 206 ASP cc_start: 0.8697 (t0) cc_final: 0.8477 (t70) REVERT: O 209 ASP cc_start: 0.7373 (t0) cc_final: 0.6617 (t0) REVERT: O 214 ARG cc_start: 0.4959 (mtp85) cc_final: 0.4564 (mtt90) outliers start: 139 outliers final: 113 residues processed: 471 average time/residue: 0.4199 time to fit residues: 305.3306 Evaluate side-chains 469 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 352 time to evaluate : 3.440 ------------------------------------------------------------------------------- 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 131 GLU Chi-restraints excluded: chain B residue 25 SER 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 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 182 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 200 GLU 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 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 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 169 ASP Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain G residue 25 SER 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 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 67 SER Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 129 LEU 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 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 L residue 227 LEU Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 THR 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 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 129 LEU 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 O residue 213 VAL 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 212 VAL 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 129 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 347 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 295 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 G 132 ASN G 228 ASN H 102 GLN J 228 ASN L 34 GLN N 132 ASN N 228 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.091511 restraints weight = 48216.909| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.05 r_work: 0.3054 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29088 Z= 0.121 Angle : 0.570 6.833 39760 Z= 0.294 Chirality : 0.043 0.139 4464 Planarity : 0.006 0.071 5344 Dihedral : 5.908 57.164 4106 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.29 % Allowed : 19.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.12), residues: 3744 helix: -1.91 (0.25), residues: 416 sheet: -0.43 (0.18), residues: 816 loop : -2.85 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 76 PHE 0.006 0.001 PHE O 65 TYR 0.012 0.001 TYR F 194 ARG 0.007 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.02741 ( 767) hydrogen bonds : angle 6.36986 ( 2526) covalent geometry : bond 0.00302 (29088) covalent geometry : angle 0.56984 (39760) *********************** 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 497 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 395 time to evaluate : 3.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 GLN cc_start: 0.8198 (mp10) cc_final: 0.7976 (mp10) REVERT: B 73 GLU cc_start: 0.7632 (tp30) cc_final: 0.7407 (tm-30) REVERT: B 207 GLU cc_start: 0.8082 (pm20) cc_final: 0.7871 (pm20) REVERT: C 22 MET cc_start: 0.9025 (ptm) cc_final: 0.8340 (ptp) REVERT: C 95 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8657 (tt) REVERT: D 37 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7835 (mt-10) REVERT: E 37 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8434 (tt0) REVERT: F 131 GLU cc_start: 0.8216 (mp0) cc_final: 0.7674 (mp0) REVERT: F 138 ARG cc_start: 0.8300 (ptt-90) cc_final: 0.7790 (ttp-110) REVERT: F 159 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7800 (pp20) REVERT: F 207 GLU cc_start: 0.7156 (mp0) cc_final: 0.6910 (mp0) REVERT: G 79 MET cc_start: 0.8895 (mmt) cc_final: 0.8584 (mmt) REVERT: G 131 GLU cc_start: 0.8113 (mp0) cc_final: 0.7549 (mp0) REVERT: G 202 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6523 (pm20) REVERT: G 209 ASP cc_start: 0.7640 (t0) cc_final: 0.6749 (t0) REVERT: G 218 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7963 (mmt-90) REVERT: H 138 ARG cc_start: 0.8212 (ptm-80) cc_final: 0.7969 (ptm-80) REVERT: I 175 ASN cc_start: 0.7958 (m-40) cc_final: 0.7628 (m-40) REVERT: J 169 ASP cc_start: 0.7006 (p0) cc_final: 0.6518 (p0) REVERT: K 131 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: M 79 MET cc_start: 0.8705 (mmt) cc_final: 0.8294 (mtt) REVERT: M 194 TYR cc_start: 0.8333 (m-80) cc_final: 0.7944 (m-80) REVERT: M 218 ARG cc_start: 0.8353 (mmt90) cc_final: 0.8097 (mmm-85) REVERT: N 131 GLU