Starting phenix.real_space_refine on Fri Jul 3 19:10:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sik_40508/07_2026/8sik_40508.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sik_40508/07_2026/8sik_40508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8sik_40508/07_2026/8sik_40508.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sik_40508/07_2026/8sik_40508.cif" model { file = "/net/cci-nas-00/data/ceres_data/8sik_40508/07_2026/8sik_40508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sik_40508/07_2026/8sik_40508.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sik_40508/07_2026/8sik_40508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sik_40508/07_2026/8sik_40508.map" } resolution = 2.9 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= 0.002 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 80 5.16 5 C 10196 2.51 5 N 2708 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15832 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "D" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "C" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "E" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="CA CA B 202 " occ=0.46 residue: pdb="CA CA F 201 " occ=0.45 residue: pdb="CA CA H 201 " occ=0.51 residue: pdb="CA CA H 203 " occ=0.49 Time building chain proxies: 3.60, per 1000 atoms: 0.23 Number of scatterers: 15832 At special positions: 0 Unit cell: (113.265, 113.265, 124.172, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 80 16.00 O 2840 8.00 N 2708 7.00 C 10196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 659.9 milliseconds 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 4 sheets defined 81.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'B' and resid 6 through 22 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.604A pdb=" N GLU B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 56 " --> pdb=" O MET B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 79 through 92 removed outlier: 3.593A pdb=" N VAL B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 139 through 149 removed outlier: 3.745A pdb=" N LYS B 149 " --> pdb=" O MET B 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 Processing helix chain 'A' and resid 120 through 144 removed outlier: 3.783A pdb=" N THR A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 178 removed outlier: 3.539A pdb=" N PHE A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TRP A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 185 through 196 removed outlier: 3.720A pdb=" N GLY A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 216 Processing helix chain 'A' and resid 224 through 237 removed outlier: 4.179A pdb=" N ILE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.527A pdb=" N VAL A 241 " --> pdb=" O MET A 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 242' Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.607A pdb=" N VAL A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 284 Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 322 through 358 removed outlier: 3.863A pdb=" N ILE A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SER A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 367 through 384 Processing helix chain 'A' and resid 389 through 396 removed outlier: 3.862A pdb=" N TRP A 392 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 394 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 395 " --> pdb=" O TRP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 533 removed outlier: 4.024A pdb=" N THR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 568 removed outlier: 3.585A pdb=" N VAL A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 22 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 45 through 57 removed outlier: 3.560A pdb=" N GLU D 55 " --> pdb=" O ASP D 51 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 56 " --> pdb=" O MET D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 79 through 92 removed outlier: 3.593A pdb=" N VAL D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 118 through 129 Processing helix chain 'D' and resid 139 through 149 removed outlier: 3.525A pdb=" N VAL D 143 " --> pdb=" O TYR D 139 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D 149 " --> pdb=" O MET D 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 22 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 removed outlier: 3.571A pdb=" N GLU F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 79 through 92 removed outlier: 3.589A pdb=" N VAL F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 118 through 129 Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'H' and resid 7 through 22 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 removed outlier: 3.564A pdb=" N GLU H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL H 56 " --> pdb=" O MET H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 79 through 92 removed outlier: 3.616A pdb=" N VAL H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 113 Processing helix chain 'H' and resid 118 through 129 Processing helix chain 'H' and resid 139 through 149 removed outlier: 3.839A pdb=" N LYS H 149 " --> pdb=" O MET H 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 115 Processing helix chain 'G' and resid 120 through 145 removed outlier: 3.830A pdb=" N THR G 144 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE G 145 " --> pdb=" O VAL G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 178 removed outlier: 3.541A pdb=" N PHE