Starting phenix.real_space_refine on Fri Nov 21 02:13:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6d8c_7831/11_2025/6d8c_7831_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d8c_7831/11_2025/6d8c_7831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6d8c_7831/11_2025/6d8c_7831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d8c_7831/11_2025/6d8c_7831.map" model { file = "/net/cci-nas-00/data/ceres_data/6d8c_7831/11_2025/6d8c_7831_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d8c_7831/11_2025/6d8c_7831_trim.cif" } resolution = 3.54 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= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4475 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 128 5.16 5 C 12425 2.51 5 N 3374 2.21 5 O 3723 1.98 5 H 19591 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39256 Number of models: 1 Model: "" Number of chains: 18 Chain: "D" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2012 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "H" Number of atoms: 5750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5750 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2012 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "J" Number of atoms: 5750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5750 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "B" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2012 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "K" Number of atoms: 5750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5750 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2012 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "L" Number of atoms: 5750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5750 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "E" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2012 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "M" Number of atoms: 5750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5750 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "N" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 102 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'G5G:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 102 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'G5G:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 102 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'G5G:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.64, per 1000 atoms: 0.19 Number of scatterers: 39256 At special positions: 0 Unit cell: (95.76, 129.01, 202.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 128 16.00 P 10 15.00 Mg 5 11.99 O 3723 8.00 N 3374 7.00 C 12425 6.00 H 19591 1.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4642 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 30 sheets defined 51.7% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'D' and resid 29 through 33 removed outlier: 4.042A pdb=" N LYS D 33 " --> pdb=" O ALA D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 57 removed outlier: 3.795A pdb=" N HIS D 56 " --> pdb=" O TRP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 71 removed outlier: 4.138A pdb=" N LEU D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 86 Processing helix chain 'D' and resid 99 through 117 removed outlier: 3.676A pdb=" N GLN D 103 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 133 through 148 removed outlier: 3.713A pdb=" N LEU D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY D 139 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 61 removed outlier: 3.672A pdb=" N GLN H 59 " --> pdb=" O GLY H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 91 removed outlier: 3.664A pdb=" N LYS H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 127 removed outlier: 4.273A pdb=" N THR H 120 " --> pdb=" O ARG H 116 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET H 123 " --> pdb=" O MET H 119 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE H 124 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU H 125 " --> pdb=" O GLN H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 146 removed outlier: 4.141A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 197 removed outlier: 4.119A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 217 removed outlier: 3.585A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS H 215 " --> pdb=" O ASP H 211 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU H 216 " --> pdb=" O ILE H 212 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS H 217 " --> pdb=" O LYS H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 233 removed outlier: 3.547A pdb=" N ALA H 228 " --> pdb=" O GLU H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 255 Processing helix chain 'H' and resid 257 through 261 Processing helix chain 'H' and resid 273 through 285 removed outlier: 3.650A pdb=" N CYS H 285 " --> pdb=" O SER H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 296 Processing helix chain 'H' and resid 308 through 321 removed outlier: 3.551A pdb=" N ALA H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 349 Processing helix chain 'H' and resid 350 through 356 removed outlier: 3.981A pdb=" N TRP H 356 " --> pdb=" O GLN H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 removed outlier: 3.617A pdb=" N GLU H 364 " --> pdb=" O GLN H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 374 removed outlier: 3.567A pdb=" N LYS H 373 " --> pdb=" O ILE H 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 33 removed outlier: 4.042A pdb=" N LYS A 33 " --> pdb=" O ALA A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 57 removed outlier: 3.795A pdb=" N HIS A 56 " --> pdb=" O TRP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 71 removed outlier: 4.138A pdb=" N LEU A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.677A pdb=" N GLN A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.713A pdb=" N LEU A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.672A pdb=" N GLN J 59 " --> pdb=" O GLY J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 91 removed outlier: 3.664A pdb=" N LYS J 84 " --> pdb=" O ASP J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 127 removed outlier: 4.273A pdb=" N THR J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET J 123 " --> pdb=" O MET J 119 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE J 124 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU J 125 " --> pdb=" O GLN J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 146 removed outlier: 4.140A pdb=" N LEU J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR J 143 " --> pdb=" O VAL J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 197 removed outlier: 4.119A pdb=" N THR J 194 " --> pdb=" O MET J 190 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU J 195 " --> pdb=" O LYS J 191 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG J 196 " --> pdb=" O ILE J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 217 removed outlier: 3.585A pdb=" N GLU J 207 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS J 215 " --> pdb=" O ASP J 211 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU J 216 " --> pdb=" O ILE J 212 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS J 217 " --> pdb=" O LYS J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 233 removed outlier: 3.548A pdb=" N ALA J 228 " --> pdb=" O GLU J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 255 Processing helix chain 'J' and resid 257 through 261 Processing helix chain 'J' and resid 273 through 285 removed outlier: 3.649A pdb=" N