Starting phenix.real_space_refine on Sat Sep 12 09:16:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vx6_21431/09_2026/6vx6_21431.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vx6_21431/09_2026/6vx6_21431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6vx6_21431/09_2026/6vx6_21431.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vx6_21431/09_2026/6vx6_21431.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vx6_21431/09_2026/6vx6_21431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vx6_21431/09_2026/6vx6_21431.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vx6_21431/09_2026/6vx6_21431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vx6_21431/09_2026/6vx6_21431.map" } resolution = 3.0 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= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 95 5.16 5 Cl 1 4.86 5 C 9870 2.51 5 N 2485 2.21 5 O 2605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15061 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "A" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "B" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "C" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "D" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.53, per 1000 atoms: 0.23 Number of scatterers: 15061 At special positions: 0 Unit cell: (97.94, 96.28, 109.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 Cl 1 17.00 S 95 16.00 O 2605 8.00 N 2485 7.00 C 9870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 679.0 milliseconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 69.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'E' and resid 5 through 10 removed outlier: 3.968A pdb=" N ALA E 10 " --> pdb=" O ALA E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU E 22 " --> pdb=" O LYS E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 52 removed outlier: 5.927A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 37 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 72 removed outlier: 3.533A pdb=" N ARG E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 3.959A pdb=" N VAL E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE E 80 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR E 85 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR E 97 " --> pdb=" O TRP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.790A pdb=" N CYS E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 149 Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 164 through 173 removed outlier: 3.940A pdb=" N LYS E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.568A pdb=" N CYS E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.565A pdb=" N GLY E 263 " --> pdb=" O PRO E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 294 removed outlier: 3.839A pdb=" N GLN E 280 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER E 318 " --> pdb=" O CYS E 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 10 removed outlier: 3.969A pdb=" N ALA A 10 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU A 22 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 52 removed outlier: 5.927A pdb=" N ARG A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 37 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 3.960A pdb=" N VAL A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 97 " --> pdb=" O TRP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.789A pdb=" N CYS A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.940A pdb=" N LYS A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.568A pdb=" N CYS A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.565A pdb=" N GLY A 263 " --> pdb=" O PRO A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 294 removed outlier: 3.839A pdb=" N GLN A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 4.346A pdb=" N SER A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 removed outlier: 3.969A pdb=" N ALA B 10 " --> pdb=" O ALA B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.726A pdb=" N LEU B 22 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 52 removed outlier: 5.928A pdb=" N ARG B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 37 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.959A pdb=" N VAL B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR B 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 97 " --> pdb=" O TRP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.791A pdb=" N CYS B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 164 through 173 removed