cc_start: 0.8075 (mp0) cc_final: 0.7670 (mp0) REVERT: N 200 GLU cc_start: 0.7259 (mp0) cc_final: 0.6878 (mp0) REVERT: O 206 ASP cc_start: 0.8653 (t0) cc_final: 0.8409 (t70) REVERT: O 209 ASP cc_start: 0.7146 (t0) cc_final: 0.6467 (t0) REVERT: O 214 ARG cc_start: 0.4782 (mtp85) cc_final: 0.4424 (mtt90) REVERT: P 2 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8283 (mt) outliers start: 102 outliers final: 72 residues processed: 468 average time/residue: 0.4312 time to fit residues: 307.2372 Evaluate side-chains 441 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 364 time to evaluate : 3.025 ------------------------------------------------------------------------------- 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 131 GLU Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 33 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 5 GLU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 LEU 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 22 MET Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 114 ASP 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 G residue 93 LEU Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 202 GLN 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 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 131 GLU 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 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 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 22 MET Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 129 LEU 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 O residue 95 ILE Chi-restraints excluded: chain O residue 97 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 O residue 213 VAL Chi-restraints excluded: chain P residue 2 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 47 optimal weight: 0.5980 chunk 227 optimal weight: 7.9990 chunk 210 optimal weight: 0.7980 chunk 355 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 275 optimal weight: 0.9980 chunk 109 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 341 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN E 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 = 0.3437 r_free = 0.3437 target = 0.110831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.092888 restraints weight = 48100.297| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.07 r_work: 0.3076 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2014 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 : 0.561 6.778 39760 Z= 0.289 Chirality : 0.043 0.155 4464 Planarity : 0.006 0.069 5344 Dihedral : 5.649 56.081 4101 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.77 % Allowed : 19.78 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.12), residues: 3744 helix: -1.82 (0.25), residues: 416 sheet: -0.31 (0.18), residues: 816 loop : -2.80 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 76 PHE 0.006 0.001 PHE O 184 TYR 0.014 0.001 TYR F 194 ARG 0.008 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.02630 ( 767) hydrogen bonds : angle 6.23056 ( 2526) covalent geometry : bond 0.00275 (29088) covalent geometry : angle 0.56105 (39760) *********************** 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 487 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 401 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7475 (pt0) cc_final: 0.7005 (mp0) REVERT: B 73 GLU cc_start: 0.7643 (tp30) cc_final: 0.7429 (tm-30) REVERT: B 207 GLU cc_start: 0.7943 (pm20) cc_final: 0.7678 (pm20) REVERT: C 22 MET cc_start: 0.8961 (ptm) cc_final: 0.8315 (ptp) REVERT: C 37 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6612 (mt-10) REVERT: C 95 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8645 (tt) REVERT: C 200 GLU cc_start: 0.7581 (mp0) cc_final: 0.7022 (mp0) REVERT: D 37 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7794 (mt-10) REVERT: D 200 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: F 131 GLU cc_start: 0.8176 (mp0) cc_final: 0.7637 (mp0) REVERT: F 138 ARG cc_start: 0.8294 (ptt-90) cc_final: 0.7813 (ttp-110) REVERT: F 207 GLU cc_start: 0.7179 (mp0) cc_final: 0.6924 (mp0) REVERT: G 79 MET cc_start: 0.8849 (mmt) cc_final: 0.8481 (mmt) REVERT: G 131 GLU cc_start: 0.8083 (mp0) cc_final: 0.7598 (mp0) REVERT: G 202 GLN cc_start: 0.6821 (OUTLIER) cc_final: 0.6513 (pm20) REVERT: G 209 ASP cc_start: 0.7604 (t0) cc_final: 0.6711 (t0) REVERT: H 138 ARG cc_start: 0.8165 (ptm-80) cc_final: 0.7919 (ptm-80) REVERT: I 65 PHE cc_start: 0.9068 (t80) cc_final: 0.8589 (t80) REVERT: I 175 ASN cc_start: 0.7874 (m-40) cc_final: 0.7536 (m-40) REVERT: J 169 ASP cc_start: 