Starting phenix.real_space_refine on Thu Mar 5 07:14:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vgn_21198/03_2026/6vgn_21198.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vgn_21198/03_2026/6vgn_21198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vgn_21198/03_2026/6vgn_21198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vgn_21198/03_2026/6vgn_21198.map" model { file = "/net/cci-nas-00/data/ceres_data/6vgn_21198/03_2026/6vgn_21198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vgn_21198/03_2026/6vgn_21198.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.360 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: 5 Type Number sf(0) Gaussians S 119 5.16 5 C 12922 2.51 5 N 3444 2.21 5 O 3948 1.98 5 F 14 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20447 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1508 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "H" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "V" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Unusual residues: {'R0M': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="R0M V 1 " pdbres="WFP V 2 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'R0M:plan-1': 1, 'WFP:plan-2': 1, 'ALO:plan-1': 1, 'YCP:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 5 Restraints were copied for chains: B, C, D, E, F, G, I, J, K, L, M, N, W, X, Y, Z, a, b Time building chain proxies: 2.33, per 1000 atoms: 0.11 Number of scatterers: 20447 At special positions: 0 Unit cell: (115.54, 115.54, 117.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 119 16.00 F 14 9.00 O 3948 8.00 N 3444 7.00 C 12922 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4956 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 35 sheets defined 50.3% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 49 through 67 removed outlier: 3.938A pdb=" N ASP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 110 through 118 removed outlier: 3.761A pdb=" N VAL A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 173 removed outlier: 4.283A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'B' and resid 33 through 39 Processing helix chain 'B' and resid 49 through 67 removed outlier: 3.938A pdb=" N ASP B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 96 Processing helix chain 'B' and resid 110 through 118 removed outlier: 3.761A pdb=" N VAL B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 173 removed outlier: 4.284A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'C' and resid 33 through 39 Processing helix chain 'C' and resid 49 through 67 removed outlier: 3.938A pdb=" N ASP C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 96 Processing helix chain 'C' and resid 110 through 118 removed outlier: 3.760A pdb=" N VAL C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 173 removed outlier: 4.283A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'D' and resid 33 through 39 Processing helix chain 'D' and resid 49 through 67 removed outlier: 3.938A pdb=" N ASP D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 Processing helix chain 'D' and resid 110 through 118 removed outlier: 3.761A pdb=" N VAL D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 173 removed outlier: 4.283A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'E' and resid 33 through 39 Processing helix chain 'E' and resid 49 through 67 removed outlier: 3.938A pdb=" N ASP E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 96 Processing helix chain 'E' and resid 110 through 118 removed outlier: 3.761A pdb=" N VAL E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 173 removed outlier: 4.283A pdb=" N ALA E 154 " --> pdb=" O LEU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 184 Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'F' and resid 33 through 39 Processing helix chain 'F' and resid 49 through 67 removed outlier: 3.937A pdb=" N ASP F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 96 Processing helix chain 'F' and resid 110 through 118 removed outlier: 3.760A pdb=" N VAL F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 173 removed outlier: 4.283A pdb=" N ALA F 154 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 184 Processing helix chain 'F' and resid 192 through 197 Processing helix chain 'G' and resid 33 through 39 Processing helix chain 'G' and resid 49 through 67 removed outlier: 3.938A pdb=" N ASP G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 96 Processing helix chain 'G' and resid 110 through 118 removed outlier: 3.761A pdb=" N VAL G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 173 removed outlier: 4.283A pdb=" N ALA G 154 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 184 Processing helix chain 'G' and resid 192 through 197 Processing helix chain 'H' and resid 16 through 26 Processing helix chain 'H' and resid 37 through 55 Processing helix chain 'H' and resid 70 through 84 Processing helix chain 'H' and resid 98 through 106 Processing helix chain 'H' and resid 132 through 159 removed outlier: 3.900A pdb=" N ILE H 138 " --> pdb=" O ALA H 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 170 Processing helix chain 'H' and resid 177 through 183 Processing helix chain 'I' and resid 16 through 26 Processing helix chain 'I' and resid 37 through 55 Processing helix chain 'I' and resid 70 through 84 Processing helix chain 'I' and resid 98 through 106 Processing helix chain 'I' and resid 132 through 159 removed outlier: 3.900A pdb=" N ILE I 138 " --> pdb=" O ALA I 134 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU I 141 " --> pdb=" O ALA I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 170 Processing helix chain 'I' and resid 177 through 183 Processing helix chain 'J' and resid 16 through 26 Processing helix chain 'J' and resid 37 through 55 Processing helix chain 'J' and resid 70 through 84 Processing helix chain 'J' and resid 98 through 106 Processing helix chain 'J' and resid 132 through 159 removed outlier: 3.899A pdb=" N ILE J 138 " --> pdb=" O ALA J 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU J 141 " --> pdb=" O ALA J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 170 Processing helix chain 'J' and resid 177 through 183 Processing helix chain 'K' and resid 16 through 26 Processing helix chain 'K' and resid 37 through 55 Processing helix chain 'K' and resid 70 through 84 Processing helix chain 'K' and resid 98 through 106 Processing helix chain 'K' and resid 132 through 159 removed outlier: 3.900A pdb=" N ILE K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU K 141 " --> pdb=" O ALA K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 170 Processing helix chain 'K' and resid 177 through 183 Processing helix chain 'L' and resid 16 through 26 Processing helix chain 'L' and resid 37 through 55 Processing helix chain 'L' and resid 70 through 84 Processing helix chain 'L' and resid 98 through 106 Processing helix chain 'L' and resid 132 through 159 removed outlier: 3.900A pdb=" N ILE L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU L 141 " --> pdb=" O ALA L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 170 Processing helix chain 'L' and resid 177 through 183 Processing helix chain 'M' and resid 16 through 26 Processing helix chain 'M' and resid 37 through 55 Processing helix chain 'M' and resid 70 through 84 Processing helix chain 'M' and resid 98 through 106 Processing helix chain 'M' and resid 132 through 159 removed outlier: 3.900A pdb=" N ILE M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU M 141 " --> pdb=" O ALA M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 170 Processing helix chain 'M' and resid 177 through 183 Processing helix chain 'N' and resid 16 through 26 Processing helix chain 'N' and resid 37 through 55 Processing helix chain 'N' and resid 70 through 84 Processing helix chain 'N' and resid 98 through 106 Processing helix chain 'N' and resid 132 through 159 removed outlier: 3.900A pdb=" N ILE N 138 " --> pdb=" O ALA N 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 170 Processing helix chain 'N' and resid 177 through 183 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER A 78 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN A 107 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG A 131 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY A 106 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU A 133 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER A 78 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN A 107 