Starting phenix.real_space_refine on Tue Jun 24 06:54:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ikj_60656/06_2025/9ikj_60656_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ikj_60656/06_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_60656/06_2025/9ikj_60656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ikj_60656/06_2025/9ikj_60656.map" model { file = "/net/cci-nas-00/data/ceres_data/9ikj_60656/06_2025/9ikj_60656_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ikj_60656/06_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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 17.82, per 1000 atoms: 0.63 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: 7.61 Conformation dependent library (CDL) restraints added in 4.7 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: 4.75 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: 10.52 Time building geometry restraints manager: 8.59 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: 1.870 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: 1.130 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 65.690 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.500 ------------------------------------------------------------------------------- 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 : 3.192 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: 0.4420 time to fit residues: 299.6954 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 : 3.094 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.085241 restraints weight = 50168.040| |-----------------------------------------------------------------------------| 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 : 3.230 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8503 (pt0) REVERT: B 196 ARG cc_start: 0.8916 (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: 0.8172 (ptm-80) REVERT: D 200 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: F 131 GLU cc_start: 0.8265 (mp0) cc_final: 0.7859 (mp0) REVERT: F 159 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8402 (pp20) REVERT: F 194 TYR cc_start: 0.8611 (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: 0.8612 (mtp85) REVERT: G 209 ASP cc_start: 0.7879 (t0) cc_final: 0.6909 (t0) REVERT: G 218 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.8019 (mmt-90) REVERT: G 226 THR cc_start: 0.9191 (m) cc_final: 0.8958 (p) REVERT: G 233 MET cc_start: 0.8722 (ttp) cc_final: 0.8518 (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: 0.8393 (mtp85) cc_final: 0.8072 (mtp85) REVERT: J 12 MET cc_start: 0.9248 (ttp) cc_final: 0.9048 (ttp) REVERT: J 34 GLN cc_start: 0.8600 (mm110) cc_final: 0.8326 (mm110) REVERT: J 149 ARG cc_start: 0.8978 (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: 0.8869 (mmt) cc_final: 0.8625 (mmt) REVERT: N 131 GLU cc_start: 0.8460 (mp0) cc_final: 0.8216 (mp0) REVERT: N 200 GLU cc_start: 0.7453 (mp0) cc_final: 0.7082 (mp0) REVERT: O 209 ASP cc_start: 0.7317 (t0) cc_final: 0.7095 (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: 0.4405 time to fit residues: 313.5453 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 : 3.177 ------------------------------------------------------------------------------- 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: 2.9990 chunk 278 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 281 optimal weight: 0.9980 chunk 337 optimal weight: 2.9990 chunk 279 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.108735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.090400 restraints weight = 47905.145| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.17 r_work: 0.3074 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1414 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= 0.136 Angle : 0.593 7.417 39760 Z= 0.307 Chirality : 0.043 0.150 4464 Planarity : 0.006 0.071 5344 Dihedral : 6.299 47.046 4120 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.87 % Allowed : 17.24 % Favored : 79.90 % 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: -3.21 (0.12), residues: 3744 helix: -2.07 (0.24), residues: 416 sheet: -0.41 (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 A 141 TYR 0.012 0.001 TYR B 194 ARG 0.006 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 767) hydrogen bonds : angle 6.73761 ( 2526) covalent geometry : bond 0.00333 (29088) covalent geometry : angle 0.59267 (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 497 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 408 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 ASP cc_start: 0.7558 (t0) cc_final: 0.7349 (t0) REVERT: B 207 GLU cc_start: 0.7992 (pm20) cc_final: 0.7694 (pm20) REVERT: C 22 MET cc_start: 0.9192 (ptm) cc_final: 0.8441 (ptp) REVERT: C 200 GLU cc_start: 0.7567 (mp0) cc_final: 0.7251 (mp0) REVERT: C 218 ARG cc_start: 0.7675 (ptp-110) cc_final: 0.7458 (ptp-110) REVERT: D 138 ARG cc_start: 0.8614 (ptm-80) cc_final: 0.8139 (ptm-80) REVERT: D 200 GLU cc_start: 0.7941 (mp0) cc_final: 0.7521 (mp0) REVERT: F 131 GLU cc_start: 0.8286 (mp0) cc_final: 0.7778 (mp0) REVERT: F 138 ARG cc_start: 0.8248 (ptt-90) cc_final: 0.7687 (ttp-110) REVERT: F 159 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7892 (pp20) REVERT: F 194 TYR cc_start: 0.8470 (m-80) cc_final: 0.8164 (m-10) REVERT: G 79 MET cc_start: 0.9048 (mmt) cc_final: 0.8483 (mmt) REVERT: G 131 GLU cc_start: 0.8253 (mp0) cc_final: 0.7622 (mp0) REVERT: G 209 ASP cc_start: 0.7779 (t0) cc_final: 0.6838 (t0) REVERT: G 218 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.7979 (mmt-90) REVERT: H 42 LEU cc_start: 0.8914 (mt) cc_final: 0.8694 (mt) REVERT: H 138 ARG cc_start: 0.8212 (ptm-80) cc_final: 0.7922 (ptm-80) REVERT: I 175 ASN cc_start: 0.8075 (m-40) cc_final: 0.7749 (m-40) REVERT: J 12 MET cc_start: 0.9254 (ttp) cc_final: 0.8960 (ttp) REVERT: J 34 GLN cc_start: 0.8535 (mm110) cc_final: 0.8254 (mm110) REVERT: J 169 ASP cc_start: 0.7041 (p0) cc_final: 0.6576 (p0) REVERT: K 131 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: M 218 ARG cc_start: 0.8375 (mmt90) cc_final: 0.8132 (mmm-85) REVERT: O 209 ASP cc_start: 0.7175 (t0) cc_final: 0.6653 (t0) REVERT: O 214 ARG cc_start: 0.4539 (mtp85) cc_final: 0.4259 (mtt90) outliers start: 89 outliers final: 58 residues processed: 467 average time/residue: 0.4847 time to fit residues: 346.7867 Evaluate side-chains 431 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 371 time to evaluate : 2.931 ------------------------------------------------------------------------------- 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 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 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 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 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 M residue 190 LEU 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: 0.0870 chunk 288 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 327 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 364 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN C 7 ASN E 228 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 ASN L 34 GLN L 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.103927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.085553 restraints weight = 48790.738| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.11 r_work: 0.2972 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 29088 Z= 0.267 Angle : 0.681 9.719 39760 Z= 0.349 Chirality : 0.046 0.145 4464 Planarity : 0.006 0.075 5344 Dihedral : 6.509 52.566 4106 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 3.87 % Allowed : 17.72 % Favored : 78.41 % 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: -2.07 (0.23), residues: 416 sheet: -0.48 (0.17), residues: 816 loop : -2.96 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 76 PHE 0.013 0.001 PHE O 65 TYR 0.014 0.002 TYR D 61 ARG 0.007 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 767) hydrogen bonds : angle 6.89754 ( 2526) covalent geometry : bond 0.00645 (29088) covalent geometry : angle 0.68111 (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 478 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 358 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLU cc_start: 0.8051 (pm20) cc_final: 0.7764 (pm20) REVERT: C 159 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7651 (pp20) REVERT: C 218 ARG cc_start: 0.7662 (ptp-110) cc_final: 0.7450 (ptp-110) REVERT: D 37 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7876 (tt0) REVERT: D 200 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: F 131 GLU cc_start: 0.8235 (mp0) cc_final: 0.7631 (mp0) REVERT: F 138 ARG cc_start: 0.8278 (ptt-90) cc_final: 0.7669 (ttp-110) REVERT: F 159 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8349 (pp20) REVERT: G 131 GLU cc_start: 0.8276 (mp0) cc_final: 0.7721 (mp0) REVERT: G 209 ASP cc_start: 0.7727 (t0) cc_final: 0.6809 (t0) REVERT: G 218 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.8010 (mmt-90) REVERT: H 42 LEU cc_start: 0.9011 (mt) cc_final: 0.8798 (mt) REVERT: H 138 ARG cc_start: 0.8264 (ptm-80) cc_final: 0.7995 (ptm-80) REVERT: I 131 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8398 (mp0) REVERT: J 169 ASP cc_start: 0.7086 (p0) cc_final: 0.6540 (p0) REVERT: K 131 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: M 79 MET cc_start: 0.8835 (mmt) cc_final: 0.8603 (mmt) REVERT: N 131 GLU cc_start: 0.8294 (mp0) cc_final: 0.7788 (mp0) REVERT: N 200 GLU cc_start: 0.7338 (mp0) cc_final: 0.6950 (mp0) REVERT: O 5 GLU cc_start: 0.8806 (pt0) cc_final: 0.8567 (pt0) REVERT: O 209 ASP cc_start: 0.7266 (t0) cc_final: 0.6633 (t0) REVERT: O 214 ARG cc_start: 0.4693 (mtp85) cc_final: 0.4352 (mtt90) outliers start: 120 outliers final: 94 residues processed: 449 average time/residue: 0.4566 time to fit residues: 317.4465 Evaluate side-chains 439 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 340 time to evaluate : 2.972 ------------------------------------------------------------------------------- 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 159 GLU Chi-restraints excluded: chain C residue 169 ASP 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 D residue 234 VAL Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 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 97 VAL Chi-restraints excluded: chain H residue 112 THR 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 131 GLU 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 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 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 90 ILE Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 110 ASN Chi-restraints excluded: chain O residue 131 GLU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 73 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 219 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 364 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** C 75 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 ASN L 34 GLN N 132 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.090863 restraints weight = 48126.776| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.04 r_work: 0.3046 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1683 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= 0.135 Angle : 0.579 7.135 39760 Z= 0.298 Chirality : 0.043 0.143 4464 Planarity : 0.006 0.070 5344 Dihedral : 6.018 51.321 4106 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.38 % Allowed : 18.36 % 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: -3.11 (0.12), residues: 3744 helix: -1.93 (0.24), residues: 416 sheet: -0.40 (0.18), residues: 816 loop : -2.88 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 76 PHE 0.007 0.001 PHE O 65 TYR 0.010 0.001 TYR K 179 ARG 0.010 0.000 ARG J 149 Details of bonding type rmsd hydrogen bonds : bond 0.02859 ( 767) hydrogen bonds : angle 6.48638 ( 2526) covalent geometry : bond 0.00332 (29088) covalent geometry : angle 0.57920 (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 494 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 389 time to evaluate : 2.838 Fit side-chains revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8166 (mt0) cc_final: 0.7952 (mt0) REVERT: B 73 GLU cc_start: 0.7549 (tp30) cc_final: 0.7159 (tm-30) REVERT: C 22 MET cc_start: 0.9008 (ptm) cc_final: 0.8318 (ptp) REVERT: C 45 TYR cc_start: 0.8838 (m-80) cc_final: 0.8536 (m-80) REVERT: C 182 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8501 (mt) REVERT: C 218 ARG cc_start: 0.7664 (ptp-110) cc_final: 0.7399 (ptp-110) REVERT: D 37 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7844 (tt0) REVERT: D 131 GLU cc_start: 0.7938 (mp0) cc_final: 0.7574 (mp0) REVERT: D 200 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: F 131 GLU cc_start: 0.8194 (mp0) cc_final: 0.7687 (mp0) REVERT: F 138 ARG cc_start: 0.8279 (ptt-90) cc_final: 0.7752 (ttp-110) REVERT: F 207 GLU cc_start: 0.7217 (mp0) cc_final: 0.6897 (mp0) REVERT: G 131 GLU cc_start: 0.8223 (mp0) cc_final: 0.7707 (mp0) REVERT: G 209 ASP cc_start: 0.7687 (t0) cc_final: 0.6808 (t0) REVERT: G 218 ARG cc_start: 0.8158 (mmm-85) cc_final: 0.7942 (mmt-90) REVERT: H 131 GLU cc_start: 0.7973 (mp0) cc_final: 0.7655 (mp0) REVERT: H 138 ARG cc_start: 0.8175 (ptm-80) cc_final: 0.7938 (ptm-80) REVERT: I 175 ASN cc_start: 0.7996 (m-40) cc_final: 0.7693 (m-40) REVERT: J 169 ASP cc_start: 0.7053 (p0) cc_final: 0.6588 (p0) REVERT: J 227 LEU cc_start: 0.9106 (tp) cc_final: 0.8836 (tp) REVERT: K 131 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8151 (mp0) REVERT: M 194 TYR cc_start: 0.8328 (m-80) cc_final: 0.7941 (m-80) REVERT: M 218 ARG cc_start: 0.8356 (mmt90) cc_final: 0.8094 (mmm-85) REVERT: N 200 GLU cc_start: 0.7284 (mp0) cc_final: 0.6936 (mp0) REVERT: O 5 GLU cc_start: 0.8676 (pt0) cc_final: 0.8440 (pt0) REVERT: O 206 ASP cc_start: 0.8635 (t0) cc_final: 0.8388 (t70) REVERT: O 209 ASP cc_start: 0.7117 (t0) cc_final: 0.6427 (t0) REVERT: O 214 ARG cc_start: 0.4706 (mtp85) cc_final: 0.4348 (mtt90) REVERT: O 218 ARG cc_start: 0.8189 (ptp-170) cc_final: 0.7971 (ptp-110) outliers start: 105 outliers final: 76 residues processed: 467 average time/residue: 0.4504 time to fit residues: 322.8849 Evaluate side-chains 442 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 363 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain B residue 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 95 ILE 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 200 GLU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 