0.7054 (p0) cc_final: 0.6619 (p0) REVERT: J 227 LEU cc_start: 0.9067 (tp) cc_final: 0.8855 (tp) REVERT: K 131 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: M 194 TYR cc_start: 0.8315 (m-80) cc_final: 0.7902 (m-80) REVERT: M 218 ARG cc_start: 0.8243 (mmt90) cc_final: 0.8010 (mmm-85) REVERT: N 131 GLU cc_start: 0.8025 (mp0) cc_final: 0.7630 (mp0) REVERT: N 200 GLU cc_start: 0.7272 (mp0) cc_final: 0.6910 (mp0) REVERT: O 5 GLU cc_start: 0.8672 (pt0) cc_final: 0.8440 (pt0) REVERT: O 206 ASP cc_start: 0.8633 (t0) cc_final: 0.8391 (t70) REVERT: O 209 ASP cc_start: 0.7175 (t0) cc_final: 0.6514 (t0) REVERT: O 214 ARG cc_start: 0.4957 (mtp85) cc_final: 0.4471 (mtt90) REVERT: P 2 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8263 (mt) REVERT: P 149 ARG cc_start: 0.8673 (mtp180) cc_final: 0.8454 (mtm-85) REVERT: P 209 ASP cc_start: 0.7318 (t0) cc_final: 0.6538 (t0) outliers start: 86 outliers final: 69 residues processed: 459 average time/residue: 0.4319 time to fit residues: 301.7101 Evaluate side-chains 445 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 371 time to evaluate : 3.029 ------------------------------------------------------------------------------- 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 131 GLU Chi-restraints excluded: chain B residue 33 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 5 GLU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 LEU 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 182 ILE Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 67 SER 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 226 THR 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 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 131 GLU 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 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 129 LEU 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 22 MET Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 95 ILE 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 129 LEU 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 O residue 213 VAL Chi-restraints excluded: chain P residue 2 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 264 optimal weight: 0.6980 chunk 284 optimal weight: 0.0870 chunk 153 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 183 optimal weight: 0.5980 chunk 174 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- 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** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN J 102 GLN L 34 GLN P 102 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.090902 restraints weight = 47523.402| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.12 r_work: 0.3062 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2082 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= 0.130 Angle : 0.576 6.943 39760 Z= 0.296 Chirality : 0.043 0.153 4464 Planarity : 0.006 0.068 5344 Dihedral : 5.647 54.977 4100 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 2.87 % Allowed : 19.94 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.12), residues: 3744 helix: -1.83 (0.25), residues: 416 sheet: -0.27 (0.18), residues: 816 loop : -2.75 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 76 PHE 0.014 0.001 PHE D 65 TYR 0.011 0.001 TYR H 38 ARG 0.009 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.02693 ( 767) hydrogen bonds : angle 6.23077 ( 2526) covalent geometry : bond 0.00322 (29088) covalent geometry : angle 0.57584 (39760) *********************** 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 469 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 380 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: A 207 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: B 73 GLU cc_start: 0.7634 (tp30) cc_final: 0.7388 (tm-30) REVERT: B 207 GLU cc_start: 0.7960 (pm20) cc_final: 0.7647 (pm20) REVERT: C 22 MET cc_start: 0.9016 (ptm) cc_final: 0.8361 (ptp) REVERT: C 34 GLN cc_start: 0.8459 (mp10) cc_final: 0.7935 (pm20) REVERT: C 200 GLU cc_start: 0.7609 (mp0) cc_final: 0.7035 (mp0) REVERT: C 218 ARG cc_start: 0.7130 (ptp-110) cc_final: 0.6871 (ptp-110) REVERT: D 200 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: E 38 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.7607 (t80) REVERT: F 131 GLU cc_start: 0.8233 (mp0) cc_final: 0.7655 (mp0) REVERT: F 138 ARG cc_start: 0.8328 (ptt-90) cc_final: 0.7856 (ttp-110) REVERT: F 207 GLU cc_start: 0.7128 (mp0) cc_final: 0.6846 (mp0) REVERT: G 79 MET cc_start: 0.8910 (mmt) cc_final: 0.8557 (mmt) REVERT: G 131 GLU cc_start: 0.8017 (mp0) cc_final: 0.7546 (mp0) REVERT: G 202 