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N MET A 125 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR A 102 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 23 Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER B 78 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN B 107 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG B 131 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY B 106 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU B 133 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER B 78 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN B 107 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N MET B 125 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR B 102 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 41 through 44 removed outlier: 5.243A pdb=" N SER C 78 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN C 107 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG C 131 " --> pdb=" O CYS C 104 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY C 106 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU C 133 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA C 108 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 41 through 44 removed outlier: 5.243A pdb=" N SER C 78 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN C 107 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N MET C 125 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR C 102 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 41 through 44 removed outlier: 5.243A pdb=" N SER D 78 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN D 107 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG D 131 " --> pdb=" O CYS D 104 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY D 106 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU D 133 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA D 108 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 41 through 44 removed outlier: 5.243A pdb=" N SER D 78 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN D 107 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N MET D 125 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR D 102 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'E' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER E 78 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN E 107 " --> pdb=" O SER E 78 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ARG E 131 " --> pdb=" O CYS E 104 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY E 106 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU E 133 " --> pdb=" O GLY E 106 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA E 108 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER E 78 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN E 107 " --> pdb=" O SER E 78 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N MET E 125 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR E 102 " --> pdb=" O MET E 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AB8, first strand: chain 'F' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER F 78 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN F 107 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG F 131 " --> pdb=" O CYS F 104 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY F 106 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU F 133 " --> pdb=" O GLY F 106 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA F 108 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER F 78 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN F 107 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N MET F 125 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR F 102 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 19 through 23 Processing sheet with id=AC2, first strand: chain 'G' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER G 78 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN G 107 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG G 131 " --> pdb=" O CYS G 104 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY G 106 " --> pdb=" O ARG G 131 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU G 133 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER G 78 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN G 107 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N MET G 125 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR G 102 " --> pdb=" O MET G 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE H 30 " --> pdb=" O TYR H 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN H 65 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU H 32 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER H 66 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET H 95 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG H 119 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY H 94 " --> pdb=" O ARG H 119 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU H 121 " --> pdb=" O GLY H 94 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA H 96 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET H 122 " --> pdb=" O ARG H 173 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ARG H 173 " --> pdb=" O MET H 122 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE H 30 " --> pdb=" O TYR H 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN H 65 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU H 32 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER H 66 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET H 95 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR H 113 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR H 90 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.587A pdb=" N ILE I 30 " --> pdb=" O TYR I 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN I 65 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU I 32 " --> pdb=" O ASN I 65 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N SER I 66 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N MET I 95 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG I 119 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY I 94 " --> pdb=" O ARG I 119 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU I 121 " --> pdb=" O GLY I 94 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA I 96 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET I 122 " --> pdb=" O ARG I 173 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG I 173 " --> pdb=" O MET I 122 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.587A pdb=" N ILE I 30 " --> pdb=" O TYR I 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN I 65 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU I 32 " --> pdb=" O ASN I 65 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N SER I 66 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N MET I 95 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N TYR I 113 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR I 90 " --> pdb=" O TYR I 113 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE J 30 " --> pdb=" O TYR J 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN J 65 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU J 32 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER J 66 " --> pdb=" O MET J 93 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG J 119 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY J 94 " --> pdb=" O ARG J 119 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU J 121 " --> pdb=" O GLY J 94 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA J 96 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET J 122 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG J 173 " --> pdb=" O MET J 122 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE J 30 " --> pdb=" O TYR J 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN J 65 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU J 32 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER J 66 " --> pdb=" O MET J 93 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR J 113 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR J 90 " --> pdb=" O TYR J 113 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.587A pdb=" N ILE K 30 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN K 65 " --> pdb=" O ILE K 30 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU K 32 " --> pdb=" O ASN K 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER K 66 " --> pdb=" O MET K 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET K 95 " --> pdb=" O