234 VAL 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 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 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 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 J residue 95 ILE Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 134 VAL 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 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 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 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 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 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 95 ILE Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 167 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: 4.9990 chunk 117 optimal weight: 3.9990 chunk 316 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 282 optimal weight: 7.9990 chunk 319 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 182 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** B 228 ASN C 7 ASN C 228 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 GLN G 228 ASN J 228 ASN K 1 ASN K 228 ASN L 34 GLN N 228 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.101847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.084066 restraints weight = 49477.548| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.03 r_work: 0.2933 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.114 29088 Z= 0.414 Angle : 0.796 11.571 39760 Z= 0.406 Chirality : 0.050 0.173 4464 Planarity : 0.007 0.080 5344 Dihedral : 6.849 59.978 4103 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 4.32 % Allowed : 18.52 % Favored : 77.16 % 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: -3.31 (0.12), residues: 3744 helix: -2.23 (0.23), residues: 416 sheet: -0.62 (0.17), residues: 816 loop : -2.96 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 58 PHE 0.016 0.002 PHE L 184 TYR 0.016 0.002 TYR C 194 ARG 0.009 0.001 ARG J 149 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 767) hydrogen bonds : angle 7.11264 ( 2526) covalent geometry : bond 0.00997 (29088) covalent geometry : angle 0.79615 (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 493 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 359 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 GLN cc_start: 0.7987 (mp10) cc_final: 0.7352 (mp10) REVERT: B 207 GLU cc_start: 0.8172 (pm20) cc_final: 0.7946 (pm20) REVERT: C 159 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7299 (pp20) REVERT: C 182 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8556 (mt) REVERT: C 218 ARG cc_start: 0.7702 (ptp-110) cc_final: 0.7488 (ptp-110) REVERT: D 200 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: F 131 GLU cc_start: 0.8249 (mp0) cc_final: 0.7592 (mp0) REVERT: F 138 ARG cc_start: 0.8287 (ptt-90) cc_final: 0.7948 (ptt90) REVERT: F 159 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8439 (pp20) REVERT: G 104 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.9062 (ptpp) REVERT: G 131 GLU cc_start: 0.8359 (mp0) cc_final: 0.7747 (mp0) REVERT: G 209 ASP cc_start: 0.7777 (t0) cc_final: 0.6857 (t0) REVERT: G 218 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.8028 (mmt-90) REVERT: H 38 TYR cc_start: 0.9259 (m-80) cc_final: 0.9040 (m-80) REVERT: H 138 ARG cc_start: 0.8332 (ptm-80) cc_final: 0.8050 (ptm-80) REVERT: J 169 ASP cc_start: 0.7090 (p0) cc_final: 0.6553 (p0) REVERT: K 131 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: M 79 MET cc_start: 0.8635 (mmt) cc_final: 0.8383 (mmt) REVERT: M 194 TYR cc_start: 0.8325 (m-80) cc_final: 0.7903 (m-80) REVERT: N 34 GLN cc_start: 0.8706 (mt0) cc_final: 0.8406 (mt0) REVERT: N 131 GLU cc_start: 0.8295 (mp0) cc_final: 0.7840 (mp0) REVERT: O 209 ASP cc_start: 0.7400 (t0) cc_final: 0.6771 (t0) REVERT: O 214 ARG cc_start: 0.4956 (mtp85) cc_final: 0.4636 (mtt90) REVERT: P 2 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8303 (mt) outliers start: 134 outliers final: 106 residues processed: 459 average time/residue: 0.4308 time to fit residues: 304.6737 Evaluate side-chains 459 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 346 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain B residue 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 42 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 145 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 39 ILE 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 187 VAL Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain F residue 22 MET Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain 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 95 ILE Chi-restraints excluded: chain G residue 104 LYS 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 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 37 GLU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 