CYS J 285 " --> pdb=" O SER J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 296 Processing helix chain 'J' and resid 308 through 321 removed outlier: 3.552A pdb=" N ALA J 319 " --> pdb=" O LYS J 315 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 349 Processing helix chain 'J' and resid 350 through 356 removed outlier: 3.981A pdb=" N TRP J 356 " --> pdb=" O GLN J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 366 removed outlier: 3.617A pdb=" N GLU J 364 " --> pdb=" O GLN J 360 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 374 removed outlier: 3.566A pdb=" N LYS J 373 " --> pdb=" O ILE J 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 removed outlier: 4.043A pdb=" N LYS B 33 " --> pdb=" O ALA B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 57 removed outlier: 3.795A pdb=" N HIS B 56 " --> pdb=" O TRP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 removed outlier: 4.138A pdb=" N LEU B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 99 through 117 removed outlier: 3.676A pdb=" N GLN B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 132 Processing helix chain 'B' and resid 133 through 148 removed outlier: 3.713A pdb=" N LEU B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 61 removed outlier: 3.672A pdb=" N GLN K 59 " --> pdb=" O GLY K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 91 removed outlier: 3.665A pdb=" N LYS K 84 " --> pdb=" O ASP K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 127 removed outlier: 4.273A pdb=" N THR K 120 " --> pdb=" O ARG K 116 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET K 123 " --> pdb=" O MET K 119 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU K 125 " --> pdb=" O GLN K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 146 removed outlier: 4.140A pdb=" N LEU K 142 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 197 removed outlier: 4.119A pdb=" N THR K 194 " --> pdb=" O MET K 190 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU K 195 " --> pdb=" O LYS K 191 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG K 196 " --> pdb=" O ILE K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 217 removed outlier: 3.586A pdb=" N GLU K 207 " --> pdb=" O THR K 203 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS K 215 " --> pdb=" O ASP K 211 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU K 216 " --> pdb=" O ILE K 212 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS K 217 " --> pdb=" O LYS K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 233 removed outlier: 3.546A pdb=" N ALA K 228 " --> pdb=" O GLU K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 255 Processing helix chain 'K' and resid 257 through 261 Processing helix chain 'K' and resid 273 through 285 removed outlier: 3.650A pdb=" N CYS K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 289 through 296 Processing helix chain 'K' and resid 308 through 321 removed outlier: 3.552A pdb=" N ALA K 319 " --> pdb=" O LYS K 315 " (cutoff:3.500A) Processing helix chain 'K' and resid 337 through 349 Processing helix chain 'K' and resid 350 through 356 removed outlier: 3.981A pdb=" N TRP K 356 " --> pdb=" O GLN K 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 366 removed outlier: 3.617A pdb=" N GLU K 364 " --> pdb=" O GLN K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 374 removed outlier: 3.567A pdb=" N LYS K 373 " --> pdb=" O ILE K 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 removed outlier: 4.042A pdb=" N LYS C 33 " --> pdb=" O ALA C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 57 removed outlier: 3.795A pdb=" N HIS C 56 " --> pdb=" O TRP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 4.137A pdb=" N LEU C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.676A pdb=" N GLN C 103 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 133 through 148 removed outlier: 3.712A pdb=" N LEU C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY C 139 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 61 removed outlier: 3.671A pdb=" N GLN L 59 " --> pdb=" O GLY L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 91 removed outlier: 3.664A pdb=" N LYS L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 127 removed outlier: 4.273A pdb=" N THR L 120 " --> pdb=" O ARG L 116 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET L 123 " --> pdb=" O MET L 119 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE L 124 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU L 125 " --> pdb=" O GLN L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 146 removed outlier: 4.139A pdb=" N LEU L 142 " --> pdb=" O ALA L 138 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR L 143 " --> pdb=" O VAL L 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 197 removed outlier: 4.118A pdb=" N THR L 194 " --> pdb=" O MET L 190 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU L 195 " --> pdb=" O LYS L 191 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG L 196 " --> pdb=" O ILE L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 217 removed outlier: 3.585A pdb=" N GLU L 207 " --> pdb=" O THR L 203 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE L 208 " --> pdb=" O ALA L 204 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS L 215 " --> pdb=" O ASP L 211 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU L 216 " --> pdb=" O ILE L 212 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS L 217 " --> pdb=" O LYS L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 233 removed outlier: 3.547A pdb=" N ALA L 228 " --> pdb=" O GLU L 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 255 Processing helix chain 'L' and resid 257 through 261 Processing helix chain 'L' and resid 273 through 285 removed outlier: 3.650A pdb=" N CYS L 285 " --> pdb=" O SER L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 289 through 296 Processing helix chain 'L' and resid 308 through 321 removed outlier: 3.551A pdb=" N ALA L 319 " --> pdb=" O LYS L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 337 through 349 Processing helix chain 'L' and resid 350 through 356 removed outlier: 3.981A pdb=" N TRP L 356 " --> pdb=" O GLN L 353 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 366 removed outlier: 3.617A pdb=" N GLU L 364 " --> pdb=" O GLN L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 369 through 374 removed outlier: 3.566A pdb=" N LYS L 373 " --> pdb=" O ILE L 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 33 removed outlier: 4.043A pdb=" N LYS E 33 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 57 removed outlier: 3.795A pdb=" N HIS E 56 " --> pdb=" O TRP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 71 removed outlier: 4.139A pdb=" N LEU E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.676A pdb=" N GLN E 103 " --> pdb=" O PHE E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'E' and resid 133 through 148 removed outlier: 3.713A pdb=" N LEU E 138 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 61 removed outlier: 3.671A pdb=" N GLN M 59 " --> pdb=" O GLY M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 91 removed outlier: 3.665A pdb=" N LYS M 84 " --> pdb=" O ASP M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 127 removed outlier: 4.274A pdb=" N THR M 120 " --> pdb=" O ARG M 116 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET M 123 " --> pdb=" O MET M 119 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE M 124 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU M 125 " --> pdb=" O GLN