SER K 66 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG K 119 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY K 94 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU K 121 " --> pdb=" O GLY K 94 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA K 96 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET K 122 " --> pdb=" O ARG K 173 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG K 173 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.587A pdb=" N ILE K 30 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN K 65 " --> pdb=" O ILE K 30 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU K 32 " --> pdb=" O ASN K 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER K 66 " --> pdb=" O MET K 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET K 95 " --> pdb=" O SER K 66 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR K 113 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR K 90 " --> pdb=" O TYR K 113 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE L 30 " --> pdb=" O TYR L 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN L 65 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU L 32 " --> pdb=" O ASN L 65 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N SER L 66 " --> pdb=" O MET L 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET L 95 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG L 119 " --> pdb=" O ALA L 92 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY L 94 " --> pdb=" O ARG L 119 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU L 121 " --> pdb=" O GLY L 94 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA L 96 " --> pdb=" O LEU L 121 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET L 122 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ARG L 173 " --> pdb=" O MET L 122 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE L 30 " --> pdb=" O TYR L 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN L 65 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU L 32 " --> pdb=" O ASN L 65 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N SER L 66 " --> pdb=" O MET L 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET L 95 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR L 113 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR L 90 " --> pdb=" O TYR L 113 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.587A pdb=" N ILE M 30 " --> pdb=" O TYR M 63 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN M 65 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU M 32 " --> pdb=" O ASN M 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER M 66 " --> pdb=" O MET M 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET M 95 " --> pdb=" O SER M 66 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG M 119 " --> pdb=" O ALA M 92 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY M 94 " --> pdb=" O ARG M 119 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU M 121 " --> pdb=" O GLY M 94 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA M 96 " --> pdb=" O LEU M 121 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET M 122 " --> pdb=" O ARG M 173 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG M 173 " --> pdb=" O MET M 122 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.587A pdb=" N ILE M 30 " --> pdb=" O TYR M 63 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN M 65 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU M 32 " --> pdb=" O ASN M 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER M 66 " --> pdb=" O MET M 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET M 95 " --> pdb=" O SER M 66 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR M 113 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR M 90 " --> pdb=" O TYR M 113 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE N 30 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN N 65 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU N 32 " --> pdb=" O ASN N 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER N 66 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG N 119 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY N 94 " --> pdb=" O ARG N 119 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU N 121 " --> pdb=" O GLY N 94 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA N 96 " --> pdb=" O LEU N 121 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET N 122 " --> pdb=" O ARG N 173 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG N 173 " --> pdb=" O MET N 122 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE N 30 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN N 65 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU N 32 " --> pdb=" O ASN N 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER N 66 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N TYR N 113 " --> pdb=" O ILE N 88 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR N 90 " --> pdb=" O TYR N 113 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3528 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: 3.58 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4123 1.31 - 1.44: 5408 1.44 - 1.57: 10971 1.57 - 1.70: 43 1.70 - 1.83: 217 Bond restraints: 20762 Sorted by residual: bond pdb=" N MP8 X 7 " pdb=" CA MP8 X 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.06e+02 bond pdb=" N MP8 b 7 " pdb=" CA MP8 b 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.05e+02 bond pdb=" N MP8 Z 7 " pdb=" CA MP8 Z 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.05e+02 bond pdb=" N MP8 V 7 " pdb=" CA MP8 V 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.05e+02 bond pdb=" N MP8 W 7 " pdb=" CA MP8 W 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.05e+02 ... (remaining 20757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 26226 3.40 - 6.80: 1744 6.80 - 10.20: 58 10.20 - 13.60: 28 13.60 - 17.00: 7 Bond angle restraints: 28063 Sorted by residual: angle pdb=" C MP8 a 7 " pdb=" CA MP8 a 7 " pdb=" CB MP8 a 7 " ideal model delta sigma weight residual 110.10 127.10 -17.00 1.90e+00 2.77e-01 8.01e+01 angle pdb=" C MP8 Y 7 " pdb=" CA MP8 Y 7 " pdb=" CB MP8 Y 7 " ideal model delta sigma weight residual 110.10 127.10 -17.00 1.90e+00 2.77e-01 8.00e+01 angle pdb=" C MP8 W 7 " pdb=" CA MP8 W 7 " pdb=" CB MP8 W 7 " ideal model delta sigma weight residual 110.10 127.07 -16.97 1.90e+00 2.77e-01 7.98e+01 angle pdb=" C MP8 V 7 " pdb=" CA MP8 V 7 " pdb=" CB MP8 V 7 " ideal model delta sigma weight residual 110.10 127.06 -16.96 1.90e+00 2.77e-01 7.97e+01 angle pdb=" C MP8 b 7 " pdb=" CA MP8 b 7 " pdb=" CB MP8 b 7 " ideal model delta sigma weight residual 110.10 127.06 -16.96 1.90e+00 2.77e-01 7.97e+01 ... (remaining 28058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.31: 12348 24.31 - 48.62: 217 48.62 - 72.93: 49 72.93 - 97.24: 35 97.24 - 121.56: 7 Dihedral angle restraints: 12656 sinusoidal: 4977 harmonic: 7679 Sorted by residual: dihedral pdb=" C MP8 b 7 " pdb=" N MP8 b 7 " pdb=" CA MP8 b 7 " pdb=" CB MP8 b 7 " ideal model delta harmonic sigma weight residual -122.60 -170.85 48.25 0 2.50e+00 1.60e-01 3.73e+02 dihedral pdb=" C MP8 W 7 " pdb=" N MP8 W 7 " pdb=" CA MP8 W 7 " pdb=" CB MP8 W 7 " ideal model delta harmonic sigma weight residual -122.60 -170.83 48.23 0 2.50e+00 1.60e-01 3.72e+02 dihedral pdb=" C MP8 X 7 " pdb=" N MP8 X 7 " pdb=" CA MP8 X 7 " pdb=" CB MP8 X 7 " ideal model delta harmonic sigma weight residual -122.60 -170.81 48.21 0 2.50e+00 1.60e-01 3.72e+02 ... (remaining 12653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.480: 3241 0.480 - 0.961: 0 0.961 - 1.441: 0 1.441 - 1.921: 0 1.921 - 2.402: 7 Chirality restraints: 3248 Sorted by residual: chirality pdb=" CA MP8 b 7 " pdb=" N MP8 b 7 " pdb=" C MP8 b 7 " pdb=" CB MP8 b 7 " both_signs ideal model delta sigma weight residual False 2.72 0.32 2.40 2.00e-01 2.50e+01 1.44e+02 chirality pdb=" CA MP8 W 7 " pdb=" N MP8 W 7 " pdb=" C MP8 W 7 " pdb=" CB MP8 W 7 " both_signs ideal model delta sigma weight residual False 2.72 0.32 2.40 2.00e-01 2.50e+01 1.44e+02 chirality pdb=" CA MP8 X 7 " pdb=" N MP8 X 7 " pdb=" C MP8 X 7 " pdb=" CB MP8 X 7 " both_signs ideal model delta sigma weight residual False 2.72 0.32 2.40 2.00e-01 2.50e+01 1.44e+02 ... (remaining 3245 not shown) Planarity restraints: 3640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 149 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C ASP E 149 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP E 149 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU E 150 