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6495 (pm20) REVERT: G 209 ASP cc_start: 0.7695 (t0) cc_final: 0.6752 (t0) REVERT: H 138 ARG cc_start: 0.8179 (ptm-80) cc_final: 0.7927 (ptm-80) REVERT: I 65 PHE cc_start: 0.9080 (t80) cc_final: 0.8623 (t80) REVERT: I 175 ASN cc_start: 0.7920 (m-40) cc_final: 0.7580 (m-40) REVERT: J 169 ASP cc_start: 0.7017 (p0) cc_final: 0.6639 (p0) REVERT: J 227 LEU cc_start: 0.9079 (tp) cc_final: 0.8866 (tp) REVERT: K 131 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: K 209 ASP cc_start: 0.7576 (t0) cc_final: 0.7088 (t0) REVERT: M 218 ARG cc_start: 0.8239 (mmt90) cc_final: 0.7983 (mmm-85) REVERT: N 131 GLU cc_start: 0.8089 (mp0) cc_final: 0.7645 (mp0) REVERT: N 200 GLU cc_start: 0.7274 (mp0) cc_final: 0.6897 (mp0) REVERT: O 5 GLU cc_start: 0.8676 (pt0) cc_final: 0.8426 (pt0) REVERT: O 209 ASP cc_start: 0.7209 (t0) cc_final: 0.6539 (t0) REVERT: O 214 ARG cc_start: 0.4886 (mtp85) cc_final: 0.4370 (mtt90) REVERT: P 2 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8262 (mt) REVERT: P 209 ASP cc_start: 0.7363 (t0) cc_final: 0.6572 (t0) outliers start: 89 outliers final: 74 residues processed: 441 average time/residue: 0.4457 time to fit residues: 301.5428 Evaluate side-chains 450 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 369 time to evaluate : 3.276 ------------------------------------------------------------------------------- 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 131 GLU Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 207 GLU 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 5 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 LEU 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 38 TYR 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 95 ILE 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 F residue 227 LEU Chi-restraints excluded: chain G residue 67 SER 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 G residue 226 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 49 ASP Chi-restraints excluded: chain H residue 67 SER 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 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 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 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 114 ASP Chi-restraints excluded: chain L residue 129 LEU 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 22 MET Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 67 SER 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 129 LEU 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 O residue 213 VAL Chi-restraints excluded: chain P residue 2 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 130 optimal weight: 8.9990 chunk 279 optimal weight: 5.9990 chunk 203 optimal weight: 0.0370 chunk 140 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 217 optimal weight: 0.7980 chunk 269 optimal weight: 8.9990 chunk 239 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- 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 ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 ASN H 102 GLN L 34 GLN M 175 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.092268 restraints weight = 48007.660| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.05 r_work: 0.3067 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29088 Z= 0.131 Angle : 0.577 6.984 39760 Z= 0.296 Chirality : 0.043 0.152 4464 Planarity : 0.006 0.068 5344 Dihedral : 5.581 53.792 4097 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.74 % Allowed : 20.20 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.12), residues: 3744 helix: -1.85 (0.25), residues: 416 sheet: -0.26 (0.18), residues: 816 loop : -2.72 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 76 PHE 0.013 0.001 PHE D 65 TYR 0.015 0.001 TYR K 179 ARG 0.010 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.02687 ( 767) hydrogen bonds : angle 6.21043 ( 2526) covalent geometry : bond 0.00325 (29088) covalent geometry : angle 0.57661 (39760) ********************** 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 462 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 377 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: A 207 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: B 73 GLU cc_start: 0.7596 (tp30) cc_final: 0.7359 (tm-30) REVERT: B 207 GLU cc_start: 0.7961 (pm20) cc_final: 0.7648 (pm20) REVERT: C 22 MET cc_start: 0.8988 (ptm) cc_final: 0.8341 (ptp) REVERT: C 200 GLU cc_start: 0.7588 (mp0) cc_final: 0.7029 (mp0) REVERT: C 218 ARG cc_start: 0.7106 (ptp-110) cc_final: 0.6863 (ptp-110) REVERT: D 38 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.7056 (t80) REVERT: D 200 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: F 131 GLU cc_start: 0.8198 (mp0) cc_final: 0.7644 (mp0) REVERT: F 138 ARG cc_start: 0.8333 (ptt-90) cc_final: 0.7862 (ttp-110) REVERT: F 207 GLU cc_start: 0.7116 (mp0) cc_final: 0.6849 (mp0) REVERT: G 79 MET cc_start: 0.8861 (mmt) cc_final: 0.8528 (mmt) REVERT: G 202 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6530 (pm20) REVERT: G 209 ASP cc_start: 0.7711 (t0) cc_final: 0.6836 (t0) REVERT: H 26 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8148 (mm-30) REVERT: H 138 ARG cc_start: 0.8170 (ptm-80) cc_final: 0.7928 (ptm-80) REVERT: H 218 ARG cc_start: 0.8581 (ptp-110) cc_final: 0.8356 (ptp-110) REVERT: I 65 PHE cc_start: 0.9069 (t80) cc_final: 0.8618 (t80) REVERT: I 175 ASN cc_start: 0.7904 (m-40) cc_final: 0.7586 (m-40) REVERT: J 169 ASP cc_start: 0.7054 (p0) cc_final: 0.6682 (p0) REVERT: J 227 LEU cc_start: 0.9072 (tp) cc_final: 0.8859 (tp) REVERT: K 131 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: K 209 ASP cc_start: 0.7553 (t0) cc_final: 0.7100 (t0) REVERT: M 79 MET cc_start: 0.8701 (mmt) cc_final: 0.8413 (mtt) REVERT: M 218 ARG cc_start: 0.8243 (mmt90) cc_final: 0.8005 (mmm-85) REVERT: N 131 GLU cc_start: 0.8059 (mp0) cc_final: 0.7632 (mp0) REVERT: N 200 GLU cc_start: 0.7249 (mp0) cc_final: 0.6895 (mp0) REVERT: O 5 GLU cc_start: 0.8641 (pt0) cc_final: 0.8407 (pt0) REVERT: O 209 ASP cc_start: 0.7167 (t0) cc_final: 0.6503 (t0) REVERT: O 214 ARG cc_start: 0.5003 (mtp85) cc_final: 0.4558 (mtt90) REVERT: P 2 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8245 (mt) REVERT: P 209 ASP cc_start: 0.7355 (t0) cc_final: 0.6586 (t0) outliers start: 85 outliers final: 75 residues processed: 435 average time/residue: 0.4441 time to fit residues: 296.3557 Evaluate side-chains 448 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 366 time to evaluate : 3.404 ------------------------------------------------------------------------------- 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 131 GLU Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 25 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 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 200 GLU 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 95 ILE 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 F residue 212 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain G residue 67 SER 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 200 GLU Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 49 ASP Chi-restraints excluded: chain H residue 67 SER 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 97 VAL 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 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 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 114 ASP 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 22 MET Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 67 SER 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 167 VAL Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 22 MET 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 276 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 163 optimal weight: 0.6980 chunk 365 optimal weight: 5.9990 chunk 336 optimal weight: 0.8980 chunk 288 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 345 optimal weight: 8.9990 chunk 169 optimal weight: 9.9990 chunk 330 optimal weight: 1.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 92 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN H 102 GLN J 228 ASN L 34 GLN N 228 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.089003 restraints weight = 48418.108| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.05 r_work: 0.3013 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 29088 Z= 0.213 Angle : 0.646 9.569 39760 Z= 0.330 Chirality : 0.045 0.174 4464 Planarity : 0.006 0.068 5344 Dihedral : 5.990 56.014 4097 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.06 % Allowed : 20.04 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.12), residues: 3744 helix: -1.98 (0.24), residues: 416 sheet: -0.36 (0.18), residues: 816 loop : -2.74 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 76 PHE 0.015 0.001 PHE D 65 TYR 0.017 0.001 TYR K 179 ARG 0.009 0.001 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03044 ( 767) hydrogen bonds : angle 6.47306 ( 2526) covalent geometry : bond 0.00516 (29088) covalent geometry : angle 0.64586 (39760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13236.11 seconds wall clock time: 230 minutes 8.23 seconds (13808.23 seconds total)