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 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 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 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 208 THR Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain P residue 1 ASN Chi-restraints excluded: chain P residue 2 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 134 VAL Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 129 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 225 optimal weight: 0.9980 chunk 347 optimal weight: 1.9990 chunk 194 optimal weight: 0.3980 chunk 76 optimal weight: 6.9990 chunk 230 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 295 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 228 ASN C 7 ASN C 15 GLN C 34 GLN E 228 ASN G 132 ASN G 228 ASN J 228 ASN K 228 ASN L 34 GLN L 86 ASN M 99 GLN N 228 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.092363 restraints weight = 48098.048| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.04 r_work: 0.3065 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29088 Z= 0.112 Angle : 0.571 6.769 39760 Z= 0.297 Chirality : 0.043 0.174 4464 Planarity : 0.006 0.072 5344 Dihedral : 5.942 57.018 4103 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.61 % Allowed : 20.20 % 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: -3.16 (0.12), residues: 3744 helix: -2.06 (0.24), residues: 416 sheet: -0.51 (0.18), residues: 816 loop : -2.87 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 76 PHE 0.008 0.001 PHE O 184 TYR 0.011 0.001 TYR K 194 ARG 0.007 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.02722 ( 767) hydrogen bonds : angle 6.38486 ( 2526) covalent geometry : bond 0.00280 (29088) covalent geometry : angle 0.57131 (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 472 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 391 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: B 207 GLU cc_start: 0.7849 (pm20) cc_final: 0.7576 (pm20) REVERT: C 22 MET cc_start: 0.9023 (ptm) cc_final: 0.8345 (ptp) REVERT: C 37 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7205 (mt-10) REVERT: C 45 TYR cc_start: 0.8872 (m-80) cc_final: 0.8485 (m-80) REVERT: C 126 ARG cc_start: 0.8186 (ptt90) cc_final: 0.7773 (ttp80) REVERT: C 218 ARG cc_start: 0.7610 (ptp-110) cc_final: 0.7358 (ptp-110) REVERT: D 37 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7863 (mt-10) REVERT: D 200 GLU cc_start: 0.8017 (mp0) cc_final: 0.7461 (mp0) REVERT: F 131 GLU cc_start: 0.8212 (mp0) cc_final: 0.7694 (mp0) REVERT: F 138 ARG cc_start: 0.8258 (ptt-90) cc_final: 0.7769 (ttp-110) REVERT: F 159 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7437 (pp20) REVERT: F 207 GLU cc_start: 0.7185 (mp0) cc_final: 0.6947 (mp0) REVERT: G 104 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.9039 (ptpp) REVERT: G 131 GLU cc_start: 0.8145 (mp0) cc_final: 0.7598 (mp0) REVERT: G 202 GLN cc_start: 0.6847 (OUTLIER) cc_final: 0.6477 (pm20) REVERT: G 209 ASP cc_start: 0.7673 (t0) cc_final: 0.6772 (t0) REVERT: G 218 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.8017 (mmt-90) REVERT: H 138 ARG cc_start: 0.8202 (ptm-80) cc_final: 0.7960 (ptm-80) REVERT: I 175 ASN cc_start: 0.7972 (m-40) cc_final: 0.7655 (m-40) REVERT: J 169 ASP cc_start: 0.7038 (p0) cc_final: 0.6543 (p0) REVERT: K 131 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: M 79 MET cc_start: 0.8615 (mmt) cc_final: 0.8310 (mtt) REVERT: M 218 ARG cc_start: 0.8305 (mmt90) cc_final: 0.8064 (mmm-85) REVERT: N 131 GLU cc_start: 0.8099 (mp0) cc_final: 0.7681 (mp0) REVERT: N 200 GLU cc_start: 0.7252 (mp0) cc_final: 0.6868 (mp0) REVERT: O 206 ASP cc_start: 0.8608 (t0) cc_final: 0.8350 (t70) REVERT: O 209 ASP cc_start: 0.7096 (t0) cc_final: 0.6401 (t0) REVERT: O 214 ARG cc_start: 0.4762 (mtp85) cc_final: 0.4393 (mtt90) outliers start: 81 outliers final: 58 residues processed: 451 average time/residue: 0.4730 time to fit residues: 325.3127 Evaluate side-chains 429 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 366 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain B residue 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 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 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 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 104 LYS Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 22 MET Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 129 LEU 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 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 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 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 160 VAL 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 131 GLU Chi-restraints excluded: chain O residue 167 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 