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 149 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ASP C 149 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP C 149 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU C 150 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 149 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ASP B 149 " 0.056 2.00e-02 2.50e+03 pdb=" O ASP B 149 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 150 " -0.019 2.00e-02 2.50e+03 ... (remaining 3637 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 8682 2.90 - 3.40: 20650 3.40 - 3.90: 36080 3.90 - 4.40: 42999 4.40 - 4.90: 67943 Nonbonded interactions: 176354 Sorted by model distance: nonbonded pdb=" N PRO E 32 " pdb=" O PRO E 32 " model vdw 2.401 2.496 nonbonded pdb=" N PRO B 32 " pdb=" O PRO B 32 " model vdw 2.401 2.496 nonbonded pdb=" N PRO A 32 " pdb=" O PRO A 32 " model vdw 2.401 2.496 nonbonded pdb=" N PRO D 32 " pdb=" O PRO D 32 " model vdw 2.401 2.496 nonbonded pdb=" N PRO G 32 " pdb=" O PRO G 32 " model vdw 2.401 2.496 ... (remaining 176349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } 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: 0.010 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.430 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 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 : 0.021 0.213 20776 Z= 1.127 Angle : 1.786 17.003 28063 Z= 1.172 Chirality : 0.141 2.402 3248 Planarity : 0.009 0.040 3640 Dihedral : 12.019 121.555 7700 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 2590 helix: -0.38 (0.12), residues: 1358 sheet: 2.07 (0.31), residues: 231 loop : 0.36 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 124 TYR 0.038 0.008 TYR N 183 PHE 0.022 0.004 PHE D 43 TRP 0.007 0.004 TRP L 174 HIS 0.010 0.003 HIS I 123 Details of bonding type rmsd covalent geometry : bond 0.02090 (20762) covalent geometry : angle 1.78604 (28063) hydrogen bonds : bond 0.16131 ( 1106) hydrogen bonds : angle 7.12939 ( 3528) Misc. bond : bond 0.08146 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 0.726 Fit side-chains REVERT: A 21 GLU cc_start: 0.8015 (tt0) cc_final: 0.7114 (pt0) REVERT: A 164 MET cc_start: 0.6760 (ttm) cc_final: 0.6526 (ttt) REVERT: A 175 ASP cc_start: 0.7455 (t70) cc_final: 0.7217 (m-30) REVERT: B 21 GLU cc_start: 0.7723 (tt0) cc_final: 0.7047 (pt0) REVERT: B 25 PHE cc_start: 0.5660 (m-10) cc_final: 0.5370 (m-80) REVERT: B 135 HIS cc_start: 0.6670 (m-70) cc_final: 0.6443 (m170) REVERT: B 164 MET cc_start: 0.6959 (ttm) cc_final: 0.6564 (ttt) REVERT: B 175 ASP cc_start: 0.7556 (t70) cc_final: 0.7194 (m-30) REVERT: C 21 GLU cc_start: 0.7347 (tt0) cc_final: 0.7034 (pt0) REVERT: C 135 HIS cc_start: 0.6446 (m-70) cc_final: 0.6100 (m-70) REVERT: C 164 MET cc_start: 0.6904 (ttm) cc_final: 0.6570 (ttt) REVERT: C 175 ASP cc_start: 0.7664 (t70) cc_final: 0.6878 (m-30) REVERT: D 164 MET cc_start: 0.6615 (ttm) cc_final: 0.6242 (ttt) REVERT: D 190 THR cc_start: 0.8332 (p) cc_final: 0.7975 (t) REVERT: E 21 GLU cc_start: 0.7310 (tt0) cc_final: 0.6957 (pt0) REVERT: E 164 MET cc_start: 0.6483 (ttm) cc_final: 0.6117 (ttt) REVERT: F 21 GLU cc_start: 0.7898 (tt0) cc_final: 0.7157 (pt0) REVERT: F 95 TYR cc_start: 0.8138 (t80) cc_final: 0.7915 (t80) REVERT: F 164 MET cc_start: 0.6634 (ttm) cc_final: 0.6249 (ttt) REVERT: G 164 MET cc_start: 0.7029 (ttm) cc_final: 0.6675 (ttt) REVERT: G 175 ASP cc_start: 0.7464 (t70) cc_final: 0.6848 (m-30) REVERT: G 200 ILE cc_start: 0.8180 (mm) cc_final: 0.7971 (mt) REVERT: H 70 SER cc_start: 0.7951 (m) cc_final: 0.7720 (p) REVERT: H 150 MET cc_start: 0.7473 (ttt) cc_final: 0.7068 (ttt) REVERT: H 179 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8327 (mt-10) REVERT: I 70 SER cc_start: 0.8154 (m) cc_final: 0.7807 (p) REVERT: J 70 SER cc_start: 0.8173 (m) cc_final: 0.7889 (p) REVERT: J 166 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8261 (mt-10) REVERT: J 179 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8176 (mt-10) REVERT: K 75 MET cc_start: 0.8426 (mmt) cc_final: 0.8129 (tpp) REVERT: L 158 THR cc_start: 0.8268 (p) cc_final: 0.8053 (p) REVERT: L 163 GLU cc_start: 0.8364 (mp0) cc_final: 0.7685 (pm20) REVERT: M 79 ASP cc_start: 0.8229 (m-30) cc_final: 0.7992 (m-30) REVERT: M 163 GLU cc_start: 0.8287 (mp0) cc_final: 0.7809 (pm20) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.1449 time to fit residues: 101.3278 Evaluate side-chains 308 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.149145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.125074 restraints weight = 23695.250| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.27 r_work: 0.3300 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20776 Z= 0.172 Angle : 0.631 7.080 28063 Z= 0.331 Chirality : 0.043 0.183 3248 Planarity : 0.004 0.031 3640 Dihedral : 10.484 101.294 2975 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.71 % Allowed : 4.38 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.16), residues: 2590 helix: 1.19 (0.14), residues: 1379 sheet: 3.22 (0.29), residues: 245 loop : -0.43 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 97 TYR 0.013 0.002 TYR M 21 PHE 0.015 0.002 PHE K 175 TRP 0.008 0.001 TRP M 174 HIS 0.006 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00401 (20762) covalent geometry : angle 0.63134 (28063) hydrogen bonds : bond 0.03608 ( 1106) hydrogen bonds : angle 4.75137 ( 3528) Misc. bond : bond 0.00106 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 456 time to evaluate : 0.674 Fit side-chains REVERT: A 93 MET cc_start: 0.8360 (mtp) cc_final: 0.8138 (mtp) REVERT: A 164 MET cc_start: 0.7318 (ttm) cc_final: 0.6913 (ttt) REVERT: A 175 ASP cc_start: 0.7535 (t70) cc_final: 0.7151 (m-30) REVERT: B 164 MET cc_start: 0.7576 (ttm) cc_final: 0.7124 (ttt) REVERT: B 175 ASP cc_start: 0.7584 (t70) cc_final: 0.7144 (m-30) REVERT: C 93 MET cc_start: 0.8652 (mtp) cc_final: 0.8313 (mtp) REVERT: C 164 MET cc_start: 0.7428 (ttm) cc_final: 0.7034 (ttt) REVERT: C 175 ASP cc_start: 0.7477 (t70) cc_final: 0.6847 (m-30) REVERT: D 74 MET cc_start: 0.8638 (ttm) cc_final: 0.8376 (mtp) REVERT: D 164 MET cc_start: 0.7197 (ttm) cc_final: 0.6834 (ttt) REVERT: D 175 ASP cc_start: 0.6976 (t70) cc_final: 0.6455 (m-30) REVERT: E 135 HIS cc_start: 0.7647 (t-170) cc_final: 0.7275 (t-170) REVERT: E 164 MET cc_start: 0.7279 (ttm) cc_final: 0.6895 (ttt) REVERT: F 21 GLU cc_start: 0.7987 (tt0) cc_final: 0.7763 (pt0) REVERT: F 93 MET cc_start: 0.8418 (mtp) cc_final: 0.8048 (mtp) REVERT: F 164 MET cc_start: 0.7210 (ttm) cc_final: 0.6846 (ttt) REVERT: F 175 ASP cc_start: 0.7444 (t70) cc_final: 0.6830 (m-30) REVERT: G 164 MET cc_start: 0.7431 (ttm) cc_final: 0.6994 (ttt) REVERT: G 175 ASP cc_start: 0.7423 (t70) cc_final: 0.6864 (m-30) REVERT: H 122 MET cc_start: 0.7113 (ttp) cc_final: 0.6894 (ttp) REVERT: H 150 MET cc_start: 0.8044 (ttt) cc_final: 0.7567 (ttt) REVERT: H 158 THR cc_start: 0.8581 (p) cc_final: 0.8315 (p) REVERT: H 163 GLU cc_start: 0.8116 (mp0) cc_final: 0.7647 (pm20) REVERT: H 183 TYR cc_start: 0.8480 (t80) cc_final: 0.8120 (t80) REVERT: I 75 MET cc_start: 0.8303 (mmt) cc_final: 0.7904 (mmp) REVERT: I 79 ASP cc_start: 0.7865 (m-30) cc_final: 0.7579 (m-30) REVERT: I 109 LYS cc_start: 0.8422 (mttp) cc_final: 0.8172 (mmtm) REVERT: J 166 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7693 (mt-10) REVERT: J 183 TYR cc_start: 0.8471 (t80) cc_final: 0.8269 (t80) REVERT: K 150 MET cc_start: 0.7870 (ttt) cc_final: 0.7522 (ttt) REVERT: K 162 ILE cc_start: 0.7713 (tp) cc_final: 0.7499 (tt) REVERT: K 163 GLU cc_start: 0.8198 (mp0) cc_final: 0.7692 (pm20) REVERT: K 183 TYR cc_start: 0.8424 (t80) cc_final: 0.8126 (t80) REVERT: L 109 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8135 (mttp) REVERT: L 158 THR cc_start: 0.8534 (p) cc_final: 0.8298 (p) REVERT: L 163 GLU cc_start: 0.8450 (mp0) cc_final: 0.7734 (pm20) REVERT: M 109 LYS cc_start: 0.8382 (mttp) cc_final: 0.8159 (mmtm) REVERT: M 141 GLU cc_start: 0.7437 (tp30) cc_final: 0.7191 (tp30) REVERT: M 163 GLU cc_start: 0.8354 (mp0) cc_final: 0.7802 (pm20) REVERT: N 109 LYS cc_start: 0.8518 (mttp) cc_final: 0.7752 (mmtm) outliers start: 15 outliers final: 9 residues processed: 463 average time/residue: 0.1509 time to fit residues: 105.1904 Evaluate side-chains 370 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 360 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 115 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 221 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 199 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN C 77 ASN C 129 ASN F 