G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 185 through 194 removed outlier: 3.646A pdb=" N GLY G 189 " --> pdb=" O VAL G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 216 Processing helix chain 'G' and resid 224 through 237 removed outlier: 4.338A pdb=" N ILE G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 242 removed outlier: 3.562A pdb=" N VAL G 241 " --> pdb=" O MET G 238 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP G 242 " --> pdb=" O LEU G 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 238 through 242' Processing helix chain 'G' and resid 245 through 258 removed outlier: 3.609A pdb=" N VAL G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 284 Processing helix chain 'G' and resid 298 through 311 Processing helix chain 'G' and resid 322 through 358 removed outlier: 3.838A pdb=" N ILE G 337 " --> pdb=" O SER G 333 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER G 338 " --> pdb=" O VAL G 334 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE G 339 " --> pdb=" O PHE G 335 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) Proline residue: G 343 - end of helix Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 363 through 366 Processing helix chain 'G' and resid 367 through 384 Processing helix chain 'G' and resid 389 through 396 removed outlier: 3.911A pdb=" N TRP G 392 " --> pdb=" O SER G 389 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS G 393 " --> pdb=" O SER G 390 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE G 394 " --> pdb=" O THR G 391 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR G 395 " --> pdb=" O TRP G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 509 through 533 removed outlier: 4.185A pdb=" N THR G 513 " --> pdb=" O HIS G 509 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 519 " --> pdb=" O LYS G 515 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG G 533 " --> pdb=" O PHE G 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 568 removed outlier: 3.572A pdb=" N VAL G 541 " --> pdb=" O ASP G 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 120 through 145 removed outlier: 3.702A pdb=" N THR C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 178 removed outlier: 3.593A pdb=" N PHE C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 185 through 195 removed outlier: 3.654A pdb=" N GLY C 189 " --> pdb=" O VAL C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 216 Processing helix chain 'C' and resid 224 through 237 removed outlier: 4.236A pdb=" N ILE C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 removed outlier: 3.593A pdb=" N ASP C 242 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.604A pdb=" N VAL C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 284 Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 322 through 358 removed outlier: 3.891A pdb=" N ILE C 337 " --> pdb=" O SER C 333 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N SER C 338 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 359 through 361 No H-bonds generated for 'chain 'C' and resid 359 through 361' Processing helix chain 'C' and resid 363 through 366 Processing helix chain 'C' and resid 367 through 384 Processing helix chain 'C' and resid 389 through 396 removed outlier: 3.876A pdb=" N TRP C 392 " --> pdb=" O SER C 389 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS C 393 " --> pdb=" O SER C 390 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 394 " --> pdb=" O THR C 391 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR C 395 " --> pdb=" O TRP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 533 removed outlier: 4.337A pdb=" N THR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 568 removed outlier: 3.587A pdb=" N VAL C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 115 Processing helix chain 'E' and resid 120 through 145 removed outlier: 3.804A pdb=" N THR E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 178 removed outlier: 3.708A pdb=" N PHE E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TRP E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET E 159 " --> pdb=" O THR E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 185 through 194 removed outlier: 3.626A pdb=" N GLY E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 216 Processing helix chain 'E' and resid 224 through 237 removed outlier: 4.242A pdb=" N ILE E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 removed outlier: 3.571A pdb=" N ASP E 242 " --> pdb=" O LEU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 258 removed outlier: 3.630A pdb=" N VAL E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 285 Processing helix chain 'E' and resid 298 through 311 Processing helix chain 'E' and resid 322 through 358 removed outlier: 3.877A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER E 338 " --> pdb=" O VAL E 334 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE E 339 " --> pdb=" O PHE E 335 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Proline residue: E 343 - end of helix Processing helix chain 'E' and resid 359 through 361 No H-bonds generated for 'chain 'E' and resid 359 through 361' Processing helix chain 'E' and resid 363 through 366 Processing helix chain 'E' and resid 367 through 384 Processing helix chain 'E' and resid 389 through 396 removed outlier: 3.856A pdb=" N TRP E 392 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS E 393 " --> pdb=" O SER E 390 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE E 394 " --> pdb=" O THR E 391 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR E 395 " --> pdb=" O TRP E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 533 removed outlier: 4.267A pdb=" N THR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG E 519 " --> pdb=" O LYS E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 567 removed outlier: 3.581A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 1112 hydrogen bonds defined for protein. 