outlier: 3.940A pdb=" N LYS B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.569A pdb=" N CYS B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 230 removed outlier: 3.654A pdb=" N LEU B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.565A pdb=" N GLY B 263 " --> pdb=" O PRO B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 294 removed outlier: 3.838A pdb=" N GLN B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.968A pdb=" N ALA C 10 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU C 22 " --> pdb=" O LYS C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 52 removed outlier: 5.928A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 37 " --> pdb=" O TRP C 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 removed outlier: 3.960A pdb=" N VAL C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR C 85 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.791A pdb=" N CYS C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.725A pdb=" N ARG C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 164 through 173 removed outlier: 3.941A pdb=" N LYS C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.568A pdb=" N CYS C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.566A pdb=" N GLY C 263 " --> pdb=" O PRO C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 294 removed outlier: 3.839A pdb=" N GLN C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 10 removed outlier: 3.969A pdb=" N ALA D 10 " --> pdb=" O ALA D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU D 22 " --> pdb=" O LYS D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 52 removed outlier: 5.927A pdb=" N ARG D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 37 " --> pdb=" O TRP D 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 removed outlier: 3.959A pdb=" N VAL D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR D 97 " --> pdb=" O TRP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.791A pdb=" N CYS D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 139 " --> pdb=" O SER D 135 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 164 through 173 removed outlier: 3.941A pdb=" N LYS D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.569A pdb=" N CYS D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN D 215 " --> pdb=" O LEU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.566A pdb=" N GLY D 263 " --> pdb=" O PRO D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 294 removed outlier: 3.838A pdb=" N GLN D 280 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER D 318 " --> pdb=" O CYS D 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 2250 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: 2.85 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4103 1.33 - 1.45: 3153 1.45 - 1.57: 8069 1.57 - 1.69: 0 1.69 - 1.81: 145 Bond restraints: 15470 Sorted by residual: bond pdb=" N VAL A 183 " pdb=" CA VAL A 183 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.23e-02 6.61e+03 8.90e+00 bond pdb=" N VAL D 183 " pdb=" CA VAL D 183 " ideal model delta sigma weight residual 1.461 1.498 -0.036 1.23e-02 6.61e+03 8.75e+00 bond pdb=" N VAL E 183 " pdb=" CA VAL E 183 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.58e+00 bond pdb=" N VAL C 183 " pdb=" CA VAL C 183 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.51e+00 bond pdb=" N VAL B 183 " pdb=" CA VAL B 183 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.47e+00 ... (remaining 15465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 20235 1.91 - 3.83: 599 3.83 - 5.74: 117 5.74 - 7.65: 24 7.65 - 9.56: 5 Bond angle restraints: 20980 Sorted by residual: angle pdb=" N LEU B 88 " pdb=" CA LEU B 88 " pdb=" C LEU B 88 " ideal model delta sigma weight residual 111.82 106.39 5.43 1.16e+00 7.43e-01 2.19e+01 angle pdb=" N LEU D 88 " pdb=" CA LEU D 88 " pdb=" C LEU D 88 " ideal model delta sigma weight residual 111.82 106.39 5.43 1.16e+00 7.43e-01 2.19e+01 angle pdb=" N LEU E 88 " pdb=" CA LEU E 88 " pdb=" C LEU E 88 " ideal model delta sigma weight residual 111.82 106.42 5.40 1.16e+00 7.43e-01 2.17e+01 angle pdb=" N LEU A 88 " pdb=" CA LEU A 88 " pdb=" C LEU A 88 " ideal model delta sigma weight residual 111.82 106.43 5.39 1.16e+00 7.43e-01 2.16e+01 angle pdb=" N LEU C 88 " pdb=" CA LEU C 88 " pdb=" C LEU C 88 " ideal model delta sigma weight residual 111.82 106.44 5.38 1.16e+00 7.43e-01 2.15e+01 ... (remaining 20975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 7840 15.45 - 30.91: 910 30.91 - 46.36: 155 46.36 - 61.82: 