129 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.154642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129579 restraints weight = 23551.116| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.40 r_work: 0.3321 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20776 Z= 0.111 Angle : 0.539 7.662 28063 Z= 0.280 Chirality : 0.041 0.160 3248 Planarity : 0.004 0.033 3640 Dihedral : 9.540 108.284 2975 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.94 % Allowed : 6.88 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.16), residues: 2590 helix: 1.80 (0.14), residues: 1358 sheet: 2.32 (0.31), residues: 259 loop : -0.40 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 23 TYR 0.019 0.001 TYR F 197 PHE 0.010 0.001 PHE L 185 TRP 0.004 0.001 TRP M 174 HIS 0.006 0.001 HIS G 135 Details of bonding type rmsd covalent geometry : bond 0.00239 (20762) covalent geometry : angle 0.53901 (28063) hydrogen bonds : bond 0.03023 ( 1106) hydrogen bonds : angle 4.27328 ( 3528) Misc. bond : bond 0.00034 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 385 time to evaluate : 0.727 Fit side-chains REVERT: A 93 MET cc_start: 0.8320 (mtp) cc_final: 0.8099 (mtp) REVERT: A 135 HIS cc_start: 0.6705 (m170) cc_final: 0.6376 (m170) REVERT: A 164 MET cc_start: 0.7207 (ttm) cc_final: 0.6804 (ttt) REVERT: A 175 ASP cc_start: 0.7341 (t70) cc_final: 0.7047 (m-30) REVERT: B 164 MET cc_start: 0.7336 (ttm) cc_final: 0.6917 (ttt) REVERT: B 175 ASP cc_start: 0.7400 (t70) cc_final: 0.6854 (m-30) REVERT: C 93 MET cc_start: 0.8393 (mtp) cc_final: 0.8004 (mtp) REVERT: C 164 MET cc_start: 0.7279 (ttm) cc_final: 0.6883 (ttt) REVERT: C 175 ASP cc_start: 0.7468 (t70) cc_final: 0.6681 (m-30) REVERT: D 74 MET cc_start: 0.8774 (ttm) cc_final: 0.8540 (mtp) REVERT: D 135 HIS cc_start: 0.7268 (t-170) cc_final: 0.6958 (t-170) REVERT: D 164 MET cc_start: 0.7203 (ttm) cc_final: 0.6795 (ttt) REVERT: D 175 ASP cc_start: 0.7068 (t70) cc_final: 0.6557 (m-30) REVERT: E 135 HIS cc_start: 0.7580 (t-170) cc_final: 0.7354 (t-170) REVERT: E 164 MET cc_start: 0.7133 (ttm) cc_final: 0.6772 (ttt) REVERT: F 50 ASP cc_start: 0.6771 (t70) cc_final: 0.6551 (t70) REVERT: F 93 MET cc_start: 0.8278 (mtp) cc_final: 0.7916 (mtp) REVERT: F 164 MET cc_start: 0.7075 (ttm) cc_final: 0.6752 (ttt) REVERT: F 175 ASP cc_start: 0.7481 (t70) cc_final: 0.6830 (m-30) REVERT: G 164 MET cc_start: 0.7268 (ttm) cc_final: 0.6847 (ttt) REVERT: G 175 ASP cc_start: 0.7468 (t70) cc_final: 0.6796 (m-30) REVERT: H 150 MET cc_start: 0.7959 (ttt) cc_final: 0.7540 (ttt) REVERT: H 158 THR cc_start: 0.8358 (p) cc_final: 0.8101 (p) REVERT: H 163 GLU cc_start: 0.8039 (mp0) cc_final: 0.7592 (pm20) REVERT: H 173 ARG cc_start: 0.7200 (ttt180) cc_final: 0.6906 (ptm160) REVERT: H 183 TYR cc_start: 0.8414 (t80) cc_final: 0.8049 (t80) REVERT: I 75 MET cc_start: 0.8332 (mmt) cc_final: 0.8086 (mmt) REVERT: I 173 ARG cc_start: 0.7356 (ttt180) cc_final: 0.7023 (ptm160) REVERT: J 166 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7759 (mt-10) REVERT: K 150 MET cc_start: 0.7782 (ttt) cc_final: 0.7511 (ttt) REVERT: K 162 ILE cc_start: 0.7652 (tp) cc_final: 0.7451 (tt) REVERT: K 163 GLU cc_start: 0.8147 (mp0) cc_final: 0.7645 (pm20) REVERT: K 182 GLU cc_start: 0.8376 (tp30) cc_final: 0.8169 (tp30) REVERT: L 158 THR cc_start: 0.8257 (p) cc_final: 0.8001 (p) REVERT: L 163 GLU cc_start: 0.8477 (mp0) cc_final: 0.7674 (pm20) REVERT: L 183 TYR cc_start: 0.8442 (t80) cc_final: 0.8192 (t80) REVERT: M 163 GLU cc_start: 0.8220 (mp0) cc_final: 0.7635 (pm20) REVERT: M 166 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7370 (mt-10) REVERT: N 79 ASP cc_start: 0.7991 (m-30) cc_final: 0.7774 (m-30) REVERT: N 141 GLU cc_start: 0.7012 (tp30) cc_final: 0.6750 (tp30) outliers start: 20 outliers final: 10 residues processed: 400 average time/residue: 0.1560 time to fit residues: 94.8543 Evaluate side-chains 352 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 342 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 196 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114184 restraints weight = 24812.196| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.31 r_work: 0.3161 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 20776 Z= 0.318 Angle : 0.725 9.375 28063 Z= 0.374 Chirality : 0.048 0.182 3248 Planarity : 0.005 0.037 3640 Dihedral : 9.580 104.460 2975 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.25 % Favored : 95.71 % Rotamer: Outliers : 1.56 % Allowed : 8.30 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.16), residues: 2590 helix: 1.30 (0.14), residues: 1372 sheet: 1.99 (0.29), residues: 259 loop : -0.84 (0.18), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 97 TYR 0.029 0.003 TYR I 183 PHE 0.017 0.002 PHE A 25 TRP 0.009 0.001 TRP M 174 HIS 0.006 0.002 HIS G 135 Details of bonding type rmsd covalent geometry : bond 0.00767 (20762) covalent geometry : angle 0.72493 (28063) hydrogen bonds : bond 0.04497 ( 1106) hydrogen bonds : angle 4.59574 ( 3528) Misc. bond : bond 0.00144 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 354 time to evaluate : 0.609 Fit side-chains REVERT: A 95 TYR cc_start: 0.8623 (t80) cc_final: 0.8346 (t80) REVERT: A 175 ASP cc_start: 0.7423 (t70) cc_final: 0.7197 (m-30) REVERT: A 200 ILE cc_start: 0.8626 (mm) cc_final: 0.8323 (mt) REVERT: B 21 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8219 (mt-10) REVERT: B 161 ARG cc_start: 0.7631 (mtp180) cc_final: 0.7288 (mtp-110) REVERT: B 164 MET cc_start: 0.7744 (ttm) cc_final: 0.7345 (ttt) REVERT: B 175 ASP cc_start: 0.7619 (t70) cc_final: 0.6996 (m-30) REVERT: B 207 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.6795 (ttm-80) REVERT: C 39 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7864 (mm-30) REVERT: C 164 MET cc_start: 0.7365 (ttm) cc_final: 0.7063 (ttt) REVERT: C 175 ASP cc_start: 0.7640 (t70) cc_final: 0.7022 (m-30) REVERT: C 200 ILE cc_start: 0.8600 (mm) cc_final: 0.8303 (mt) REVERT: D 135 HIS cc_start: 0.7616 (t-170) cc_final: 0.7310 (t-170) REVERT: D 161 ARG cc_start: 0.7712 (mtp180) cc_final: 0.7489 (mtp180) REVERT: D 164 MET cc_start: 0.7524 (ttm) cc_final: 0.7175 (ttt) REVERT: D 175 ASP cc_start: 0.7303 (t70) cc_final: 0.6997 (m-30) REVERT: D 207 ARG cc_start: 0.7475 (ttm-80) cc_final: 0.6922 (ttm-80) REVERT: E 74 MET cc_start: 0.8801 (ttm) cc_final: 0.8586 (ttm) REVERT: E 125 MET cc_start: 0.8988 (mtm) cc_final: 0.8661 (mtm) REVERT: E 135 HIS cc_start: 0.7759 (t-170) cc_final: 0.7514 (t-170) REVERT: E 164 MET cc_start: 0.7389 (ttm) cc_final: 0.7132 (ttt) REVERT: E 175 ASP cc_start: 0.7421 (t70) cc_final: 0.7045 (m-30) REVERT: E 200 ILE cc_start: 0.8483 (mm) cc_final: 0.8151 (mt) REVERT: F 125 MET cc_start: 0.9051 (mtm) cc_final: 0.8555 (mtm) REVERT: F 164 MET cc_start: 0.7551 (ttm) cc_final: 0.7225 (ttt) REVERT: F 175 ASP cc_start: 0.7462 (t70) cc_final: 0.7028 (m-30) REVERT: G 164 MET cc_start: 0.7502 (ttm) cc_final: 0.7160 (ttt) REVERT: G 175 ASP cc_start: 0.7614 (t70) cc_final: 0.7052 (m-30) REVERT: G 201 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8095 (m-30) REVERT: G 207 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.7021 (ttm-80) REVERT: H 150 MET cc_start: 0.7904 (ttt) cc_final: 0.7514 (ttt) REVERT: H 171 ARG cc_start: 0.6789 (mtm180) cc_final: 0.6414 (ttm170) REVERT: H 183 TYR cc_start: 0.8799 (t80) cc_final: 0.8474 (t80) REVERT: I 22 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: I 75 MET cc_start: 0.8444 (mmt) cc_final: 0.8170 (mmp) REVERT: K 150 MET cc_start: 0.8009 (ttt) cc_final: 0.7648 (ttt) REVERT: K 162 ILE cc_start: 0.8075 (tp) cc_final: 0.7875 (tt) REVERT: K 163 GLU cc_start: 0.8190 (mp0) cc_final: 0.7782 (pm20) REVERT: L 22 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8078 (tm-30) REVERT: M 163 GLU cc_start: 0.8268 (mp0) cc_final: 0.7805 (pm20) REVERT: N 75 MET cc_start: 0.8414 (mmt) cc_final: 0.8200 (tpp) REVERT: N 79 ASP cc_start: 0.8090 (m-30) cc_final: 0.7874 (m-30) REVERT: N 183 TYR cc_start: 0.8989 (t80) cc_final: 0.8728 (t80) outliers start: 33 outliers final: 22 residues processed: 374 average time/residue: 0.1907 time to fit residues: 103.1308 Evaluate side-chains 344 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 319 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 201 ASP Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 57 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.145936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121883 restraints weight = 23870.100| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.29 r_work: 0.3251 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20776 