47 optimal weight: 0.5980 chunk 227 optimal weight: 9.9990 chunk 210 optimal weight: 0.7980 chunk 355 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 275 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 341 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 34 GLN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN J 228 ASN L 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.106329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088556 restraints weight = 48737.689| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.04 r_work: 0.3006 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29088 Z= 0.211 Angle : 0.643 9.399 39760 Z= 0.330 Chirality : 0.045 0.161 4464 Planarity : 0.006 0.076 5344 Dihedral : 6.160 59.891 4101 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 3.09 % Allowed : 19.62 % Favored : 77.29 % 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: -3.10 (0.12), residues: 3744 helix: -2.00 (0.24), residues: 416 sheet: -0.47 (0.18), residues: 816 loop : -2.83 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 76 PHE 0.009 0.001 PHE O 65 TYR 0.011 0.001 TYR M 61 ARG 0.009 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03074 ( 767) hydrogen bonds : angle 6.57727 ( 2526) covalent geometry : bond 0.00512 (29088) covalent geometry : angle 0.64341 (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 461 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 365 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7466 (pm20) REVERT: B 207 GLU cc_start: 0.7982 (pm20) cc_final: 0.7676 (pm20) REVERT: C 22 MET cc_start: 0.9064 (ptm) cc_final: 0.8379 (ptp) REVERT: C 34 GLN cc_start: 0.7975 (mp-120) cc_final: 0.7676 (mp10) REVERT: C 95 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8642 (tt) REVERT: C 182 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8495 (mt) REVERT: D 37 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7867 (mt-10) REVERT: D 200 GLU cc_start: 0.8005 (mp0) cc_final: 0.7594 (mp0) REVERT: F 131 GLU cc_start: 0.8271 (mp0) cc_final: 0.7662 (mp0) REVERT: F 138 ARG cc_start: 0.8317 (ptt-90) cc_final: 0.7787 (ttp-110) REVERT: F 159 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7995 (pp20) REVERT: F 190 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7562 (tp) REVERT: G 131 GLU cc_start: 0.8037 (mp0) cc_final: 0.7534 (mp0) REVERT: G 209 ASP cc_start: 0.7754 (t0) cc_final: 0.6833 (t0) REVERT: G 218 ARG cc_start: 0.8237 (mmm-85) cc_final: 0.7988 (mmt-90) REVERT: H 38 TYR cc_start: 0.9111 (m-80) cc_final: 0.8863 (m-80) REVERT: H 138 ARG cc_start: 0.8229 (ptm-80) cc_final: 0.7970 (ptm-80) REVERT: I 175 ASN cc_start: 0.8046 (m-40) cc_final: 0.7716 (m-40) REVERT: J 169 ASP cc_start: 0.7033 (p0) cc_final: 0.6569 (p0) REVERT: K 131 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: M 79 MET cc_start: 0.8739 (mmt) cc_final: 0.8511 (mmt) REVERT: N 200 GLU cc_start: 0.7296 (mp0) cc_final: 0.6905 (mp0) REVERT: O 5 GLU cc_start: 0.8789 (pt0) cc_final: 0.8559 (pt0) REVERT: O 209 ASP cc_start: 0.7285 (t0) cc_final: 0.6573 (t0) REVERT: O 214 ARG cc_start: 0.4762 (mtp85) cc_final: 0.4308 (mtt90) outliers start: 96 outliers final: 79 residues processed: 437 average time/residue: 0.4359 time to fit residues: 293.4392 Evaluate side-chains 440 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 355 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain B residue 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 126 ARG Chi-restraints excluded: chain B residue 131 GLU 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 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 134 VAL 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 F residue 190 LEU 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 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 112 THR 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 129 LEU Chi-restraints excluded: chain I residue 182 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 208 THR 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 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 134 VAL Chi-restraints excluded: chain L residue 183 SER 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 160 VAL 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 131 GLU Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain O residue 213 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 264 optimal weight: 8.9990 chunk 284 optimal weight: 7.9990 chunk 153 optimal weight: 0.2980 chunk 98 optimal weight: 4.9990 chunk 197 optimal weight: 9.9990 chunk 257 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 174 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN H 102 GLN K 228 ASN L 34 GLN N 228 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.087684 restraints weight = 