45 61.82 - 77.27: 25 Dihedral angle restraints: 8975 sinusoidal: 3575 harmonic: 5400 Sorted by residual: dihedral pdb=" C VAL A 183 " pdb=" N VAL A 183 " pdb=" CA VAL A 183 " pdb=" CB VAL A 183 " ideal model delta harmonic sigma weight residual -122.00 -131.87 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" C VAL D 183 " pdb=" N VAL D 183 " pdb=" CA VAL D 183 " pdb=" CB VAL D 183 " ideal model delta harmonic sigma weight residual -122.00 -131.87 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" C VAL C 183 " pdb=" N VAL C 183 " pdb=" CA VAL C 183 " pdb=" CB VAL C 183 " ideal model delta harmonic sigma weight residual -122.00 -131.83 9.83 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 8972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1739 0.053 - 0.105: 419 0.105 - 0.158: 76 0.158 - 0.210: 26 0.210 - 0.263: 15 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA PRO C 77 " pdb=" N PRO C 77 " pdb=" C PRO C 77 " pdb=" CB PRO C 77 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO D 77 " pdb=" N PRO D 77 " pdb=" C PRO D 77 " pdb=" CB PRO D 77 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO E 77 " pdb=" N PRO E 77 " pdb=" C PRO E 77 " pdb=" CB PRO E 77 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2272 not shown) Planarity restraints: 2625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 351 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C THR A 351 " -0.051 2.00e-02 2.50e+03 pdb=" O THR A 351 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 352 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 351 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C THR B 351 " 0.051 2.00e-02 2.50e+03 pdb=" O THR B 351 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA B 352 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 351 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.54e+00 pdb=" C THR C 351 " 0.051 2.00e-02 2.50e+03 pdb=" O THR C 351 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 352 " -0.016 2.00e-02 2.50e+03 ... (remaining 2622 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4107 2.79 - 3.32: 12796 3.32 - 3.84: 25125 3.84 - 4.37: 32863 4.37 - 4.90: 53533 Nonbonded interactions: 128424 Sorted by model distance: nonbonded pdb=" O ASN C 296 " pdb="CA CA C 501 " model vdw 2.260 2.510 nonbonded pdb=" O ASN E 296 " pdb="CA CA E 501 " model vdw 2.273 2.510 nonbonded pdb=" O ALA C 10 " pdb="CA CA D 501 " model vdw 2.277 2.510 nonbonded pdb=" O LEU A 75 " pdb=" OH TYR A 284 " model vdw 2.289 3.040 nonbonded pdb=" O LEU B 75 " pdb=" OH TYR B 284 " model vdw 2.289 3.040 ... (remaining 128419 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 367) selection = (chain 'B' and resid 2 through 367) selection = (chain 'C' and resid 2 through 367) selection = (chain 'D' and resid 2 through 367) selection = (chain 'E' and resid 2 through 367) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.190 Find NCS groups from input model: 0.420 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:9.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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 : 0.005 0.045 15470 Z= 0.268 Angle : 0.819 9.563 20980 Z= 0.492 Chirality : 0.053 0.263 2275 Planarity : 0.004 0.040 2625 Dihedral : 14.085 77.272 5505 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.94 % Allowed : 8.49 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.69 (0.12), residues: 1820 helix: -4.58 (0.05), residues: 1055 sheet: None (None), residues: 0 loop : -2.27 (0.18), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 344 TYR 0.031 0.002 TYR D 236 PHE 0.020 0.002 PHE D 282 TRP 0.010 0.001 TRP C 93 HIS 0.002 0.000 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.27 (15470) covalent geometry : angle 0.81938 / 0.49 (20980) hydrogen bonds : bond 0.30767 / 19.51 ( 770) hydrogen bonds : angle 11.88766 / 8.17 ( 2250) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7512 (mpt180) REVERT: A 175 ASN cc_start: 0.7994 (t0) cc_final: 0.7779 (m-40) REVERT: A 203 ASP cc_start: 0.7708 (m-30) cc_final: 0.7472 (m-30) REVERT: D 64 LYS cc_start: 0.7760 (mttm) cc_final: 0.7468 (mtpt) REVERT: D 68 TYR cc_start: 0.7975 (t80) cc_final: 0.7758 (t80) outliers start: 15 outliers final: 0 residues processed: 278 average time/residue: 0.7259 time to fit residues: 219.0496 Evaluate side-chains 162 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 58 GLN E 293 GLN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 296 ASN A 361 GLN B 58 