Z= 0.111 Angle : 0.527 6.021 28063 Z= 0.275 Chirality : 0.041 0.163 3248 Planarity : 0.004 0.051 3640 Dihedral : 9.149 106.558 2975 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.79 % Allowed : 9.43 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.16), residues: 2590 helix: 1.78 (0.14), residues: 1379 sheet: 2.00 (0.29), residues: 245 loop : -0.68 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 185 TYR 0.021 0.001 TYR I 183 PHE 0.010 0.001 PHE L 185 TRP 0.005 0.001 TRP J 174 HIS 0.004 0.001 HIS G 135 Details of bonding type rmsd covalent geometry : bond 0.00250 (20762) covalent geometry : angle 0.52657 (28063) hydrogen bonds : bond 0.02963 ( 1106) hydrogen bonds : angle 4.20315 ( 3528) Misc. bond : bond 0.00025 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 348 time to evaluate : 0.766 Fit side-chains REVERT: A 175 ASP cc_start: 0.7589 (t70) cc_final: 0.7203 (m-30) REVERT: A 201 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: B 21 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: B 164 MET cc_start: 0.7393 (ttm) cc_final: 0.7016 (ttt) REVERT: B 175 ASP cc_start: 0.7506 (t70) cc_final: 0.7019 (m-30) REVERT: B 205 GLU cc_start: 0.8120 (pm20) cc_final: 0.7777 (mp0) REVERT: C 93 MET cc_start: 0.8590 (mtp) cc_final: 0.8198 (mtp) REVERT: C 164 MET cc_start: 0.7309 (ttm) cc_final: 0.6974 (ttt) REVERT: C 175 ASP cc_start: 0.7615 (t70) cc_final: 0.6999 (m-30) REVERT: C 200 ILE cc_start: 0.8426 (mm) cc_final: 0.8066 (mt) REVERT: D 57 MET cc_start: 0.8384 (mtm) cc_final: 0.8171 (mtm) REVERT: D 164 MET cc_start: 0.7263 (ttm) cc_final: 0.6928 (ttt) REVERT: D 175 ASP cc_start: 0.7363 (t70) cc_final: 0.7023 (m-30) REVERT: D 200 ILE cc_start: 0.8552 (mm) cc_final: 0.8241 (mt) REVERT: E 135 HIS cc_start: 0.7680 (t-170) cc_final: 0.7436 (t-170) REVERT: E 164 MET cc_start: 0.7219 (ttm) cc_final: 0.6874 (ttt) REVERT: E 175 ASP cc_start: 0.7453 (t70) cc_final: 0.7055 (m-30) REVERT: E 200 ILE cc_start: 0.8331 (mm) cc_final: 0.7965 (mt) REVERT: F 164 MET cc_start: 0.7442 (ttm) cc_final: 0.7154 (ttt) REVERT: F 175 ASP cc_start: 0.7587 (t70) cc_final: 0.7062 (m-30) REVERT: G 50 ASP cc_start: 0.7500 (t70) cc_final: 0.7186 (t70) REVERT: G 164 MET cc_start: 0.7337 (ttm) cc_final: 0.6961 (ttt) REVERT: G 175 ASP cc_start: 0.7611 (t70) cc_final: 0.7079 (m-30) REVERT: G 200 ILE cc_start: 0.8282 (mm) cc_final: 0.7971 (mt) REVERT: H 150 MET cc_start: 0.8117 (ttt) cc_final: 0.7703 (ttt) REVERT: H 173 ARG cc_start: 0.7362 (ttt180) cc_final: 0.7111 (ptm160) REVERT: H 183 TYR cc_start: 0.8730 (t80) cc_final: 0.8404 (t80) REVERT: I 75 MET cc_start: 0.8342 (mmt) cc_final: 0.8114 (mmp) REVERT: J 166 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7802 (mt-10) REVERT: J 171 ARG cc_start: 0.6400 (mtp180) cc_final: 0.5869 (ttp-110) REVERT: J 183 TYR cc_start: 0.8686 (t80) cc_final: 0.8382 (t80) REVERT: K 150 MET cc_start: 0.7981 (ttt) cc_final: 0.7644 (ttt) REVERT: K 163 GLU cc_start: 0.8186 (mp0) cc_final: 0.7723 (pm20) REVERT: K 171 ARG cc_start: 0.6387 (mtm-85) cc_final: 0.6046 (mtm110) REVERT: M 163 GLU cc_start: 0.8266 (mp0) cc_final: 0.7776 (pm20) REVERT: M 166 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7427 (mt-10) REVERT: M 171 ARG cc_start: 0.6529 (mtp180) cc_final: 0.5843 (ttp-110) REVERT: N 79 ASP cc_start: 0.8031 (m-30) cc_final: 0.7731 (m-30) REVERT: N 183 TYR cc_start: 0.8919 (t80) cc_final: 0.8513 (t80) outliers start: 38 outliers final: 20 residues processed: 373 average time/residue: 0.1620 time to fit residues: 91.5506 Evaluate side-chains 346 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 324 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 54 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 135 HIS E 135 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.139371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115747 restraints weight = 24405.366| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.28 r_work: 0.3183 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20776 Z= 0.227 Angle : 0.618 7.539 28063 Z= 0.320 Chirality : 0.045 0.174 3248 Planarity : 0.005 0.045 3640 Dihedral : 9.254 106.390 2975 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.17 % Allowed : 9.71 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.16), residues: 2590 helix: 1.66 (0.14), residues: 1372 sheet: 1.82 (0.29), residues: 245 loop : -0.81 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 185 TYR 0.027 0.002 TYR I 183 PHE 0.014 0.002 PHE K 175 TRP 0.008 0.001 TRP J 174 HIS 0.005 0.001 HIS M 123 Details of bonding type rmsd covalent geometry : bond 0.00549 (20762) covalent geometry : angle 0.61846 (28063) hydrogen bonds : bond 0.03807 ( 1106) hydrogen bonds : angle 4.35796 ( 3528) Misc. bond : bond 0.00088 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 325 time to evaluate : 0.654 Fit side-chains REVERT: A 175 ASP cc_start: 0.7554 (t70) cc_final: 0.7264 (m-30) REVERT: A 201 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: B 21 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8194 (mt-10) REVERT: B 164 MET cc_start: 0.7570 (ttm) cc_final: 0.7172 (ttt) REVERT: B 175 ASP cc_start: 0.7544 (t70) cc_final: 0.7091 (m-30) REVERT: B 205 GLU cc_start: 0.8222 (pm20) cc_final: 0.7876 (mp0) REVERT: C 135 HIS cc_start: 0.7619 (t-170) cc_final: 0.7257 (t-170) REVERT: C 164 MET cc_start: 0.7320 (ttm) cc_final: 0.6972 (ttt) REVERT: C 175 ASP cc_start: 0.7592 (t70) cc_final: 0.7065 (m-30) REVERT: C 200 ILE cc_start: 0.8570 (mm) cc_final: 0.8259 (mt) REVERT: D 57 MET cc_start: 0.8359 (mtm) cc_final: 0.8103 (mtm) REVERT: D 161 ARG cc_start: 0.7603 (mtp180) cc_final: 0.7391 (mtp180) REVERT: D 164 MET cc_start: 0.7457 (ttm) cc_final: 0.7097 (ttt) REVERT: D 175 ASP cc_start: 0.7424 (t70) cc_final: 0.7161 (m-30) REVERT: D 200 ILE cc_start: 0.8651 (mm) cc_final: 0.8435 (mt) REVERT: D 207 ARG cc_start: 0.7434 (ttm-80) cc_final: 0.7049 (ttm-80) REVERT: E 125 MET cc_start: 0.8848 (mtp) cc_final: 0.8586 (mtm) REVERT: E 164 MET cc_start: 0.7316 (ttm) cc_final: 0.7052 (ttt) REVERT: E 175 ASP cc_start: 0.7474 (t70) cc_final: 0.7094 (m-30) REVERT: E 200 ILE cc_start: 0.8518 (mm) cc_final: 0.8194 (mt) REVERT: F 125 MET cc_start: 0.9007 (mtm) cc_final: 0.8548 (mtm) REVERT: F 164 MET cc_start: 0.7540 (ttm) cc_final: 0.7222 (ttt) REVERT: F 175 ASP cc_start: 0.7529 (t70) cc_final: 0.7130 (m-30) REVERT: G 164 MET cc_start: 0.7557 (ttm) cc_final: 0.7178 (ttt) REVERT: G 175 ASP cc_start: 0.7641 (t70) cc_final: 0.7109 (m-30) REVERT: G 200 ILE cc_start: 0.8410 (mm) cc_final: 0.8177 (mt) REVERT: H 150 MET cc_start: 0.8115 (ttt) cc_final: 0.7683 (ttt) REVERT: H 183 TYR cc_start: 0.8859 (t80) cc_final: 0.8514 (t80) REVERT: I 75 MET cc_start: 0.8351 (mmt) cc_final: 0.8080 (mmp) REVERT: J 91 TYR cc_start: 0.8886 (m-80) cc_final: 0.8665 (m-80) REVERT: J 183 TYR cc_start: 0.8899 (t80) cc_final: 0.8545 (t80) REVERT: K 171 ARG cc_start: 0.6424 (mtm-85) cc_final: 0.6053 (mtm110) REVERT: M 163 GLU cc_start: 0.8254 (mp0) cc_final: 0.7799 (pm20) REVERT: M 171 ARG cc_start: 0.6776 (mtp180) cc_final: 0.6063 (ttp-110) REVERT: N 75 MET cc_start: 0.8507 (mmt) cc_final: 0.8240 (tpp) REVERT: N 79 ASP cc_start: 0.8081 (m-30) cc_final: 0.7793 (m-30) REVERT: N 171 ARG cc_start: 0.6308 (mtm-85) cc_final: 0.5690 (ttp-110) REVERT: N 172 ASP cc_start: 0.7323 (m-30) cc_final: 0.7035 (m-30) outliers start: 46 outliers final: 34 residues processed: 353 average time/residue: 0.1630 time to fit residues: 86.2562 Evaluate side-chains 349 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 313 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 171 ARG Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 138 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 201 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.147025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123396 restraints weight = 23847.537| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.32 r_work: 0.3240 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20776 Z= 0.123 Angle : 0.530 6.089 28063 Z= 0.276 Chirality : 0.041 0.161 3248 Planarity : 0.004 0.035 3640 Dihedral : 8.982 107.269 2975 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.89 % Allowed : 10.04 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.16), residues: 2590 helix: 1.92 (0.14), residues: 1379 sheet: 1.71 (0.29), residues: 245 loop : -0.74 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 185 TYR 0.021 0.001 TYR N 183 PHE 0.011 0.001 PHE L 185 TRP 0.006 0.001 TRP M 174 HIS 0.003 0.001 HIS G 135 Details of bonding type rmsd