M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 146 removed outlier: 4.141A pdb=" N LEU M 142 " --> pdb=" O ALA M 138 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR M 143 " --> pdb=" O VAL M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 197 removed outlier: 4.119A pdb=" N THR M 194 " --> pdb=" O MET M 190 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU M 195 " --> pdb=" O LYS M 191 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG M 196 " --> pdb=" O ILE M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 202 through 217 removed outlier: 3.585A pdb=" N GLU M 207 " --> pdb=" O THR M 203 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE M 208 " --> pdb=" O ALA M 204 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS M 215 " --> pdb=" O ASP M 211 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU M 216 " --> pdb=" O ILE M 212 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS M 217 " --> pdb=" O LYS M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 233 removed outlier: 3.547A pdb=" N ALA M 228 " --> pdb=" O GLU M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 255 Processing helix chain 'M' and resid 257 through 261 Processing helix chain 'M' and resid 273 through 285 removed outlier: 3.650A pdb=" N CYS M 285 " --> pdb=" O SER M 281 " (cutoff:3.500A) Processing helix chain 'M' and resid 289 through 296 Processing helix chain 'M' and resid 308 through 321 removed outlier: 3.552A pdb=" N ALA M 319 " --> pdb=" O LYS M 315 " (cutoff:3.500A) Processing helix chain 'M' and resid 337 through 349 Processing helix chain 'M' and resid 350 through 356 removed outlier: 3.980A pdb=" N TRP M 356 " --> pdb=" O GLN M 353 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 366 removed outlier: 3.617A pdb=" N GLU M 364 " --> pdb=" O GLN M 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 369 through 374 removed outlier: 3.566A pdb=" N LYS M 373 " --> pdb=" O ILE M 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.709A pdb=" N THR H 106 " --> pdb=" O CYS H 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'H' and resid 150 through 152 removed outlier: 3.591A pdb=" N VAL H 163 " --> pdb=" O VAL H 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 238 through 240 removed outlier: 3.537A pdb=" N LYS H 238 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE H 248 " --> pdb=" O TYR H 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 297 through 298 removed outlier: 6.474A pdb=" N ASN H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'J' and resid 29 through 32 removed outlier: 3.709A pdb=" N THR J 106 " --> pdb=" O CYS J 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'J' and resid 150 through 152 removed outlier: 3.591A pdb=" N VAL J 163 " --> pdb=" O VAL J 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 238 through 240 removed outlier: 3.538A pdb=" N LYS J 238 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE J 248 " --> pdb=" O TYR J 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 297 through 298 removed outlier: 6.473A pdb=" N ASN J 297 " --> pdb=" O ILE J 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 29 through 32 removed outlier: 3.709A pdb=" N THR K 106 " --> pdb=" O CYS K 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'K' and resid 150 through 152 removed outlier: 3.591A pdb=" N VAL K 163 " --> pdb=" O VAL K 152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 238 through 240 removed outlier: 3.538A pdb=" N LYS K 238 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE K 248 " --> pdb=" O TYR K 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 297 through 298 removed outlier: 6.474A pdb=" N ASN K 297 " --> pdb=" O ILE K 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'L' and resid 29 through 32 removed outlier: 3.710A pdb=" N THR L 106 " --> pdb=" O CYS L 10 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'L' and resid 150 through 152 removed outlier: 3.590A pdb=" N VAL L 163 " --> pdb=" O VAL L 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 238 through 240 removed outlier: 3.537A pdb=" N LYS L 238 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE L 248 " --> pdb=" O TYR L 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 297 through 298 removed outlier: 6.474A pdb=" N ASN L 297 " --> pdb=" O ILE L 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'M' and resid 29 through 32 removed outlier: 3.710A pdb=" N THR M 106 " --> pdb=" O CYS M 10 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'M' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'M' and resid 150 through 152 removed outlier: 3.590A pdb=" N VAL M 163 " --> pdb=" O VAL M 152 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 238 through 240 removed outlier: 3.538A pdb=" N LYS M 238 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE M 248 " --> pdb=" O TYR M 240 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 297 through 298 removed outlier: 6.473A pdb=" N ASN M 297 " --> pdb=" O ILE M 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 845 hydrogen bonds defined for protein. 2295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.30 Time building geometry restraints manager: 5.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 19556 1.02 - 1.22: 56 1.22 - 1.42: 8128 1.42 - 1.62: 11699 1.62 - 1.82: 218 Bond restraints: 39657 Sorted by residual: bond pdb=" C HYP O 1 " pdb=" N ALA O 2 " ideal model delta sigma weight residual 1.329 1.460 -0.131 1.40e-02 5.10e+03 8.71e+01 bond pdb=" C HYP P 1 " pdb=" N ALA P 2 " ideal model delta sigma weight residual 1.329 1.459 -0.130 1.40e-02 5.10e+03 8.63e+01 bond pdb=" C HYP N 1 " pdb=" N ALA N 2 " ideal model delta sigma weight residual 1.329 1.459 -0.130 1.40e-02 5.10e+03 8.59e+01 bond pdb=" C ALA O 5 " pdb=" N ALO O 6 " ideal model delta sigma weight residual 1.329 1.458 -0.129 1.40e-02 5.10e+03 8.47e+01 bond pdb=" C ALA N 5 " pdb=" N ALO N 6 " ideal model delta sigma weight residual 1.329 1.457 -0.128 1.40e-02 5.10e+03 8.38e+01 ... (remaining 39652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 70936 2.35 - 4.70: 725 4.70 - 7.05: 109 7.05 - 9.40: 11 9.40 - 11.75: 6 Bond angle restraints: 71787 Sorted by residual: angle pdb=" N THR M 194 " pdb=" CA THR M 194 " pdb=" C THR M 194 " ideal model delta sigma weight residual 111.71 105.25 6.46 1.15e+00 7.56e-01 3.16e+01 angle pdb=" N THR L 194 " pdb=" CA THR L 194 " pdb=" C THR L 194 " ideal model delta sigma weight residual 111.71 105.26 6.45 1.15e+00 7.56e-01 3.15e+01 angle pdb=" N THR H 194 " pdb=" CA THR H 194 " pdb=" C THR H 194 " ideal model delta sigma weight residual 111.71 105.27 6.44 1.15e+00 7.56e-01 3.14e+01 angle pdb=" N THR K 194 " pdb=" CA THR K 194 " pdb=" C THR K 194 " ideal model delta sigma weight residual 111.71 105.28 6.43 1.15e+00 7.56e-01 3.13e+01 angle pdb=" N THR J 194 " pdb=" CA THR J 194 " pdb=" C THR J 194 " ideal model delta sigma weight residual 111.71 105.29 6.42 1.15e+00 7.56e-01 3.12e+01 ... (remaining 71782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.81: 18262 33.81 - 67.63: 362 67.63 - 101.44: 6 101.44 - 135.25: 9 135.25 - 169.06: 10 Dihedral angle restraints: 18649 sinusoidal: 10352 harmonic: 8297 Sorted by residual: dihedral pdb=" O2A ADP J 401 " pdb=" O3A ADP J 401 " pdb=" PA ADP J 401 " pdb=" PB ADP J 401 " ideal model delta sinusoidal sigma weight residual -60.00 109.06 -169.06 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP K 401 " pdb=" O3A ADP K 401 " pdb=" PA ADP K 401 " pdb=" PB ADP K 401 " ideal model delta sinusoidal sigma weight residual -60.00 109.00 -169.00 