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN D 115 HIS D 293 GLN D 361 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.143481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.110301 restraints weight = 18768.985| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.92 r_work: 0.2964 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15470 Z= 0.172 Angle : 0.583 10.961 20980 Z= 0.300 Chirality : 0.039 0.134 2275 Planarity : 0.004 0.024 2625 Dihedral : 4.354 15.135 2055 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.89 % Allowed : 14.59 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.16), residues: 1820 helix: -2.08 (0.12), residues: 1090 sheet: None (None), residues: 0 loop : -1.65 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 218 TYR 0.021 0.002 TYR D 236 PHE 0.021 0.002 PHE E 283 TRP 0.014 0.001 TRP D 182 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (15470) covalent geometry : angle 0.58279 / 0.30 (20980) hydrogen bonds : bond 0.05135 / 3.22 ( 770) hydrogen bonds : angle 4.86170 / 3.36 ( 2250) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 TYR cc_start: 0.7593 (t80) cc_final: 0.7288 (t80) REVERT: E 165 ARG cc_start: 0.8402 (tpp80) cc_final: 0.8080 (mpt180) REVERT: A 68 TYR cc_start: 0.8059 (t80) cc_final: 0.7791 (t80) REVERT: A 72 TYR cc_start: 0.7304 (m-10) cc_final: 0.7045 (m-10) REVERT: A 203 ASP cc_start: 0.8252 (m-30) cc_final: 0.7915 (m-30) REVERT: A 334 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.7718 (mmtp) REVERT: A 337 TYR cc_start: 0.8068 (m-80) cc_final: 0.7800 (m-80) REVERT: B 64 LYS cc_start: 0.7540 (mttm) cc_final: 0.7191 (mtpt) REVERT: D 68 TYR cc_start: 0.8149 (t80) cc_final: 0.7787 (t80) outliers start: 30 outliers final: 8 residues processed: 216 average time/residue: 0.6656 time to fit residues: 157.8337 Evaluate side-chains 173 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 149 optimal weight: 0.2980 chunk 38 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 144 optimal weight: 0.0770 chunk 120 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN D 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.146149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.113175 restraints weight = 18952.626| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.91 r_work: 0.3121 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15470 Z= 0.107 Angle : 0.482 10.334 20980 Z= 0.246 Chirality : 0.037 0.122 2275 Planarity : 0.003 0.023 2625 Dihedral : 3.944 15.354 2055 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.89 % Allowed : 15.97 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.30 (0.17), residues: 1820 helix: -0.42 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : -1.41 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 168 TYR 0.009 0.001 TYR B 61 PHE 0.023 0.001 PHE E 80 TRP 0.009 0.001 TRP D 182 HIS 0.002 0.000 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (15470) covalent geometry : angle 0.48230 / 0.25 (20980) hydrogen bonds : bond 0.04106 / 2.58 ( 770) hydrogen bonds : angle 4.13469 / 2.85 ( 2250) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.8325 (tpp80) cc_final: 0.8038 (mpt180) REVERT: E 168 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8180 (ttm170) REVERT: A 13 ARG cc_start: 0.7420 (mtm110) cc_final: 0.7101 (mtm-85) REVERT: A 175 ASN cc_start: 0.8494 (t0) cc_final: 0.7900 (m-40) REVERT: A 203 ASP cc_start: 0.8220 (m-30) cc_final: 0.7921 (m-30) REVERT: A 262 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7367 (mm110) REVERT: B 34 ARG cc_start: 0.8095 (ttm110) cc_final: 0.7860 (mtm110) REVERT: B 64 LYS cc_start: 0.7552 (mttm) cc_final: 0.7293 (mtpt) REVERT: B 163 MET cc_start: 0.9410 (ttm) cc_final: 0.9173 (ttp) REVERT: B 212 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8543 (mt-10) REVERT: C 165 ARG cc_start: 0.8098 (tpp-160) cc_final: 0.7686 (mpt180) REVERT: C 328 ASP cc_start: 0.8889 (t70) cc_final: 0.8411 (t70) REVERT: D 68 TYR cc_start: 0.7877 (t80) cc_final: 0.7648 (t80) outliers start: 30 outliers final: 14 residues processed: 234 average time/residue: 0.6830 time to fit residues: 174.8302 Evaluate side-chains 190 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 159 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN A 280 GLN A 296 ASN A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN D 280 GLN D 361 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.143118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109922 restraints weight = 18968.438| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.93 