3306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5098 1.34 - 1.46: 2385 1.46 - 1.57: 8533 1.57 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 16152 Sorted by residual: bond pdb=" C ILE A 368 " pdb=" N PRO A 369 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.13e+00 bond pdb=" C ILE C 368 " pdb=" N PRO C 369 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.05e+00 bond pdb=" C GLY D 26 " pdb=" O GLY D 26 " ideal model delta sigma weight residual 1.239 1.222 0.017 1.09e-02 8.42e+03 2.44e+00 bond pdb=" CA LYS D 22 " pdb=" C LYS D 22 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.34e-02 5.57e+03 1.85e+00 bond pdb=" CB ILE B 131 " pdb=" CG1 ILE B 131 " ideal model delta sigma weight residual 1.530 1.550 -0.020 2.00e-02 2.50e+03 1.00e+00 ... (remaining 16147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 21507 1.74 - 3.47: 271 3.47 - 5.21: 35 5.21 - 6.94: 7 6.94 - 8.68: 4 Bond angle restraints: 21824 Sorted by residual: angle pdb=" N ILE A 227 " pdb=" CA ILE A 227 " pdb=" C ILE A 227 " ideal model delta sigma weight residual 112.96 109.20 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CB ILE B 131 " pdb=" CG1 ILE B 131 " pdb=" CD1 ILE B 131 " ideal model delta sigma weight residual 113.80 120.89 -7.09 2.10e+00 2.27e-01 1.14e+01 angle pdb=" N GLY D 26 " pdb=" CA GLY D 26 " pdb=" C GLY D 26 " ideal model delta sigma weight residual 114.95 110.49 4.46 1.41e+00 5.03e-01 1.00e+01 angle pdb=" CG ARG E 507 " pdb=" CD ARG E 507 " pdb=" NE ARG E 507 " ideal model delta sigma weight residual 112.00 118.29 -6.29 2.20e+00 2.07e-01 8.17e+00 angle pdb=" CA GLU D 12 " pdb=" CB GLU D 12 " pdb=" CG GLU D 12 " ideal model delta sigma weight residual 114.10 119.41 -5.31 2.00e+00 2.50e-01 7.04e+00 ... (remaining 21819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 8299 17.48 - 34.96: 897 34.96 - 52.44: 251 52.44 - 69.93: 20 69.93 - 87.41: 25 Dihedral angle restraints: 9492 sinusoidal: 3776 harmonic: 5716 Sorted by residual: dihedral pdb=" CA GLN E 234 " pdb=" C GLN E 234 " pdb=" N ILE E 235 " pdb=" CA ILE E 235 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CG ARG G 109 " pdb=" CD ARG G 109 " pdb=" NE ARG G 109 " pdb=" CZ ARG G 109 " ideal model delta sinusoidal sigma weight residual 90.00 134.49 -44.49 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU A 170 " pdb=" CG GLU A 170 " pdb=" CD GLU A 170 " pdb=" OE1 GLU A 170 " ideal model delta sinusoidal sigma weight residual 0.00 -86.93 86.93 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 9489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1972 0.049 - 0.097: 406 0.097 - 0.146: 60 0.146 - 0.194: 1 0.194 - 0.243: 5 Chirality restraints: 2444 Sorted by residual: chirality pdb=" CG LEU G 191 " pdb=" CB LEU G 191 " pdb=" CD1 LEU G 191 " pdb=" CD2 LEU G 191 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA ASN F 43 " pdb=" N ASN F 43 " pdb=" C ASN F 43 " pdb=" CB ASN F 43 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CG LEU E 191 " pdb=" CB LEU E 191 " pdb=" CD1 LEU E 191 " pdb=" CD2 LEU E 191 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2441 not shown) Planarity restraints: 2752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 21 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.54e+00 pdb=" C ASP D 21 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP D 21 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS D 22 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 507 " 0.196 9.50e-02 1.11e+02 8.81e-02 5.33e+00 pdb=" NE ARG G 507 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG G 507 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 507 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 507 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 131 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.15e+00 pdb=" C ILE B 131 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE B 131 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP B 132 " 0.008 2.00e-02 2.50e+03 ... (remaining 2749 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1625 2.74 - 3.28: 16120 3.28 - 3.82: 26892 3.82 - 4.36: 31323 4.36 - 4.90: 55056 Nonbonded interactions: 131016 Sorted by model distance: nonbonded pdb=" OE2 GLU H 68 " pdb="CA CA H 203 " model vdw 2.206 2.510 nonbonded pdb=" OE1 GLU H 55 " pdb=" NZ LYS G 527 " model vdw 2.209 3.120 nonbonded pdb=" OD1 ASN H 61 " pdb="CA CA H 203 " model vdw 2.211 2.510 nonbonded pdb=" OE1 GLU H 124 " pdb=" OG SER G 390 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLU B 124 " pdb=" OG SER A 390 " model vdw 2.268 3.040 ... (remaining 131011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 6 through 201) selection = (chain 'D' and resid 6 through 201) selection = chain 'F' selection = (chain 'H' and resid 6 through 201) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.880 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.003 0.026 16152 Z= 0.130 Angle : 0.506 8.678 21824 Z= 0.296 Chirality : 0.039 0.243 2444 Planarity : 0.004 0.088 2752 Dihedral : 15.666 87.408 5812 