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP H 401 " pdb=" O3A ADP H 401 " pdb=" PA ADP H 401 " pdb=" PB ADP H 401 " ideal model delta sinusoidal sigma weight residual -60.00 109.00 -169.00 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 18646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2657 0.065 - 0.131: 383 0.131 - 0.196: 17 0.196 - 0.262: 8 0.262 - 0.327: 5 Chirality restraints: 3070 Sorted by residual: chirality pdb=" CA HIS J 161 " pdb=" N HIS J 161 " pdb=" C HIS J 161 " pdb=" CB HIS J 161 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA HIS M 161 " pdb=" N HIS M 161 " pdb=" C HIS M 161 " pdb=" CB HIS M 161 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA HIS H 161 " pdb=" N HIS H 161 " pdb=" C HIS H 161 " pdb=" CB HIS H 161 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 3067 not shown) Planarity restraints: 5791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN K 263 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO K 264 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO K 264 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 264 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN M 263 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO M 264 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO M 264 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO M 264 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 263 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO L 264 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO L 264 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 264 " -0.033 5.00e-02 4.00e+02 ... (remaining 5788 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 448 2.08 - 2.71: 65705 2.71 - 3.34: 113002 3.34 - 3.97: 144457 3.97 - 4.60: 231939 Nonbonded interactions: 555551 Sorted by model distance: nonbonded pdb=" HE1 MET H 47 " pdb=" HG1 THR M 148 " model vdw 1.448 2.270 nonbonded pdb=" HG1 THR K 148 " pdb=" HE1 MET L 47 " model vdw 1.460 2.270 nonbonded pdb=" HG1 THR H 148 " pdb=" HE1 MET J 47 " model vdw 1.488 2.270 nonbonded pdb=" HE3 LYS D 127 " pdb=" HG2 GLU M 167 " model vdw 1.540 2.440 nonbonded pdb=" HG2 GLU K 167 " pdb=" HE3 LYS C 127 " model vdw 1.542 2.440 ... (remaining 555546 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.210 Extract box with map and model: 0.430 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 39.400 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 : 0.006 0.131 20069 Z= 0.363 Angle : 0.819 10.405 27190 Z= 0.481 Chirality : 0.046 0.327 3070 Planarity : 0.005 0.059 3436 Dihedral : 11.945 169.063 7543 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.85 % Allowed : 3.06 % Favored : 96.10 % 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: -2.35 (0.15), residues: 2435 helix: -1.88 (0.12), residues: 1050 sheet: -1.71 (0.28), residues: 305 loop : -0.94 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 312 TYR 0.019 0.001 TYR K 166 PHE 0.010 0.001 PHE A 49 TRP 0.019 0.002 TRP H 340 HIS 0.004 0.001 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00588 (20066) covalent geometry : angle 0.81924 (27190) hydrogen bonds : bond 0.30239 ( 845) hydrogen bonds : angle 8.93154 ( 2295) Misc. bond : bond 0.01555 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 712 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 66 ASN cc_start: 0.8414 (t0) cc_final: 0.8204 (t0) REVERT: D 87 LYS cc_start: 0.8367 (mttt) cc_final: 0.8053 (mtmt) REVERT: D 92 LYS cc_start: 0.8069 (mttp) cc_final: 0.7858 (mtpp) REVERT: H 113 LYS cc_start: 0.7627 (mtpt) cc_final: 0.7409 (mtmt) REVERT: H 171 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8826 (mt) REVERT: H 283 MET cc_start: 0.7860 (mmt) cc_final: 0.7602 (mmt) REVERT: H 361 GLU cc_start: 0.6217 (tt0) cc_final: 0.5998 (tt0) REVERT: A 119 ILE cc_start: 0.7738 (mt) cc_final: 0.7458 (mt) REVERT: J 176 MET cc_start: 0.7878 (mmm) cc_final: 0.7298 (mtp) REVERT: J 361 GLU cc_start: 0.6563 (tt0) cc_final: 0.6262 (tt0) REVERT: B 100 ARG cc_start: 0.7917 (ttt90) cc_final: 0.5922 (ptt180) REVERT: K 107 GLU cc_start: 0.7663 (pp20) cc_final: 0.7305 (pp20) REVERT: K 244 ASP cc_start: 0.5371 (OUTLIER) cc_final: 0.4908 (p0) REVERT: L 78 ASN cc_start: 0.7495 (m110) cc_final: 0.7224 (m-40) REVERT: L 244 ASP cc_start: 0.5293 (OUTLIER) cc_final: 0.5030 (p0) REVERT: E 89 MET cc_start: 0.7801 (mmm) cc_final: 0.6451 (mmt) REVERT: E 100 ARG cc_start: 0.8061 (ttt90) cc_final: 0.6002 (ptt90) REVERT: M 12 ASN cc_start: 0.7717 (t0) cc_final: 0.7308 (t0) REVERT: M 44 MET cc_start: 0.8580 (mmt) cc_final: 0.8324 (mmt) REVERT: M 157 ASP cc_start: 0.7040 (t0) cc_final: 0.6838 (t0) REVERT: M 176 MET cc_start: 0.8081 (mmm) cc_final: 0.7758 (mtp) outliers start: 18 outliers final: 13 residues processed: 728 average time/residue: 0.4163 time to fit residues: 435.8784 Evaluate side-chains 396 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 380 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain N residue 7 CYS Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain P residue 7 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 133 ASN H 137 GLN H 275 HIS A 68 GLN J 87 HIS J 137 GLN J 296 ASN B 133 ASN K 137 GLN L 137 GLN L 275 HIS M 87 HIS M 137 GLN M 246 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106315 restraints weight = 97301.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109419 restraints weight = 36150.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111183 restraints weight = 17884.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112228 restraints weight = 11089.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112903 restraints weight = 8101.545| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20069 Z= 0.131 Angle : 0.611 6.223 27190 Z= 0.314 Chirality : 0.041 0.142 3070 Planarity : 0.005 0.057 3436 Dihedral : 11.985 167.686 2808 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.65 % Allowed : 10.44 % Favored : 87.91 % 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: -0.87 (0.16), residues: 2435 helix: -0.13 (0.14), residues: 1105 sheet: -1.27 (0.29), residues: 305 loop : -0.67 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 37 TYR 0.013 0.001 TYR J 166 PHE 0.014 0.001 PHE M 262 TRP 0.015 0.001 TRP J 340 HIS 0.006 0.001 HIS M 87 Details of bonding type rmsd covalent geometry : bond 0.00286 (20066) covalent geometry : angle 0.61116 (27190) hydrogen bonds : bond 0.05436 ( 845) hydrogen bonds : angle 5.83191 ( 2295) Misc. bond : bond 0.00017 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 440 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6728 (mm-30) REVERT: D 92 LYS cc_start: 0.8173 (mttp) cc_final: 0.7873 (mttm) REVERT: D 117 GLU cc_start: 0.7831 (tp30) cc_final: 0.7420 (tp30) REVERT: H 123 MET cc_start: 0.7168 (mmt) cc_final: 0.6865 (mmt) REVERT: H 171 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8954 (mt) REVERT: H 283 MET cc_start: 0.8161 (mmt) cc_final: 0.7649 (mmt) REVERT: A 119 ILE cc_start: 0.8029 (mt) cc_final: 0.7725 (mt) REVERT: J 318 THR cc_start: 0.8720 (m) cc_final: 0.8337 (p) REVERT: B 51 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7634 (mmt-90) REVERT: B 100 ARG cc_start: 0.7800 (ttt90) cc_final: 0.6082 (ptt90) REVERT: K 107 GLU cc_start: 0.7466 (pp20) cc_final: 0.7187 (pp20) REVERT: K 244 ASP cc_start: 0.6283 (OUTLIER) cc_final: 0.5895 (p0) REVERT: K 353 GLN cc_start: 0.7342 (mm-40) cc_final: 0.7084 (mp10) REVERT: L 78 ASN cc_start: 0.7962 (m110) cc_final: 0.7513 (m-40) REVERT: L 244 ASP cc_start: 0.6321 (OUTLIER) cc_final: 0.5897 (p0) REVERT: E 33 LYS cc_start: 0.6708 (OUTLIER) cc_final: 0.6029 (ptpp) REVERT: E 87 LYS cc_start: 0.8031 (mtpt) cc_final: 0.7740 (mtmt) REVERT: E 100 ARG cc_start: 0.8026 (ttt90) cc_final: 0.6243 (ptt90) REVERT: M 12 ASN cc_start: 0.7886 (t0) cc_final: 0.7635 (t0) REVERT: M 44 MET cc_start: 0.8659 (mmt) cc_final: 0.8324 (mmt) REVERT: M 198 TYR cc_start: 0.8963 (m-80) cc_final: 0.8659 (m-80) outliers start: 35 outliers final: 20 residues processed: 465 average time/residue: 0.4429 time to fit residues: 293.0253 Evaluate side-chains 381 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 357 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 244 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 172 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 208 optimal weight: 0.0050 chunk 57 optimal weight: 6.