r_work: 0.2918 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15470 Z= 0.161 Angle : 0.538 11.436 20980 Z= 0.267 Chirality : 0.039 0.116 2275 Planarity : 0.003 0.023 2625 Dihedral : 3.922 15.215 2055 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.26 % Allowed : 16.29 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.60 (0.18), residues: 1820 helix: 0.12 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -1.19 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 168 TYR 0.017 0.001 TYR C 236 PHE 0.020 0.002 PHE A 80 TRP 0.012 0.001 TRP D 182 HIS 0.003 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (15470) covalent geometry : angle 0.53755 / 0.27 (20980) hydrogen bonds : bond 0.04469 / 2.81 ( 770) hydrogen bonds : angle 4.01639 / 2.76 ( 2250) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.8461 (tpp80) cc_final: 0.8091 (mpt180) REVERT: E 168 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8278 (ttm170) REVERT: A 68 TYR cc_start: 0.7975 (t80) cc_final: 0.7657 (t80) REVERT: A 203 ASP cc_start: 0.8276 (m-30) cc_final: 0.7808 (m-30) REVERT: A 334 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.7761 (mmtp) REVERT: A 337 TYR cc_start: 0.8048 (m-80) cc_final: 0.7746 (m-80) REVERT: B 64 LYS cc_start: 0.7410 (mttm) cc_final: 0.7144 (mtpt) REVERT: B 71 ARG cc_start: 0.8185 (ptm160) cc_final: 0.7866 (ppp-140) REVERT: B 212 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8552 (mt-10) REVERT: C 165 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.7752 (mpt180) REVERT: D 23 LEU cc_start: 0.8883 (mp) cc_final: 0.8670 (mp) REVERT: D 68 TYR cc_start: 0.8008 (t80) cc_final: 0.7707 (t80) REVERT: D 71 ARG cc_start: 0.8044 (ptm160) cc_final: 0.7755 (ptm-80) outliers start: 36 outliers final: 19 residues processed: 221 average time/residue: 0.6498 time to fit residues: 157.8382 Evaluate side-chains 201 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain D residue 282 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 109 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 143 optimal weight: 0.0020 chunk 65 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN D 361 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.143306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.110347 restraints weight = 18897.486| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.92 r_work: 0.3042 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15470 Z= 0.135 Angle : 0.515 11.773 20980 Z= 0.256 Chirality : 0.039 0.150 2275 Planarity : 0.003 0.023 2625 Dihedral : 3.824 15.260 2055 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.01 % Allowed : 17.04 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.19), residues: 1820 helix: 0.50 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -1.10 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 168 TYR 0.012 0.001 TYR A 68 PHE 0.020 0.001 PHE D 282 TRP 0.011 0.001 TRP D 182 HIS 0.002 0.000 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (15470) covalent geometry : angle 0.51491 / 0.26 (20980) hydrogen bonds : bond 0.04192 / 2.64 ( 770) hydrogen bonds : angle 3.91378 / 2.69 ( 2250) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.8470 (tpp80) cc_final: 0.8086 (mpt180) REVERT: E 168 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8314 (ttm170) REVERT: E 361 GLN cc_start: 0.7675 (mt0) cc_final: 0.7197 (mm-40) REVERT: A 71 ARG cc_start: 0.8046 (ptm160) cc_final: 0.7732 (ptm-80) REVERT: A 175 ASN cc_start: 0.8616 (t0) cc_final: 0.8235 (m110) REVERT: A 203 ASP cc_start: 0.8232 (m-30) cc_final: 0.7936 (m-30) REVERT: A 334 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.7816 (mmtp) REVERT: A 337 TYR cc_start: 0.8081 (m-80) cc_final: 0.7815 (m-80) REVERT: B 64 LYS cc_start: 0.7537 (mttm) cc_final: 0.7315 (mtpt) REVERT: B 71 ARG cc_start: 0.8225 (ptm160) cc_final: 0.7896 (ppp-140) REVERT: B 212 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8525 (mt-10) REVERT: C 64 LYS cc_start: 0.7676 (mttm) cc_final: 0.7400 (mtpt) REVERT: C 165 ARG cc_start: 0.8229 (tpp-160) cc_final: 0.7826 (mpt180) REVERT: C 262 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7659 (mm110) REVERT: C 337 TYR cc_start: 0.8265 (m-80) cc_final: 0.8019 (m-80) REVERT: D 71 ARG cc_start: 0.8072 (ptm160) cc_final: 0.7814 (ptm-80) REVERT: D 203 ASP cc_start: 0.8096 (m-30) cc_final: 0.7788 (m-30) outliers start: 32 outliers final: 16 residues processed: 225 average time/residue: 0.6146 time to fit residues: 152.2954 Evaluate side-chains 203 