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.96 % Allowed : 19.64 % Favored : 79.40 % 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: 2.43 (0.19), residues: 1952 helix: 2.13 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -0.12 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 507 TYR 0.017 0.001 TYR D 139 PHE 0.013 0.001 PHE E 332 TRP 0.023 0.002 TRP G 323 HIS 0.005 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (16152) covalent geometry : angle 0.50590 / 0.30 (21824) hydrogen bonds : bond 0.09180 / 6.43 ( 1112) hydrogen bonds : angle 4.47777 / 3.18 ( 3306) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.731 Fit side-chains REVERT: G 195 ARG cc_start: 0.6353 (mtp180) cc_final: 0.5956 (mtm110) REVERT: C 191 LEU cc_start: 0.6722 (mp) cc_final: 0.6407 (mm) outliers start: 16 outliers final: 12 residues processed: 216 average time/residue: 0.6942 time to fit residues: 164.1949 Evaluate side-chains 207 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.181527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.147467 restraints weight = 15656.656| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.82 r_work: 0.3477 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16152 Z= 0.139 Angle : 0.464 7.526 21824 Z= 0.257 Chirality : 0.038 0.213 2444 Planarity : 0.003 0.045 2752 Dihedral : 3.940 38.439 2182 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.43 % Allowed : 16.20 % Favored : 80.36 % 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: 2.50 (0.19), residues: 1952 helix: 2.16 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.10 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 507 TYR 0.013 0.002 TYR C 545 PHE 0.014 0.001 PHE C 332 TRP 0.015 0.001 TRP G 323 HIS 0.003 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (16152) covalent geometry : angle 0.46397 / 0.26 (21824) hydrogen bonds : bond 0.04305 / 2.93 ( 1112) hydrogen bonds : angle 3.78173 / 2.70 ( 3306) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 205 time to evaluate : 0.598 Fit side-chains REVERT: B 131 ILE cc_start: 0.4326 (OUTLIER) cc_final: 0.4036 (pp) REVERT: A 191 LEU cc_start: 0.7121 (mp) cc_final: 0.6824 (mm) REVERT: D 112 ASN cc_start: 0.8608 (m-40) cc_final: 0.8397 (m-40) REVERT: F 68 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: F 140 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6230 (mp0) REVERT: H 112 ASN cc_start: 0.8641 (m-40) cc_final: 0.8421 (m-40) REVERT: H 141 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7010 (pp20) REVERT: G 195 ARG cc_start: 0.7253 (mtp180) cc_final: 0.6873 (mtm110) REVERT: C 191 LEU cc_start: 0.7153 (mp) cc_final: 0.6804 (mm) outliers start: 57 outliers final: 19 residues processed: 246 average time/residue: 0.6659 time to fit residues: 178.9863 Evaluate side-chains 223 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 285 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 177 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 147 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.184061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.149470 restraints weight = 15835.734| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.87 r_work: 0.3486 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16152 Z= 0.115 Angle : 0.438 7.128 21824 Z= 0.239 Chirality : 0.037 0.242 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.441 23.749 2170 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.01 % Allowed : 16.63 % Favored : 80.36 % 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: 2.68 (0.19), residues: 1952 helix: 2.29 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.08 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 109 TYR 0.011 0.001 TYR C 545 PHE 0.012 0.001 PHE E 332 TRP 0.014 0.001 TRP A 379 HIS 0.003 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (16152) covalent geometry : angle 0.43751 / 0.24 (21824) hydrogen bonds : bond 0.03981 / 2.71 ( 1112) hydrogen bonds : angle 3.64555 / 2.60 ( 3306) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 0.590 Fit side-chains REVERT: A 557 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7412 (mtpt) REVERT: D 68 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: D 112 ASN cc_start: 0.8565 (m-40) cc_final: 0.8316 (m-40) REVERT: F 42 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.6852 (mp10) REVERT: F 68 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: F 140 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: H 112 ASN cc_start: 0.8583 (m-40) cc_final: 0.8326 (m-40) REVERT: H 141 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6953 (pp20) REVERT: G 195 ARG cc_start: 0.7193 (mtp180) cc_final: 0.6797 (mtm110) REVERT: G 508 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: C 533 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7577 (mtm180) outliers start: 50 outliers final: 16 residues processed: 240 average time/residue: 0.6881 time to fit residues: 179.9747 Evaluate side-chains 220 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 508 GLU Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 155 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 180 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.184559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150242 restraints weight = 15671.255| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.82 r_work: 0.3497 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16152 Z= 0.113 Angle : 0.431 6.271 21824 Z= 0.236 Chirality : 0.037 0.240 