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 296 ASN J 353 GLN C 56 HIS C 101 GLN M 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.098752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.087625 restraints weight = 103076.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.090651 restraints weight = 37711.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.092400 restraints weight = 18883.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.093436 restraints weight = 11947.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.094071 restraints weight = 8892.282| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 20069 Z= 0.285 Angle : 0.733 8.279 27190 Z= 0.383 Chirality : 0.046 0.235 3070 Planarity : 0.006 0.078 3436 Dihedral : 11.153 156.412 2801 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.07 % Allowed : 12.61 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.16), residues: 2435 helix: 0.23 (0.15), residues: 1070 sheet: -2.11 (0.28), residues: 295 loop : -0.85 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 116 TYR 0.023 0.002 TYR L 166 PHE 0.017 0.002 PHE M 262 TRP 0.021 0.002 TRP M 340 HIS 0.009 0.002 HIS H 161 Details of bonding type rmsd covalent geometry : bond 0.00674 (20066) covalent geometry : angle 0.73308 (27190) hydrogen bonds : bond 0.04295 ( 845) hydrogen bonds : angle 5.28273 ( 2295) Misc. bond : bond 0.00056 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 404 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 LYS cc_start: 0.8385 (mttp) cc_final: 0.7945 (mttm) REVERT: H 113 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7927 (mmtt) REVERT: H 187 ASP cc_start: 0.7686 (m-30) cc_final: 0.7436 (m-30) REVERT: H 244 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7945 (p0) REVERT: H 283 MET cc_start: 0.8426 (mmt) cc_final: 0.7994 (mmt) REVERT: J 195 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7368 (mm-30) REVERT: B 70 ASP cc_start: 0.8161 (m-30) cc_final: 0.7950 (m-30) REVERT: B 92 LYS cc_start: 0.8035 (tmmt) cc_final: 0.7481 (mtpt) REVERT: B 100 ARG cc_start: 0.7747 (ttt90) cc_final: 0.5949 (ptt90) REVERT: K 53 TYR cc_start: 0.8260 (m-80) cc_final: 0.7995 (m-80) REVERT: K 107 GLU cc_start: 0.7481 (pp20) cc_final: 0.6688 (pp20) REVERT: K 162 ASN cc_start: 0.7678 (m-40) cc_final: 0.7403 (m-40) REVERT: K 211 ASP cc_start: 0.8434 (t0) cc_final: 0.8161 (t0) REVERT: K 353 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7453 (mp10) REVERT: K 361 GLU cc_start: 0.7611 (tt0) cc_final: 0.7218 (tt0) REVERT: C 70 ASP cc_start: 0.8276 (m-30) cc_final: 0.7918 (m-30) REVERT: L 16 LEU cc_start: 0.8611 (tp) cc_final: 0.8367 (tp) REVERT: L 78 ASN cc_start: 0.8365 (m110) cc_final: 0.7861 (m110) REVERT: L 132 MET cc_start: 0.8876 (ttp) cc_final: 0.8656 (ttp) REVERT: L 161 HIS cc_start: 0.7463 (OUTLIER) cc_final: 0.5809 (m-70) REVERT: L 162 ASN cc_start: 0.8085 (m-40) cc_final: 0.7796 (m-40) REVERT: L 244 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7540 (p0) REVERT: E 70 ASP cc_start: 0.8232 (m-30) cc_final: 0.7948 (m-30) REVERT: E 83 VAL cc_start: 0.9184 (t) cc_final: 0.8877 (t) REVERT: E 87 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7823 (mtpt) REVERT: E 100 ARG cc_start: 0.7954 (ttt90) cc_final: 0.6072 (ptt90) REVERT: E 127 LYS cc_start: 0.7774 (tttm) cc_final: 0.7149 (ttpt) REVERT: E 131 ASP cc_start: 0.8285 (m-30) cc_final: 0.8067 (m-30) REVERT: M 44 MET cc_start: 0.8773 (mmt) cc_final: 0.8489 (mmt) outliers start: 44 outliers final: 32 residues processed: 442 average time/residue: 0.4393 time to fit residues: 274.2225 Evaluate side-chains 354 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 319 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 286 ASP Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 351 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 286 ASP Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 318 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 35 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 275 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.091216 restraints weight = 102073.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.094296 restraints weight = 37044.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.096067 restraints weight = 18364.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.097103 restraints weight = 11485.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.097759 restraints weight = 8479.425| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20069 Z= 0.108 Angle : 0.565 8.566 27190 Z= 0.280 Chirality : 0.041 0.151 3070 Planarity : 0.004 0.051 3436 Dihedral : 10.728 164.353 2797 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.51 % Allowed : 15.19 % Favored : 83.30 % 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: -0.42 (0.17), residues: 2435 helix: 0.70 (0.16), residues: 1095 sheet: -2.03 (0.28), residues: 285 loop : -0.70 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 116 TYR 0.009 0.001 TYR L 279 PHE 0.013 0.001 PHE K 262 TRP 0.014 0.001 TRP M 340 HIS 0.005 0.001 HIS H 161 Details of bonding type rmsd covalent geometry : bond 0.00251 (20066) covalent geometry : angle 0.56505 (27190) hydrogen bonds : bond 0.03046 ( 845) hydrogen bonds : angle 4.81455 ( 2295) Misc. bond : bond 0.00033 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 362 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 LYS cc_start: 0.8281 (mttp) cc_final: 0.7906 (mttm) REVERT: H 132 MET cc_start: 0.8733 (ttp) cc_final: 0.8261 (ttp) REVERT: H 244 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7630 (p0) REVERT: H 293 LEU cc_start: 0.8897 (mp) cc_final: 0.8552 (mp) REVERT: H 360 GLN cc_start: 0.7325 (pp30) cc_final: 0.7116 (pp30) REVERT: A 86 GLN cc_start: 0.8416 (mm110) cc_final: 0.8138 (mm110) REVERT: J 47 MET cc_start: 0.8770 (tpp) cc_final: 0.8559 (tpp) REVERT: J 82 MET cc_start: 0.8916 (tpt) cc_final: 0.8708 (tpt) REVERT: J 107 GLU cc_start: 0.7747 (pp20) cc_final: 0.7479 (pp20) REVERT: J 125 GLU cc_start: 0.7928 (mp0) cc_final: 0.7470 (mp0) REVERT: B 100 ARG cc_start: 0.7700 (ttt90) cc_final: 0.5898 (ptt90) REVERT: K 107 GLU cc_start: 0.7270 (pp20) cc_final: 0.6514 (pp20) REVERT: K 244 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7647 (p0) REVERT: C 70 ASP cc_start: 0.8218 (m-30) cc_final: 0.7850 (m-30) REVERT: L 78 ASN cc_start: 0.8328 (m110) cc_final: 0.7717 (m-40) REVERT: L 132 MET cc_start: 0.8871 (ttp) cc_final: 0.8598 (ttp) REVERT: L 161 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.6502 (m-70) REVERT: L 162 ASN cc_start: 0.7933 (m-40) cc_final: 0.7657 (m-40) REVERT: L 244 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7466 (p0) REVERT: L 372 ARG cc_start: 0.7323 (ptp-170) cc_final: 0.7038 (ptp-170) REVERT: E 66 ASN cc_start: 0.8244 (t0) cc_final: 0.7825 (t0) REVERT: E 70 ASP cc_start: 0.8108 (m-30) cc_final: 0.7742 (m-30) REVERT: E 100 ARG cc_start: 0.7901 (ttt90) cc_final: 0.6057 (ptt90) REVERT: M 44 MET cc_start: 0.8740 (mmt) cc_final: 0.8303 (mmt) outliers start: 32 outliers final: 24 residues processed: 388 average time/residue: 0.4554 time to fit residues: 250.8484 Evaluate side-chains 356 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 328 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 300 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 158 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 186 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.096425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.085363 restraints weight = 104128.