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 177 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 172 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 58 GLN ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN D 361 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.110163 restraints weight = 18846.522| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.94 r_work: 0.2968 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15470 Z= 0.143 Angle : 0.531 11.881 20980 Z= 0.261 Chirality : 0.039 0.152 2275 Planarity : 0.003 0.023 2625 Dihedral : 3.792 14.814 2055 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.82 % Allowed : 17.99 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.17 (0.19), residues: 1820 helix: 0.75 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -1.00 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 168 TYR 0.013 0.001 TYR D 236 PHE 0.018 0.001 PHE A 276 TRP 0.011 0.001 TRP D 182 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (15470) covalent geometry : angle 0.53054 / 0.26 (20980) hydrogen bonds : bond 0.04226 / 2.67 ( 770) hydrogen bonds : angle 3.87860 / 2.67 ( 2250) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.8482 (tpp80) cc_final: 0.8092 (mpt180) REVERT: E 168 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8319 (ttm170) REVERT: E 361 GLN cc_start: 0.7715 (mt0) cc_final: 0.7220 (mm-40) REVERT: A 71 ARG cc_start: 0.8048 (ptm160) cc_final: 0.7759 (ptm-80) REVERT: A 175 ASN cc_start: 0.8634 (t0) cc_final: 0.8246 (m110) REVERT: A 203 ASP cc_start: 0.8290 (m-30) cc_final: 0.7982 (m-30) REVERT: A 337 TYR cc_start: 0.8072 (m-80) cc_final: 0.7773 (m-80) REVERT: B 71 ARG cc_start: 0.8206 (ptm160) cc_final: 0.7888 (ppp-140) REVERT: B 212 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8564 (mt-10) REVERT: C 68 TYR cc_start: 0.7870 (t80) cc_final: 0.7586 (t80) REVERT: C 71 ARG cc_start: 0.8231 (ptm160) cc_final: 0.7830 (ptm-80) REVERT: C 165 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7837 (mpt180) REVERT: C 262 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7629 (mm110) REVERT: D 71 ARG cc_start: 0.8037 (ptm160) cc_final: 0.7731 (ptm-80) outliers start: 29 outliers final: 17 residues processed: 219 average time/residue: 0.6343 time to fit residues: 152.6811 Evaluate side-chains 204 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 14 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 95 optimal weight: 0.2980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 58 GLN ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.144215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.111292 restraints weight = 18688.500| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.92 r_work: 0.2983 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15470 Z= 0.125 Angle : 0.509 11.579 20980 Z= 0.252 Chirality : 0.038 0.141 2275 Planarity : 0.002 0.023 2625 Dihedral : 3.736 15.074 2055 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.76 % Allowed : 18.74 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.19), residues: 1820 helix: 1.01 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.79 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 168 TYR 0.010 0.001 TYR D 236 PHE 0.021 0.001 PHE E 282 TRP 0.010 0.001 TRP D 182 HIS 0.002 0.000 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (15470) covalent geometry : angle 0.50903 / 0.25 (20980) hydrogen bonds : bond 0.04063 / 2.57 ( 770) hydrogen bonds : angle 3.83073 / 2.63 ( 2250) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.8483 (tpp80) cc_final: 0.8102 (mpt180) REVERT: E 168 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8339 (ttm170) REVERT: E 175 ASN cc_start: 0.8552 (t0) cc_final: 0.8069 (m110) REVERT: E 361 GLN cc_start: 0.7681 (mt0) cc_final: 0.7224 (mm-40) REVERT: A 71 ARG cc_start: 0.8024 (ptm160) cc_final: 0.7763 (ptm-80) REVERT: A 168 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7881 (ttm170) REVERT: A 175 ASN cc_start: 0.8605 (t0) cc_final: 0.8256 (m110) REVERT: A 203 ASP cc_start: 0.8279 (m-30) cc_final: 0.7981 (m-30) REVERT: A 337 TYR cc_start: 0.8074 (m-80) cc_final: 0.7802 (m-80) REVERT: B 71 ARG cc_start: 0.8214 (ptm160) cc_final: 0.7908 (ppp-140) REVERT: B 175 ASN cc_start: 0.8560 (t0) cc_final: 0.8183 (m110) REVERT: B 212 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8571 (mt-10) REVERT: C 68 TYR cc_start: 0.7897 (t80) cc_final: 0.7640 (t80) REVERT: C 165 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7839 (mpt180) REVERT: C 262 