48532.345| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.03 r_work: 0.2991 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 29088 Z= 0.241 Angle : 0.669 9.612 39760 Z= 0.343 Chirality : 0.045 0.160 4464 Planarity : 0.006 0.071 5344 Dihedral : 6.339 59.961 4101 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 3.12 % Allowed : 19.65 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.16 (0.12), residues: 3744 helix: -2.12 (0.24), residues: 416 sheet: -0.53 (0.18), residues: 816 loop : -2.85 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 76 PHE 0.011 0.001 PHE O 65 TYR 0.011 0.001 TYR P 194 ARG 0.010 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 767) hydrogen bonds : angle 6.65555 ( 2526) covalent geometry : bond 0.00585 (29088) covalent geometry : angle 0.66851 (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 456 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 359 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7503 (pt0) cc_final: 0.6943 (mp0) REVERT: C 22 MET cc_start: 0.9066 (ptm) cc_final: 0.8360 (ptp) REVERT: C 182 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8492 (mt) REVERT: D 37 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7844 (mt-10) REVERT: D 126 ARG cc_start: 0.6675 (ptt90) cc_final: 0.6405 (ttp80) REVERT: D 200 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: F 131 GLU cc_start: 0.8305 (mp0) cc_final: 0.7706 (mp0) REVERT: F 138 ARG cc_start: 0.8327 (ptt-90) cc_final: 0.7782 (ttp-110) REVERT: F 159 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8160 (pp20) REVERT: F 207 GLU cc_start: 0.7199 (mp0) cc_final: 0.6888 (mp0) REVERT: G 131 GLU cc_start: 0.8102 (mp0) cc_final: 0.7655 (mp0) REVERT: G 209 ASP cc_start: 0.7781 (t0) cc_final: 0.6864 (t0) REVERT: G 218 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.7991 (mmt-90) REVERT: H 38 TYR cc_start: 0.9125 (m-80) cc_final: 0.8890 (m-80) REVERT: H 138 ARG cc_start: 0.8220 (ptm-80) cc_final: 0.7955 (ptm-80) REVERT: J 169 ASP cc_start: 0.7064 (p0) cc_final: 0.6597 (p0) REVERT: K 131 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: M 79 MET cc_start: 0.8769 (mmt) cc_final: 0.8541 (mmt) REVERT: N 131 GLU cc_start: 0.8192 (mp0) cc_final: 0.7964 (mp0) REVERT: O 5 GLU cc_start: 0.8803 (pt0) cc_final: 0.8572 (pt0) REVERT: O 209 ASP cc_start: 0.7286 (t0) cc_final: 0.6569 (t0) REVERT: O 214 ARG cc_start: 0.4861 (mtp85) cc_final: 0.4472 (mtt90) REVERT: P 209 ASP cc_start: 0.7472 (t0) cc_final: 0.6576 (t0) outliers start: 97 outliers final: 87 residues processed: 435 average time/residue: 0.4424 time to fit residues: 296.4847 Evaluate side-chains 440 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 349 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 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 126 ARG Chi-restraints excluded: chain B residue 131 GLU 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 D residue 35 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain E residue 22 MET 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 230 LYS Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 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 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 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 97 VAL Chi-restraints excluded: chain H residue 102 GLN Chi-restraints excluded: chain H residue 112 THR 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 129 LEU 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 208 THR 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 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 134 VAL Chi-restraints excluded: chain L residue 183 SER 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 160 VAL 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 110 ASN Chi-restraints excluded: chain O residue 131 GLU Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain O residue 213 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 130 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 chunk 269 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 34 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN J 34 GLN K 228 ASN L 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.090031 restraints weight = 48261.418| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.03 r_work: 0.3033 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29088 Z= 0.158 Angle : 0.610 8.771 39760 Z= 0.314 Chirality : 0.044 0.161 4464 Planarity : 0.006 0.070 5344 Dihedral : 6.064 57.999 4101 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 2.90 % Allowed : 19.97 % Favored : 77.13 % 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: -1.98 (0.24), residues: 416 sheet: -0.48 (0.18), residues: 816 loop : -2.82 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 76 PHE 0.012 0.001 PHE H 101 TYR 0.017 0.001 TYR O 179 ARG 0.010 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.02867 ( 767) hydrogen bonds : angle 6.44542 ( 2526) covalent geometry : bond 0.00389 (29088) covalent geometry : angle 0.60979 (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 457 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 367 time to evaluate : 3.