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.088329 restraints weight = 38485.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.090038 restraints weight = 19434.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.091050 restraints weight = 12417.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.091698 restraints weight = 9276.970| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.6046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20069 Z= 0.228 Angle : 0.629 7.055 27190 Z= 0.323 Chirality : 0.043 0.148 3070 Planarity : 0.005 0.051 3436 Dihedral : 10.531 165.871 2793 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.45 % Allowed : 14.68 % Favored : 82.88 % 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: -0.39 (0.17), residues: 2435 helix: 0.70 (0.16), residues: 1095 sheet: -2.11 (0.28), residues: 320 loop : -0.55 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 183 TYR 0.011 0.002 TYR J 143 PHE 0.013 0.002 PHE K 262 TRP 0.014 0.001 TRP M 340 HIS 0.006 0.001 HIS L 73 Details of bonding type rmsd covalent geometry : bond 0.00540 (20066) covalent geometry : angle 0.62936 (27190) hydrogen bonds : bond 0.03569 ( 845) hydrogen bonds : angle 4.90326 ( 2295) Misc. bond : bond 0.00033 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 336 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 LYS cc_start: 0.8370 (mttp) cc_final: 0.7940 (mttm) REVERT: H 132 MET cc_start: 0.8849 (ttp) cc_final: 0.8426 (ttp) REVERT: H 244 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8054 (p0) REVERT: H 299 MET cc_start: 0.8321 (mmt) cc_final: 0.8091 (mmt) REVERT: B 70 ASP cc_start: 0.8057 (m-30) cc_final: 0.7702 (m-30) REVERT: B 100 ARG cc_start: 0.7784 (ttt90) cc_final: 0.5859 (ptt180) REVERT: K 107 GLU cc_start: 0.7380 (pp20) cc_final: 0.6556 (pp20) REVERT: K 161 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7016 (m-70) REVERT: K 162 ASN cc_start: 0.7683 (m-40) cc_final: 0.7390 (m-40) REVERT: C 70 ASP cc_start: 0.8292 (m-30) cc_final: 0.7889 (m-30) REVERT: C 117 GLU cc_start: 0.8073 (tp30) cc_final: 0.7829 (tp30) REVERT: L 78 ASN cc_start: 0.8410 (m110) cc_final: 0.7804 (m-40) REVERT: L 82 MET cc_start: 0.8900 (tpp) cc_final: 0.8624 (tpt) REVERT: L 132 MET cc_start: 0.8929 (ttp) cc_final: 0.8662 (ttp) REVERT: L 161 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.7078 (m-70) REVERT: L 162 ASN cc_start: 0.8084 (m-40) cc_final: 0.7824 (m-40) REVERT: L 244 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7669 (p0) REVERT: L 372 ARG cc_start: 0.7421 (ptp-170) cc_final: 0.7199 (ptp-170) REVERT: E 66 ASN cc_start: 0.8430 (t0) cc_final: 0.8041 (t0) REVERT: E 70 ASP cc_start: 0.8264 (m-30) cc_final: 0.7840 (m-30) REVERT: E 100 ARG cc_start: 0.7875 (ttt90) cc_final: 0.5952 (ptt90) REVERT: M 44 MET cc_start: 0.8713 (mmt) cc_final: 0.8286 (mmt) outliers start: 52 outliers final: 40 residues processed: 379 average time/residue: 0.4151 time to fit residues: 227.9982 Evaluate side-chains 351 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 307 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 274 ILE Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 296 ASN Chi-restraints excluded: chain M residue 300 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 243 optimal weight: 0.6980 chunk 151 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 231 optimal weight: 0.0870 chunk 192 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.088485 restraints weight = 103358.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.091388 restraints weight = 38916.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.093053 restraints weight = 19766.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.094055 restraints weight = 12622.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.094690 restraints weight = 9403.271| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20069 Z= 0.112 Angle : 0.548 6.347 27190 Z= 0.271 Chirality : 0.040 0.148 3070 Planarity : 0.004 0.046 3436 Dihedral : 10.211 174.410 2793 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.30 % Allowed : 15.38 % Favored : 82.31 % 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: -0.10 (0.17), residues: 2435 helix: 1.03 (0.16), residues: 1090 sheet: -2.05 (0.27), residues: 310 loop : -0.48 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 206 TYR 0.010 0.001 TYR J 279 PHE 0.013 0.001 PHE K 262 TRP 0.012 0.001 TRP M 340 HIS 0.003 0.001 HIS M 161 Details of bonding type rmsd covalent geometry : bond 0.00261 (20066) covalent geometry : angle 0.54823 (27190) hydrogen bonds : bond 0.02882 ( 845) hydrogen bonds : angle 4.60063 ( 2295) Misc. bond : bond 0.00052 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 338 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 LYS cc_start: 0.8188 (mttp) cc_final: 0.7866 (mttm) REVERT: H 244 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7778 (p0) REVERT: H 283 MET cc_start: 0.8358 (mmt) cc_final: 0.8140 (mmt) REVERT: J 211 ASP cc_start: 0.8606 (t0) cc_final: 0.8221 (t0) REVERT: B 35 LEU cc_start: 0.7125 (mt) cc_final: 0.6889 (mt) REVERT: B 70 ASP cc_start: 0.7908 (m-30) cc_final: 0.7551 (m-30) REVERT: B 100 ARG cc_start: 0.7786 (ttt90) cc_final: 0.6017 (ptt90) REVERT: K 107 GLU cc_start: 0.7315 (pp20) cc_final: 0.6507 (pp20) REVERT: K 161 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.7210 (m-70) REVERT: K 244 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7924 (p0) REVERT: C 70 ASP cc_start: 0.8236 (m-30) cc_final: 0.7832 (m-30) REVERT: C 117 GLU cc_start: 0.7885 (tp30) cc_final: 0.7678 (tp30) REVERT: L 78 ASN cc_start: 0.8259 (m110) cc_final: 0.7608 (m-40) REVERT: L 82 MET cc_start: 0.8935 (tpp) cc_final: 0.8674 (tpt) REVERT: L 132 MET cc_start: 0.8829 (ttp) cc_final: 0.8302 (ttp) REVERT: L 161 HIS cc_start: 0.7781 (OUTLIER) cc_final: 0.7423 (m-70) REVERT: L 162 ASN cc_start: 0.7969 (m-40) cc_final: 0.7605 (m-40) REVERT: L 244 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7518 (p0) REVERT: E 66 ASN cc_start: 0.8251 (t0) cc_final: 0.7806 (t0) REVERT: E 70 ASP cc_start: 0.8203 (m-30) cc_final: 0.7775 (m-30) REVERT: E 100 ARG cc_start: 0.7843 (ttt90) cc_final: 0.6078 (ptt90) REVERT: M 44 MET cc_start: 0.8678 (mmt) cc_final: 0.8182 (mmt) outliers start: 49 outliers final: 39 residues processed: 378 average time/residue: 0.4336 time to fit residues: 237.7462 Evaluate side-chains 360 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 316 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 355 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 300 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 139 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 113 optimal weight: 0.2980 chunk 143 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.095459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.084423 restraints weight = 104740.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.087381 restraints weight = 38767.