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7690 (mm110) REVERT: D 71 ARG cc_start: 0.8044 (ptm160) cc_final: 0.7790 (ptm-80) REVERT: D 203 ASP cc_start: 0.8109 (m-30) cc_final: 0.7797 (m-30) outliers start: 28 outliers final: 18 residues processed: 222 average time/residue: 0.6346 time to fit residues: 154.9466 Evaluate side-chains 208 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 158 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106308 restraints weight = 18988.890| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.95 r_work: 0.3200 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15470 Z= 0.134 Angle : 0.525 12.134 20980 Z= 0.258 Chirality : 0.038 0.134 2275 Planarity : 0.003 0.025 2625 Dihedral : 3.734 14.567 2055 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.82 % Allowed : 19.06 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 1820 helix: 1.06 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.84 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 168 TYR 0.019 0.001 TYR A 68 PHE 0.019 0.001 PHE A 276 TRP 0.011 0.001 TRP D 182 HIS 0.002 0.000 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (15470) covalent geometry : angle 0.52539 / 0.26 (20980) hydrogen bonds : bond 0.04139 / 2.62 ( 770) hydrogen bonds : angle 3.82910 / 2.63 ( 2250) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.8430 (tpp80) cc_final: 0.8073 (mpt180) REVERT: E 168 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8337 (ttm170) REVERT: E 175 ASN cc_start: 0.8538 (t0) cc_final: 0.8064 (m110) REVERT: E 361 GLN cc_start: 0.7662 (mt0) cc_final: 0.7199 (mm-40) REVERT: A 71 ARG cc_start: 0.7976 (ptm160) cc_final: 0.7734 (ptm-80) REVERT: A 168 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7937 (ttm170) REVERT: A 175 ASN cc_start: 0.8582 (t0) cc_final: 0.8228 (m110) REVERT: A 203 ASP cc_start: 0.8304 (m-30) cc_final: 0.7983 (m-30) REVERT: B 71 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7943 (ppp-140) REVERT: B 80 PHE cc_start: 0.7633 (m-80) cc_final: 0.7431 (m-80) REVERT: B 175 ASN cc_start: 0.8579 (t0) cc_final: 0.8186 (m110) REVERT: B 212 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8564 (mt-10) REVERT: C 68 TYR cc_start: 0.7879 (t80) cc_final: 0.7678 (t80) REVERT: C 165 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7827 (mpt180) REVERT: D 71 ARG cc_start: 0.8052 (ptm160) cc_final: 0.7746 (ptm-80) REVERT: D 203 ASP cc_start: 0.8169 (m-30) cc_final: 0.7895 (m-30) outliers start: 29 outliers final: 17 residues processed: 219 average time/residue: 0.5988 time to fit residues: 144.7469 Evaluate side-chains 209 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 166 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.139847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105987 restraints weight = 18898.745| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.94 r_work: 0.3192 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15470 Z= 0.146 Angle : 0.535 12.265 20980 Z= 0.264 Chirality : 0.039 0.131 2275 Planarity : 0.003 0.025 2625 Dihedral : 3.783 15.104 2055 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.64 % Allowed : 19.50 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1820 helix: 1.07 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.80 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 168 TYR 0.013 0.001 TYR D 236 PHE 0.017 0.001 PHE A 282 TRP 0.011 0.001 TRP D 182 HIS 0.002 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (15470) covalent geometry : angle 0.53500 / 0.26 (20980) hydrogen bonds : bond 0.04237 / 2.68 ( 770) hydrogen bonds : angle 3.86259 / 2.65 ( 2250) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 42 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8710 (mp) REVERT: E 165 ARG cc_start: 0.8439 (tpp80) cc_final: 0.8076 (mpt180) REVERT: E 168 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8294 (ttm170) REVERT: E 175 ASN cc_start: 0.8546 (t0) cc_final: 0.8066 (m110) REVERT: E 361 GLN cc_start: 0.7705 (mt0) cc_final: 0.7232 (mm-40) REVERT: A 71 ARG cc_start: 0.7962 (ptm160) cc_final: 0.7728 (ptm-80) REVERT: A 168 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7949 (ttm170) REVERT: A 175 ASN cc_start: 0.8601 (t0) cc_final: 0.8227 (m110) REVERT: A 203 ASP cc_start: 0.8328 (m-30) cc_final: 0.7998 (m-30) REVERT: A 337 TYR cc_start: 0.8013 (m-80) cc_final: 0.7717 (m-80) REVERT: B 71 ARG cc_start: 0.8222 (ptm160) cc_final: 0.7939 (ppp-140) REVERT: B 175 ASN cc_start: 0.8566 (t0) cc_final: 0.8174 (m110) REVERT: B 212 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8564 (mt-10) REVERT: C 68 TYR cc_start: 0.7903 (t80) cc_final: 0.7647 (t80) REVERT: C 165 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7853 (mpt180) REVERT: C 262 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7617 (mm110) REVERT: D 71 ARG cc_start: 0.8053 (ptm160) cc_final: 0.7750 (ptm-80) REVERT: D 203 ASP cc_start: 0.8200 (m-30) cc_final: 0.7860 (m-30) outliers start: 26 outliers final: 17 residues processed: 215 average time/residue: 0.6291 time to fit residues: 149.1084 Evaluate side-chains 209 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 179 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 130 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.140612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.106469 restraints weight = 18961.383| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.96 r_work: 0.3205 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15470 Z= 0.135 Angle : 0.529 11.970 20980 Z= 0.261 Chirality : 0.039 0.129 2275 Planarity : 0.003 0.024 2625 Dihedral : 3.758 14.492 2055 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.64 % Allowed : 19.87 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.20), residues: 1820 helix: 1.11 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.78 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 168 TYR 0.020 0.001 TYR A 68 PHE 0.023 0.002 PHE E 80 TRP 0.010 0.001 TRP D 182 HIS 0.002 0.000 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15470) covalent geometry : angle 0.52943 / 0.26 (20980) hydrogen bonds : bond 0.04188 / 2.65 ( 770) hydrogen bonds : angle 3.83737 / 2.63 ( 2250) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 19 LYS cc_start: 0.8271 (mmtp) cc_final: 0.7983 (mmtp) REVERT: E 42 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8741 (mp) REVERT: E 165 ARG cc_start: 0.8427 (tpp80) cc_final: 0.8014 (mpt180) REVERT: E 168 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8335 (ttm170) REVERT: E 175 ASN cc_start: 0.8526 (t0) cc_final: 0.8054 (m110) REVERT: E 361 GLN cc_start: 0.7741 (mt0) cc_final: 0.7273 (mm-40) REVERT: A 71 ARG cc_start: 0.7958 (ptm160) cc_final: 0.7735 (ptm-80) REVERT: A 168 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7894 (ttm170) REVERT: A 175 ASN cc_start: 0.8579 (t0) cc_final: 0.8216 (m110) REVERT: A 203 ASP cc_start: 0.8330 (m-30) cc_final: 0.8004 (m-30) REVERT: A 337 TYR cc_start: 0.8020 (m-80) cc_final: 0.7744 (m-80) REVERT: B 71 ARG cc_start: 0.8219 (ptm160) cc_final: 0.7940 (ppp-140) REVERT: B 175 ASN cc_start: 0.8548 (t0) cc_final: 0.8161 (m110) REVERT: B 212 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8552 (mt-10) REVERT: C 68 TYR cc_start: 0.7814 (t80) cc_final: 0.7457 (t80) REVERT: C 165 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7831 (mpt180) REVERT: D 71 ARG cc_start: 0.8036 (ptm160) cc_final: 0.7739 (ptm-80) REVERT: D 203 ASP cc_start: 0.8228 (m-30) cc_final: 0.7941 (m-30) outliers start: 26 outliers final: 19 residues processed: 210 average time/residue: 0.6350 time to fit residues: 146.9056 Evaluate side-chains 208 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 16 optimal weight: 0.0980 chunk 128 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 174 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 167 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 95 ASN ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.141763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.107982 restraints weight = 18815.087| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.95 r_work: 0.3221 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15470 Z= 0.116 Angle : 0.513 12.687 20980 Z= 0.254 Chirality : 0.038 0.132 2275 Planarity : 0.002 0.024 2625 Dihedral : 3.706 14.957 2055 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.76 % Allowed : 19.81 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.76 (0.20), residues: 1820 helix: 1.20 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.73 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 168 TYR 0.030 0.001 TYR E 68 PHE 0.015 0.001 PHE A 282 TRP 0.010 0.001 TRP D 182 HIS 0.002 0.000 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (15470) covalent geometry : angle 0.51288 / 0.25 (20980) hydrogen bonds : bond 0.04021 / 2.55 ( 770) hydrogen bonds : angle 3.78734 / 2.60 ( 2250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4986.91 seconds wall clock time: 85 minutes 59.10 seconds (5159.10 seconds total)