covalent geometry : bond 0.00288 (20762) covalent geometry : angle 0.52994 (28063) hydrogen bonds : bond 0.02976 ( 1106) hydrogen bonds : angle 4.15460 ( 3528) Misc. bond : bond 0.00035 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 334 time to evaluate : 0.695 Fit side-chains REVERT: A 175 ASP cc_start: 0.7599 (t70) cc_final: 0.7130 (m-30) REVERT: A 201 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7759 (m-30) REVERT: A 205 GLU cc_start: 0.8135 (pm20) cc_final: 0.7591 (mp0) REVERT: A 207 ARG cc_start: 0.7457 (ttm-80) cc_final: 0.7006 (ttm-80) REVERT: B 164 MET cc_start: 0.7317 (ttm) cc_final: 0.6923 (ttt) REVERT: B 175 ASP cc_start: 0.7708 (t70) cc_final: 0.7043 (m-30) REVERT: B 205 GLU cc_start: 0.8254 (pm20) cc_final: 0.7794 (tm-30) REVERT: C 164 MET cc_start: 0.7283 (ttm) cc_final: 0.6936 (ttt) REVERT: C 175 ASP cc_start: 0.7565 (t70) cc_final: 0.6965 (m-30) REVERT: C 200 ILE cc_start: 0.8402 (mm) cc_final: 0.8063 (mt) REVERT: D 57 MET cc_start: 0.8340 (mtm) cc_final: 0.8135 (mtm) REVERT: D 164 MET cc_start: 0.7201 (ttm) cc_final: 0.6855 (ttt) REVERT: D 175 ASP cc_start: 0.7383 (t70) cc_final: 0.7108 (m-30) REVERT: D 200 ILE cc_start: 0.8528 (mm) cc_final: 0.8255 (mt) REVERT: E 125 MET cc_start: 0.8852 (mtp) cc_final: 0.8560 (mtm) REVERT: E 164 MET cc_start: 0.7072 (ttm) cc_final: 0.6685 (ttt) REVERT: E 175 ASP cc_start: 0.7547 (t70) cc_final: 0.7093 (m-30) REVERT: E 200 ILE cc_start: 0.8283 (mm) cc_final: 0.7935 (mt) REVERT: E 205 GLU cc_start: 0.8258 (pm20) cc_final: 0.7740 (tp30) REVERT: F 164 MET cc_start: 0.7303 (ttm) cc_final: 0.6969 (ttt) REVERT: F 175 ASP cc_start: 0.7518 (t70) cc_final: 0.7117 (m-30) REVERT: F 205 GLU cc_start: 0.8280 (pm20) cc_final: 0.7817 (mp0) REVERT: G 164 MET cc_start: 0.7353 (ttm) cc_final: 0.6965 (ttt) REVERT: G 175 ASP cc_start: 0.7659 (t70) cc_final: 0.7066 (m-30) REVERT: G 200 ILE cc_start: 0.8206 (mm) cc_final: 0.7936 (mt) REVERT: G 201 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: H 150 MET cc_start: 0.8009 (ttt) cc_final: 0.7644 (ttt) REVERT: H 173 ARG cc_start: 0.7218 (ttt180) cc_final: 0.6709 (ptm160) REVERT: H 183 TYR cc_start: 0.8746 (t80) cc_final: 0.8351 (t80) REVERT: I 171 ARG cc_start: 0.6455 (mtm-85) cc_final: 0.6002 (ttp-110) REVERT: J 166 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7780 (mt-10) REVERT: J 171 ARG cc_start: 0.6391 (mtp180) cc_final: 0.5905 (ttp-110) REVERT: J 173 ARG cc_start: 0.7419 (ttt180) cc_final: 0.7117 (ptm160) REVERT: J 183 TYR cc_start: 0.8754 (t80) cc_final: 0.8431 (t80) REVERT: K 150 MET cc_start: 0.7756 (ttt) cc_final: 0.7450 (ttt) REVERT: L 173 ARG cc_start: 0.7321 (ttt180) cc_final: 0.6779 (ttt90) REVERT: M 163 GLU cc_start: 0.8277 (mp0) cc_final: 0.7756 (pm20) REVERT: M 166 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7462 (mt-10) REVERT: M 171 ARG cc_start: 0.6767 (mtp180) cc_final: 0.6122 (ttp-110) REVERT: M 183 TYR cc_start: 0.8877 (t80) cc_final: 0.8666 (t80) REVERT: N 79 ASP cc_start: 0.8067 (m-30) cc_final: 0.7718 (m-30) REVERT: N 171 ARG cc_start: 0.6138 (mtm-85) cc_final: 0.5582 (ttp-110) REVERT: N 172 ASP cc_start: 0.7301 (m-30) cc_final: 0.7019 (m-30) outliers start: 40 outliers final: 31 residues processed: 360 average time/residue: 0.1529 time to fit residues: 83.8794 Evaluate side-chains 352 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 319 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 201 ASP Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 250 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 173 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 186 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118767 restraints weight = 24145.652| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.28 r_work: 0.3221 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20776 Z= 0.158 Angle : 0.557 6.641 28063 Z= 0.288 Chirality : 0.042 0.171 3248 Planarity : 0.004 0.039 3640 Dihedral : 8.974 107.547 2975 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.79 % Allowed : 10.61 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.16), residues: 2590 helix: 1.91 (0.14), residues: 1379 sheet: 1.70 (0.28), residues: 245 loop : -0.79 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 185 TYR 0.025 0.002 TYR I 183 PHE 0.011 0.001 PHE L 175 TRP 0.007 0.001 TRP M 174 HIS 0.004 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00377 (20762) covalent geometry : angle 0.55659 (28063) hydrogen bonds : bond 0.03246 ( 1106) hydrogen bonds : angle 4.21033 ( 3528) Misc. bond : bond 0.00054 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 315 time to evaluate : 0.675 Fit side-chains REVERT: A 175 ASP cc_start: 0.7577 (t70) cc_final: 0.7117 (m-30) REVERT: A 201 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: A 205 GLU cc_start: 0.8140 (pm20) cc_final: 0.7659 (mp0) REVERT: B 164 MET cc_start: 0.7436 (ttm) cc_final: 0.7044 (ttt) REVERT: B 175 ASP cc_start: 0.7528 (t70) cc_final: 0.7085 (m-30) REVERT: B 200 ILE cc_start: 0.8359 (mm) cc_final: 0.8118 (mt) REVERT: B 205 GLU cc_start: 0.8355 (pm20) cc_final: 0.7710 (tm-30) REVERT: C 175 ASP cc_start: 0.7597 (t70) cc_final: 0.7013 (m-30) REVERT: C 200 ILE cc_start: 0.8535 (mm) cc_final: 0.8217 (mt) REVERT: D 57 MET cc_start: 0.8358 (mtm) cc_final: 0.8150 (mtm) REVERT: D 161 ARG cc_start: 0.7561 (mtp180) cc_final: 0.7353 (mtp180) REVERT: D 164 MET cc_start: 0.7330 (ttm) cc_final: 0.6999 (ttt) REVERT: D 175 ASP cc_start: 0.7401 (t70) cc_final: 0.7178 (m-30) REVERT: D 200 ILE cc_start: 0.8627 (mm) cc_final: 0.8370 (mt) REVERT: D 207 ARG cc_start: 0.7512 (ttm-80) cc_final: 0.7073 (ttm-80) REVERT: E 164 MET cc_start: 0.7123 (ttm) cc_final: 0.6749 (ttt) REVERT: E 175 ASP cc_start: 0.7571 (t70) cc_final: 0.7173 (m-30) REVERT: E 200 ILE cc_start: 0.8444 (mm) cc_final: 0.8109 (mt) REVERT: E 205 GLU cc_start: 0.8228 (pm20) cc_final: 0.7817 (tp30) REVERT: F 164 MET cc_start: 0.7423 (ttm) cc_final: 0.7116 (ttt) REVERT: F 175 ASP cc_start: 0.7585 (t70) cc_final: 0.7202 (m-30) REVERT: G 164 MET cc_start: 0.7490 (ttm) cc_final: 0.7101 (ttt) REVERT: G 175 ASP cc_start: 0.7689 (t70) cc_final: 0.7152 (m-30) REVERT: G 200 ILE cc_start: 0.8310 (mm) cc_final: 0.8073 (mt) REVERT: G 201 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: H 150 MET cc_start: 0.8088 (ttt) cc_final: 0.7697 (ttt) REVERT: H 183 TYR cc_start: 0.8837 (t80) cc_final: 0.8460 (t80) REVERT: I 171 ARG cc_start: 0.6539 (mtm-85) cc_final: 0.6076 (ttp-110) REVERT: J 91 TYR cc_start: 0.8820 (m-80) cc_final: 0.8561 (m-80) REVERT: J 171 ARG cc_start: 0.6488 (mtp180) cc_final: 0.6021 (ttp-110) REVERT: J 173 ARG cc_start: 0.7608 (ttt180) cc_final: 0.7286 (ptm160) REVERT: J 183 TYR cc_start: 0.8868 (t80) cc_final: 0.8594 (t80) REVERT: L 173 ARG cc_start: 0.7473 (ttt180) cc_final: 0.6943 (ttt90) REVERT: M 163 GLU cc_start: 0.8281 (mp0) cc_final: 0.7832 (pm20) REVERT: M 171 ARG cc_start: 0.6854 (mtp180) cc_final: 0.6213 (ttp-110) REVERT: M 173 ARG cc_start: 0.7529 (ttt180) cc_final: 0.7291 (ptm160) REVERT: N 75 MET cc_start: 0.8516 (mmt) cc_final: 0.8232 (tpp) REVERT: N 79 ASP cc_start: 0.8064 (m-30) cc_final: 0.7741 (m-30) REVERT: N 171 ARG cc_start: 0.6286 (mtm-85) cc_final: 0.5739 (ttp-110) REVERT: N 172 ASP cc_start: 0.7357 (m-30) cc_final: 0.7066 (m-30) outliers start: 38 outliers final: 35 residues processed: 340 average time/residue: 0.1545 time to fit residues: 80.4316 Evaluate side-chains 351 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 314 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 201 ASP Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 171 ARG Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 132 optimal weight: 0.7980 chunk 250 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 0.2980 chunk 62 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.145774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121927 restraints weight = 23780.786| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.28 r_work: 0.3259 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20776 Z= 0.119 Angle : 0.524 5.507 28063 Z= 0.272 Chirality : 0.041 0.165 3248 Planarity : 0.004 0.035 3640 Dihedral : 8.824 106.952 2975 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.93 % Allowed : 10.47 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.16), residues: 2590 helix: 2.14 (0.14), residues: 1358 sheet: 1.33 (0.28), residues: 259 loop : -0.79 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 185 TYR 0.022 0.001 TYR I 183 PHE 0.013 0.001 PHE H 102 TRP 0.005 0.001 TRP K 174 HIS 0.003 0.001 HIS G 135 Details of bonding type rmsd covalent