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.089093 restraints weight = 19576.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.090095 restraints weight = 12447.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.090720 restraints weight = 9340.486| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20069 Z= 0.226 Angle : 0.618 8.015 27190 Z= 0.315 Chirality : 0.043 0.161 3070 Planarity : 0.005 0.042 3436 Dihedral : 10.292 176.914 2791 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.87 % Allowed : 15.38 % Favored : 81.75 % 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: -0.22 (0.17), residues: 2435 helix: 0.85 (0.16), residues: 1095 sheet: -2.03 (0.28), residues: 320 loop : -0.46 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 116 TYR 0.011 0.001 TYR K 143 PHE 0.013 0.001 PHE K 262 TRP 0.013 0.001 TRP L 340 HIS 0.009 0.001 HIS J 161 Details of bonding type rmsd covalent geometry : bond 0.00529 (20066) covalent geometry : angle 0.61841 (27190) hydrogen bonds : bond 0.03389 ( 845) hydrogen bonds : angle 4.76731 ( 2295) Misc. bond : bond 0.00048 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 324 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 LYS cc_start: 0.8336 (mttp) cc_final: 0.7894 (mtpp) REVERT: H 244 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8118 (p0) REVERT: B 35 LEU cc_start: 0.7362 (mt) cc_final: 0.7159 (mt) REVERT: B 70 ASP cc_start: 0.8086 (m-30) cc_final: 0.7713 (m-30) REVERT: B 100 ARG cc_start: 0.7868 (ttt90) cc_final: 0.5836 (ptt180) REVERT: K 44 MET cc_start: 0.8774 (mmt) cc_final: 0.8546 (mmt) REVERT: K 107 GLU cc_start: 0.7338 (pp20) cc_final: 0.6399 (pp20) REVERT: K 161 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.6766 (m-70) REVERT: K 162 ASN cc_start: 0.7836 (m-40) cc_final: 0.7523 (m-40) REVERT: L 78 ASN cc_start: 0.8337 (m110) cc_final: 0.7668 (m110) REVERT: L 82 MET cc_start: 0.8886 (tpp) cc_final: 0.8616 (tpt) REVERT: L 125 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: L 132 MET cc_start: 0.8953 (ttp) cc_final: 0.8332 (ttp) REVERT: L 162 ASN cc_start: 0.7963 (m-40) cc_final: 0.7729 (m-40) REVERT: L 244 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7733 (p0) REVERT: L 372 ARG cc_start: 0.7567 (ptp-170) cc_final: 0.7097 (ptt180) REVERT: E 66 ASN cc_start: 0.8499 (t0) cc_final: 0.8092 (t0) REVERT: E 70 ASP cc_start: 0.8210 (m-30) cc_final: 0.7782 (m-30) REVERT: E 100 ARG cc_start: 0.7978 (ttt90) cc_final: 0.6024 (ptt90) REVERT: M 44 MET cc_start: 0.8832 (mmt) cc_final: 0.8290 (mmt) REVERT: M 161 HIS cc_start: 0.8038 (OUTLIER) cc_final: 0.7274 (m-70) outliers start: 61 outliers final: 44 residues processed: 375 average time/residue: 0.4137 time to fit residues: 227.1005 Evaluate side-chains 361 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 312 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 300 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 127 optimal weight: 0.0870 chunk 186 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 196 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.098651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.087668 restraints weight = 103044.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.090692 restraints weight = 37874.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.092420 restraints weight = 18939.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.093454 restraints weight = 11926.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.094098 restraints weight = 8835.572| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20069 Z= 0.109 Angle : 0.545 6.663 27190 Z= 0.269 Chirality : 0.040 0.147 3070 Planarity : 0.004 0.042 3436 Dihedral : 9.938 177.101 2785 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.07 % Allowed : 16.75 % Favored : 81.19 % 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: 0.05 (0.17), residues: 2435 helix: 1.10 (0.16), residues: 1100 sheet: -1.90 (0.28), residues: 310 loop : -0.39 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 116 TYR 0.008 0.001 TYR J 279 PHE 0.012 0.001 PHE K 262 TRP 0.012 0.001 TRP M 340 HIS 0.008 0.001 HIS J 161 Details of bonding type rmsd covalent geometry : bond 0.00254 (20066) covalent geometry : angle 0.54456 (27190) hydrogen bonds : bond 0.02832 ( 845) hydrogen bonds : angle 4.51510 ( 2295) Misc. bond : bond 0.00056 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 341 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8555 (mm110) cc_final: 0.8308 (mm110) REVERT: D 92 LYS cc_start: 0.8280 (mttp) cc_final: 0.7868 (mtpp) REVERT: H 123 MET cc_start: 0.7875 (mmt) cc_final: 0.7516 (mmt) REVERT: H 244 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7933 (p0) REVERT: H 283 MET cc_start: 0.8300 (mmt) cc_final: 0.8095 (mmt) REVERT: A 84 LEU cc_start: 0.8841 (mp) cc_final: 0.8639 (mp) REVERT: A 85 SER cc_start: 0.9026 (p) cc_final: 0.8759 (p) REVERT: J 50 LYS cc_start: 0.6991 (ptpp) cc_final: 0.6727 (pttm) REVERT: J 195 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7098 (mm-30) REVERT: J 211 ASP cc_start: 0.8664 (t0) cc_final: 0.8250 (t0) REVERT: B 35 LEU cc_start: 0.7477 (mt) cc_final: 0.7240 (mt) REVERT: B 51 ARG cc_start: 0.8088 (mmp80) cc_final: 0.7870 (tpp-160) REVERT: B 70 ASP cc_start: 0.8016 (m-30) cc_final: 0.7564 (m-30) REVERT: B 92 LYS cc_start: 0.7992 (tmmt) cc_final: 0.7657 (mmmt) REVERT: B 100 ARG cc_start: 0.7810 (ttt90) cc_final: 0.5849 (ptt180) REVERT: K 44 MET cc_start: 0.8579 (mmt) cc_final: 0.8327 (mmt) REVERT: K 47 MET cc_start: 0.8706 (mmm) cc_final: 0.8422 (mmm) REVERT: K 107 GLU cc_start: 0.7272 (pp20) cc_final: 0.6333 (pp20) REVERT: K 161 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.6893 (m90) REVERT: K 162 ASN cc_start: 0.7800 (m-40) cc_final: 0.7490 (m-40) REVERT: C 70 ASP cc_start: 0.8242 (m-30) cc_final: 0.7847 (m-30) REVERT: L 78 ASN cc_start: 0.8321 (m110) cc_final: 0.7540 (m110) REVERT: L 132 MET cc_start: 0.8947 (ttp) cc_final: 0.8341 (ttp) REVERT: L 161 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.7806 (m-70) REVERT: L 244 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7576 (p0) REVERT: L 372 ARG cc_start: 0.7551 (ptp-170) cc_final: 0.7069 (ptt180) REVERT: E 66 ASN cc_start: 0.8383 (t0) cc_final: 0.7930 (t0) REVERT: E 70 ASP cc_start: 0.8242 (m-30) cc_final: 0.7782 (m-30) REVERT: E 100 ARG cc_start: 0.7886 (ttt90) cc_final: 0.5967 (ptt90) REVERT: M 44 MET cc_start: 0.8828 (mmt) cc_final: 0.8348 (mmt) REVERT: M 161 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7605 (m-70) outliers start: 44 outliers final: 35 residues processed: 381 average time/residue: 0.4347 time to fit residues: 240.7653 Evaluate side-chains 362 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 322 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 300 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 102 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 236 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.086889 restraints weight = 104174.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.089889 restraints weight = 38166.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.091602 restraints weight = 19064.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.092621 restraints weight = 12017.