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.6167 (t80) REVERT: A 202 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: A 207 GLU cc_start: 0.7451 (pt0) cc_final: 0.6968 (mp0) REVERT: C 22 MET cc_start: 0.9076 (ptm) cc_final: 0.8414 (ptp) REVERT: C 37 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6779 (mt-10) REVERT: D 37 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7842 (mt-10) REVERT: D 126 ARG cc_start: 0.6578 (ptt90) cc_final: 0.6356 (ttp80) REVERT: E 5 GLU cc_start: 0.8649 (pt0) cc_final: 0.8406 (pt0) REVERT: E 37 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8304 (tt0) REVERT: E 218 ARG cc_start: 0.7778 (ptp-110) cc_final: 0.7509 (ptp90) REVERT: F 131 GLU cc_start: 0.8244 (mp0) cc_final: 0.7687 (mp0) REVERT: F 138 ARG cc_start: 0.8336 (ptt-90) cc_final: 0.7820 (ttp-110) REVERT: F 159 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7903 (pp20) REVERT: F 207 GLU cc_start: 0.7169 (mp0) cc_final: 0.6899 (mp0) REVERT: G 209 ASP cc_start: 0.7689 (t0) cc_final: 0.6804 (t0) REVERT: G 218 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7807 (mmt-90) REVERT: H 138 ARG cc_start: 0.8238 (ptm-80) cc_final: 0.7979 (ptm-80) REVERT: I 175 ASN cc_start: 0.8005 (m-40) cc_final: 0.7672 (m-40) REVERT: I 218 ARG cc_start: 0.8237 (mtp85) cc_final: 0.8003 (mtp85) REVERT: J 169 ASP cc_start: 0.6998 (p0) cc_final: 0.6505 (p0) REVERT: K 131 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: M 79 MET cc_start: 0.8713 (mmt) cc_final: 0.8472 (mmt) REVERT: M 218 ARG cc_start: 0.8418 (mmt90) cc_final: 0.8215 (mmm-85) REVERT: N 200 GLU cc_start: 0.7247 (mp0) cc_final: 0.6838 (mp0) REVERT: O 5 GLU cc_start: 0.8689 (pt0) cc_final: 0.8468 (pt0) REVERT: O 209 ASP cc_start: 0.7252 (t0) cc_final: 0.6540 (t0) REVERT: O 214 ARG cc_start: 0.4961 (mtp85) cc_final: 0.4470 (mtt90) REVERT: P 131 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8332 (pt0) REVERT: P 209 ASP cc_start: 0.7435 (t0) cc_final: 0.6563 (t0) outliers start: 90 outliers final: 79 residues processed: 430 average time/residue: 0.4543 time to fit residues: 299.8307 Evaluate side-chains 442 residues out of total 3104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 358 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain B residue 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 126 ARG Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 38 TYR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 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 227 LEU Chi-restraints excluded: chain G residue 67 SER 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 67 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 112 THR 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 129 LEU 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 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 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 134 VAL Chi-restraints excluded: chain L residue 183 SER 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 160 VAL 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 131 GLU Chi-restraints excluded: chain O residue 167 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 131 GLU 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: 9.9990 chunk 20 optimal weight: 8.9990 chunk 163 optimal weight: 0.7980 chunk 365 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 345 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN H 102 GLN K 228 ASN L 34 GLN N 132 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.085654 restraints weight = 48936.239| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.04 r_work: 0.2961 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 29088 Z= 0.334 Angle : 0.744 13.252 39760 Z= 0.380 Chirality : 0.048 0.179 4464 Planarity : 0.007 0.074 5344 Dihedral : 6.601 59.452 4101 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 3.19 % Allowed : 19.88 % Favored : 76.93 % 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: -3.22 (0.12), residues: 3744 helix: -2.19 (0.23), residues: 416 sheet: -0.60 (0.18), residues: 816 loop : -2.87 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 76 PHE 0.013 0.002 PHE O 65 TYR 0.018 0.002 TYR O 179 ARG 0.009 0.001 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 767) hydrogen bonds : angle 6.83080 ( 2526) covalent geometry : bond 0.00808 (29088) covalent geometry : angle 0.74374 (39760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14545.39 seconds wall clock time: 252 minutes 13.77 seconds (15133.77 seconds total)