geometry : bond 0.00276 (20762) covalent geometry : angle 0.52387 (28063) hydrogen bonds : bond 0.02856 ( 1106) hydrogen bonds : angle 4.11943 ( 3528) Misc. bond : bond 0.00032 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 321 time to evaluate : 0.699 Fit side-chains REVERT: A 175 ASP cc_start: 0.7564 (t70) cc_final: 0.7094 (m-30) REVERT: A 201 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7751 (m-30) REVERT: A 205 GLU cc_start: 0.8128 (pm20) cc_final: 0.7916 (mt-10) REVERT: A 207 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7135 (ttm-80) REVERT: B 70 ARG cc_start: 0.8442 (mtp180) cc_final: 0.8112 (mtp180) REVERT: B 164 MET cc_start: 0.7403 (ttm) cc_final: 0.7013 (ttt) REVERT: B 175 ASP cc_start: 0.7550 (t70) cc_final: 0.7128 (m-30) REVERT: B 200 ILE cc_start: 0.8299 (mm) cc_final: 0.8029 (mt) REVERT: B 205 GLU cc_start: 0.8175 (pm20) cc_final: 0.7831 (tm-30) REVERT: C 175 ASP cc_start: 0.7603 (t70) cc_final: 0.7031 (m-30) REVERT: C 200 ILE cc_start: 0.8497 (mm) cc_final: 0.8149 (mt) REVERT: D 164 MET cc_start: 0.7291 (ttm) cc_final: 0.6935 (ttt) REVERT: D 175 ASP cc_start: 0.7449 (t70) cc_final: 0.7207 (m-30) REVERT: D 200 ILE cc_start: 0.8605 (mm) cc_final: 0.8319 (mt) REVERT: E 125 MET cc_start: 0.8972 (mtm) cc_final: 0.8685 (mtm) REVERT: E 164 MET cc_start: 0.7141 (ttm) cc_final: 0.6742 (ttt) REVERT: E 175 ASP cc_start: 0.7580 (t70) cc_final: 0.7216 (m-30) REVERT: E 200 ILE cc_start: 0.8407 (mm) cc_final: 0.8043 (mt) REVERT: E 205 GLU cc_start: 0.8286 (pm20) cc_final: 0.7807 (tp30) REVERT: F 164 MET cc_start: 0.7372 (ttm) cc_final: 0.7047 (ttt) REVERT: F 175 ASP cc_start: 0.7598 (t70) cc_final: 0.7228 (m-30) REVERT: G 164 MET cc_start: 0.7402 (ttm) cc_final: 0.7009 (ttt) REVERT: G 175 ASP cc_start: 0.7599 (t70) cc_final: 0.7173 (m-30) REVERT: G 200 ILE cc_start: 0.8234 (mm) cc_final: 0.7973 (mt) REVERT: G 201 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: H 173 ARG cc_start: 0.7316 (ttt180) cc_final: 0.6842 (ptm160) REVERT: H 183 TYR cc_start: 0.8801 (t80) cc_final: 0.8478 (t80) REVERT: I 22 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: I 171 ARG cc_start: 0.6549 (mtm-85) cc_final: 0.6097 (ttp-110) REVERT: J 171 ARG cc_start: 0.6573 (mtp180) cc_final: 0.5994 (ttp-110) REVERT: J 173 ARG cc_start: 0.7458 (ttt180) cc_final: 0.7179 (ptm160) REVERT: J 183 TYR cc_start: 0.8854 (t80) cc_final: 0.8556 (t80) REVERT: K 150 MET cc_start: 0.8004 (ttt) cc_final: 0.7704 (ttt) REVERT: K 171 ARG cc_start: 0.6483 (mtm-85) cc_final: 0.5981 (ttp-110) REVERT: L 173 ARG cc_start: 0.7449 (ttt180) cc_final: 0.6923 (ttt90) REVERT: M 163 GLU cc_start: 0.8251 (mp0) cc_final: 0.7781 (pm20) REVERT: M 166 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7486 (mt-10) REVERT: M 171 ARG cc_start: 0.6604 (mtp180) cc_final: 0.6005 (ttp-110) REVERT: N 79 ASP cc_start: 0.8055 (m-30) cc_final: 0.7722 (m-30) REVERT: N 171 ARG cc_start: 0.6245 (mtm-85) cc_final: 0.5677 (ttm170) REVERT: N 172 ASP cc_start: 0.7421 (m-30) cc_final: 0.7165 (m-30) outliers start: 41 outliers final: 31 residues processed: 348 average time/residue: 0.1550 time to fit residues: 82.8997 Evaluate side-chains 348 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 314 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 201 ASP Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 100 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 228 optimal weight: 0.5980 chunk 199 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 231 optimal weight: 7.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN E 135 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117726 restraints weight = 24267.353| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.29 r_work: 0.3208 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20776 Z= 0.185 Angle : 0.582 6.132 28063 Z= 0.301 Chirality : 0.043 0.181 3248 Planarity : 0.004 0.042 3640 Dihedral : 8.936 106.742 2975 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.84 % Allowed : 10.33 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.16), residues: 2590 helix: 1.91 (0.14), residues: 1379 sheet: 1.53 (0.28), residues: 259 loop : -0.81 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 185 TYR 0.028 0.002 TYR I 183 PHE 0.011 0.001 PHE H 175 TRP 0.006 0.001 TRP I 174 HIS 0.004 0.001 HIS M 123 Details of bonding type rmsd covalent geometry : bond 0.00446 (20762) covalent geometry : angle 0.58219 (28063) hydrogen bonds : bond 0.03417 ( 1106) hydrogen bonds : angle 4.26146 ( 3528) Misc. bond : bond 0.00065 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 311 time to evaluate : 0.760 Fit side-chains REVERT: A 175 ASP cc_start: 0.7619 (t70) cc_final: 0.7131 (m-30) REVERT: A 201 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: A 205 GLU cc_start: 0.8129 (pm20) cc_final: 0.7551 (tp30) REVERT: B 70 ARG cc_start: 0.8515 (mtp180) cc_final: 0.8160 (mtp180) REVERT: B 164 MET cc_start: 0.7439 (ttm) cc_final: 0.7052 (ttt) REVERT: B 175 ASP cc_start: 0.7613 (t70) cc_final: 0.7145 (m-30) REVERT: B 205 GLU cc_start: 0.8300 (pm20) cc_final: 0.7701 (tm-30) REVERT: C 175 ASP cc_start: 0.7590 (t70) cc_final: 0.7033 (m-30) REVERT: C 200 ILE cc_start: 0.8602 (mm) cc_final: 0.8314 (mt) REVERT: C 201 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7410 (m-30) REVERT: D 161 ARG cc_start: 0.7611 (mtp180) cc_final: 0.7388 (mtp180) REVERT: D 164 MET cc_start: 0.7350 (ttm) cc_final: 0.7018 (ttt) REVERT: D 175 ASP cc_start: 0.7454 (t70) cc_final: 0.7225 (m-30) REVERT: D 200 ILE cc_start: 0.8628 (mm) cc_final: 0.8412 (mt) REVERT: D 207 ARG cc_start: 0.7450 (ttm-80) cc_final: 0.7001 (ttm-80) REVERT: E 125 MET cc_start: 0.8926 (mtm) cc_final: 0.8656 (mtm) REVERT: E 164 MET cc_start: 0.7270 (ttm) cc_final: 0.6897 (ttt) REVERT: E 175 ASP cc_start: 0.7574 (t70) cc_final: 0.7193 (m-30) REVERT: E 200 ILE cc_start: 0.8505 (mm) cc_final: 0.8193 (mt) REVERT: E 205 GLU cc_start: 0.8377 (pm20) cc_final: 0.7827 (tp30) REVERT: F 164 MET cc_start: 0.7455 (ttm) cc_final: 0.7146 (ttt) REVERT: F 175 ASP cc_start: 0.7538 (t70) cc_final: 0.7172 (m-30) REVERT: G 164 MET cc_start: 0.7544 (ttm) cc_final: 0.7155 (ttt) REVERT: G 175 ASP cc_start: 0.7590 (t70) cc_final: 0.7214 (m-30) REVERT: G 201 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: H 183 TYR cc_start: 0.8920 (t80) cc_final: 0.8547 (t80) REVERT: I 171 ARG cc_start: 0.6628 (mtm-85) cc_final: 0.6181 (ttp-110) REVERT: J 91 TYR cc_start: 0.8842 (m-80) cc_final: 0.8580 (m-80) REVERT: J 171 ARG cc_start: 0.6524 (mtp180) cc_final: 0.5942 (ttp-110) REVERT: J 183 TYR cc_start: 0.8962 (t80) cc_final: 0.8613 (t80) REVERT: K 150 MET cc_start: 0.8084 (ttt) cc_final: 0.7769 (ttt) REVERT: L 173 ARG cc_start: 0.7505 (ttt180) cc_final: 0.6953 (ttt90) REVERT: L 183 TYR cc_start: 0.8877 (t80) cc_final: 0.8548 (t80) REVERT: M 163 GLU cc_start: 0.8199 (mp0) cc_final: 0.7745 (pm20) REVERT: N 75 MET cc_start: 0.8496 (mmt) cc_final: 0.8190 (tpp) REVERT: N 79 ASP cc_start: 0.8076 (m-30) cc_final: 0.7746 (m-30) REVERT: N 171 ARG cc_start: 0.6326 (mtm-85) cc_final: 0.5815 (ttp-110) REVERT: N 172 ASP cc_start: 0.7471 (m-30) cc_final: 0.7162 (m-30) outliers start: 39 outliers final: 35 residues processed: 337 average time/residue: 0.1657 time to fit residues: 84.9865 Evaluate side-chains 341 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 201 ASP Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 109 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 188 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 209 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122126 restraints weight = 23867.521| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.28 r_work: 0.3259 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20776 Z= 0.117 Angle : 0.527 5.808 28063 Z= 0.274 Chirality : 0.041 0.167 3248 Planarity : 0.004 0.036 3640 Dihedral : 8.771 108.163 2975 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.79 % Allowed : 10.42 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.16), residues: 2590 helix: 2.18 (0.14), residues: 1358 sheet: 1.31 (0.28), residues: 259 loop : -0.82 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 185 TYR 0.021 0.001 TYR I 183 PHE 0.015 0.001 PHE H 102 TRP 0.005 0.001 TRP J 174 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00271 (20762) covalent geometry : angle 0.52739 (28063) hydrogen bonds : bond 0.02858 ( 1106) hydrogen bonds : angle 4.14369 ( 3528) Misc. bond : bond 0.00030 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3974.54 seconds wall clock time: 69 minutes 9.37 seconds (4149.37 seconds total)