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.093253 restraints weight = 8916.449| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.6471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20069 Z= 0.145 Angle : 0.563 6.954 27190 Z= 0.280 Chirality : 0.041 0.151 3070 Planarity : 0.004 0.077 3436 Dihedral : 9.934 178.201 2785 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.49 % Allowed : 16.46 % Favored : 81.04 % 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: 0.11 (0.17), residues: 2435 helix: 1.14 (0.16), residues: 1100 sheet: -1.82 (0.28), residues: 310 loop : -0.37 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 116 TYR 0.010 0.001 TYR J 279 PHE 0.010 0.001 PHE M 262 TRP 0.012 0.001 TRP L 340 HIS 0.006 0.001 HIS J 161 Details of bonding type rmsd covalent geometry : bond 0.00341 (20066) covalent geometry : angle 0.56293 (27190) hydrogen bonds : bond 0.02957 ( 845) hydrogen bonds : angle 4.51008 ( 2295) Misc. bond : bond 0.00051 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 325 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8467 (mm110) cc_final: 0.8251 (mm110) REVERT: D 92 LYS cc_start: 0.8283 (mttp) cc_final: 0.7872 (mtpp) REVERT: H 123 MET cc_start: 0.7924 (mmt) cc_final: 0.7560 (mmt) REVERT: H 161 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.7381 (m-70) REVERT: H 244 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8063 (p0) REVERT: A 85 SER cc_start: 0.9019 (p) cc_final: 0.8804 (p) REVERT: J 107 GLU cc_start: 0.7383 (pp20) cc_final: 0.7118 (pp20) REVERT: J 195 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7114 (mm-30) REVERT: J 211 ASP cc_start: 0.8688 (t0) cc_final: 0.8281 (t0) REVERT: B 70 ASP cc_start: 0.8011 (m-30) cc_final: 0.7580 (m-30) REVERT: B 100 ARG cc_start: 0.7853 (ttt90) cc_final: 0.5885 (ptt180) REVERT: B 116 ARG cc_start: 0.8214 (mtm110) cc_final: 0.8010 (mtp-110) REVERT: K 53 TYR cc_start: 0.7858 (m-80) cc_final: 0.7584 (m-80) REVERT: K 107 GLU cc_start: 0.7277 (pp20) cc_final: 0.6305 (pp20) REVERT: K 119 MET cc_start: 0.9182 (ttm) cc_final: 0.8974 (ttp) REVERT: L 78 ASN cc_start: 0.8394 (m110) cc_final: 0.7601 (m110) REVERT: L 125 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: L 132 MET cc_start: 0.8968 (ttp) cc_final: 0.8354 (ttp) REVERT: L 244 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7628 (p0) REVERT: L 372 ARG cc_start: 0.7624 (ptp-170) cc_final: 0.7160 (ptt180) REVERT: E 66 ASN cc_start: 0.8431 (t0) cc_final: 0.7900 (t0) REVERT: E 70 ASP cc_start: 0.8265 (m-30) cc_final: 0.7811 (m-30) REVERT: E 100 ARG cc_start: 0.7893 (ttt90) cc_final: 0.5960 (ptt90) REVERT: M 44 MET cc_start: 0.8839 (mmt) cc_final: 0.8292 (mmt) REVERT: M 161 HIS cc_start: 0.8155 (OUTLIER) cc_final: 0.7529 (m-70) outliers start: 53 outliers final: 44 residues processed: 371 average time/residue: 0.4163 time to fit residues: 225.3175 Evaluate side-chains 371 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 322 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 300 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 117 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 233 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.098429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.087712 restraints weight = 103456.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.090608 restraints weight = 38975.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.092274 restraints weight = 19788.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.093272 restraints weight = 12608.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.093883 restraints weight = 9421.315| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20069 Z= 0.124 Angle : 0.552 6.700 27190 Z= 0.272 Chirality : 0.040 0.151 3070 Planarity : 0.004 0.065 3436 Dihedral : 9.772 172.661 2785 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.16 % Allowed : 17.03 % Favored : 80.81 % 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: 0.20 (0.17), residues: 2435 helix: 1.23 (0.16), residues: 1100 sheet: -1.72 (0.28), residues: 310 loop : -0.36 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 116 TYR 0.008 0.001 TYR J 279 PHE 0.011 0.001 PHE K 262 TRP 0.012 0.001 TRP L 340 HIS 0.005 0.001 HIS J 161 Details of bonding type rmsd covalent geometry : bond 0.00291 (20066) covalent geometry : angle 0.55158 (27190) hydrogen bonds : bond 0.02836 ( 845) hydrogen bonds : angle 4.44304 ( 2295) Misc. bond : bond 0.00051 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 329 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 LYS cc_start: 0.8222 (mttp) cc_final: 0.7853 (mttm) REVERT: H 123 MET cc_start: 0.7883 (mmt) cc_final: 0.7543 (mmt) REVERT: H 244 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8015 (p0) REVERT: A 85 SER cc_start: 0.8984 (p) cc_final: 0.8726 (p) REVERT: J 195 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7041 (mm-30) REVERT: J 211 ASP cc_start: 0.8650 (t0) cc_final: 0.8288 (t0) REVERT: J 283 MET cc_start: 0.8546 (mmt) cc_final: 0.8258 (mmm) REVERT: B 70 ASP cc_start: 0.7914 (m-30) cc_final: 0.7530 (m-30) REVERT: B 100 ARG cc_start: 0.7865 (ttt90) cc_final: 0.5940 (ptt180) REVERT: B 116 ARG cc_start: 0.8134 (mtm110) cc_final: 0.7930 (mtp-110) REVERT: L 78 ASN cc_start: 0.8187 (m110) cc_final: 0.7675 (m110) REVERT: L 82 MET cc_start: 0.8932 (tpp) cc_final: 0.8703 (tpt) REVERT: L 125 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: L 244 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7625 (p0) REVERT: L 372 ARG cc_start: 0.7452 (ptp-170) cc_final: 0.7072 (ptt180) REVERT: E 66 ASN cc_start: 0.8411 (t0) cc_final: 0.7923 (t0) REVERT: E 70 ASP cc_start: 0.8211 (m-30) cc_final: 0.7757 (m-30) REVERT: E 100 ARG cc_start: 0.7856 (ttt90) cc_final: 0.5982 (ptt90) REVERT: M 44 MET cc_start: 0.8815 (mmt) cc_final: 0.8267 (mmt) REVERT: M 161 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7306 (m-70) outliers start: 46 outliers final: 40 residues processed: 368 average time/residue: 0.4323 time to fit residues: 231.5113 Evaluate side-chains 370 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 326 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 300 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 161 optimal weight: 0.9990 chunk 112 optimal weight: 0.0270 chunk 218 optimal weight: 0.5980 chunk 223 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 244 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.100907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.089956 restraints weight = 102648.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.093024 restraints weight = 37571.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.094769 restraints weight = 18692.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.095783 restraints weight = 11715.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.096437 restraints weight = 8700.072| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.6522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20069 Z= 0.093 Angle : 0.535 6.411 27190 Z= 0.261 Chirality : 0.040 0.153 3070 Planarity : 0.004 0.066 3436 Dihedral : 9.399 159.713 2783 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.69 % Allowed : 17.83 % Favored : 80.48 % 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: 0.45 (0.17), residues: 2435 helix: 1.47 (0.16), residues: 1100 sheet: -1.51 (0.29), residues: 310 loop : -0.31 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 116 TYR 0.007 0.001 TYR K 53 PHE 0.009 0.001 PHE K 262 TRP 0.011 0.001 TRP L 340 HIS 0.003 0.001 HIS J 161 Details of bonding type rmsd covalent geometry : bond 0.00220 (20066) covalent geometry : angle 0.53463 (27190) hydrogen bonds : bond 0.02590 ( 845) hydrogen bonds : angle 4.25350 ( 2295) Misc. bond : bond 0.00046 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7009.27 seconds wall clock time: 120 minutes 8.11 seconds (7208.11 seconds total)