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.331 17.466 2168 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.77 % Allowed : 17.11 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.19), residues: 1952 helix: 2.23 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.27 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 109 TYR 0.012 0.001 TYR C 545 PHE 0.012 0.001 PHE E 332 TRP 0.014 0.001 TRP G 323 HIS 0.003 0.001 HIS G 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (16152) covalent geometry : angle 0.43077 / 0.24 (21824) hydrogen bonds : bond 0.03887 / 2.64 ( 1112) hydrogen bonds : angle 3.60034 / 2.57 ( 3306) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 0.458 Fit side-chains REVERT: B 141 GLU cc_start: 0.7448 (pt0) cc_final: 0.6994 (pp20) REVERT: A 557 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7392 (mtpt) REVERT: D 12 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7099 (pm20) REVERT: D 68 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7003 (mt-10) REVERT: D 112 ASN cc_start: 0.8546 (m-40) cc_final: 0.8293 (m-40) REVERT: F 42 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.6860 (mp10) REVERT: F 68 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: F 140 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6094 (mp0) REVERT: H 112 ASN cc_start: 0.8573 (m-40) cc_final: 0.8336 (m-40) REVERT: H 141 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6937 (pp20) REVERT: G 195 ARG cc_start: 0.7155 (mtp180) cc_final: 0.6748 (mtm110) REVERT: C 533 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7532 (mtm180) REVERT: E 560 GLN cc_start: 0.7357 (tp-100) cc_final: 0.6701 (mt0) outliers start: 46 outliers final: 25 residues processed: 242 average time/residue: 0.6522 time to fit residues: 172.4069 Evaluate side-chains 239 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 312 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 91 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 173 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 166 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.184883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150194 restraints weight = 15722.140| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.86 r_work: 0.3502 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16152 Z= 0.110 Angle : 0.429 6.752 21824 Z= 0.234 Chirality : 0.037 0.258 2444 Planarity : 0.003 0.028 2752 Dihedral : 3.306 17.399 2168 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.25 % Allowed : 16.87 % Favored : 79.88 % 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: 2.65 (0.19), residues: 1952 helix: 2.26 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.24 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 109 TYR 0.011 0.001 TYR C 545 PHE 0.012 0.001 PHE E 332 TRP 0.015 0.001 TRP G 323 HIS 0.004 0.001 HIS G 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (16152) covalent geometry : angle 0.42871 / 0.23 (21824) hydrogen bonds : bond 0.03805 / 2.58 ( 1112) hydrogen bonds : angle 3.56691 / 2.55 ( 3306) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 210 time to evaluate : 0.612 Fit side-chains REVERT: B 141 GLU cc_start: 0.7506 (pt0) cc_final: 0.7093 (pp20) REVERT: A 557 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7396 (mtpt) REVERT: D 12 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6774 (pm20) REVERT: D 68 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6869 (mt-10) REVERT: D 112 ASN cc_start: 0.8525 (m-40) cc_final: 0.8280 (m-40) REVERT: F 42 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.6887 (mp10) REVERT: F 68 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: F 140 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6050 (mp0) REVERT: H 112 ASN cc_start: 0.8543 (m-40) cc_final: 0.8302 (m-40) REVERT: H 141 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6963 (pp20) REVERT: G 195 ARG cc_start: 0.7140 (mtp180) cc_final: 0.6725 (mtm110) REVERT: C 533 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7233 (mtm110) REVERT: E 560 GLN cc_start: 0.7333 (tp-100) cc_final: 0.6688 (mt0) outliers start: 54 outliers final: 26 residues processed: 252 average time/residue: 0.6988 time to fit residues: 192.3224 Evaluate side-chains 238 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 390 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 9 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 32 optimal weight: 0.0270 chunk 171 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.184111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.149807 restraints weight = 15587.225| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.85 r_work: 0.3486 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16152 Z= 0.123 Angle : 0.446 7.263 21824 Z= 0.243 Chirality : 0.038 0.254 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.338 17.387 2168 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.07 % Allowed : 17.41 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.19), residues: 1952 helix: 2.23 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.20 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 109 TYR 0.013 0.001 TYR C 545 PHE 0.013 0.001 PHE E 332 TRP 0.016 0.001 TRP G 323 HIS 0.004 0.001 HIS G 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (16152) covalent geometry : angle 0.44638 / 0.24 (21824) hydrogen bonds : bond 0.03934 / 2.67 ( 1112) hydrogen bonds : angle 3.59993 / 2.57 ( 3306) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 0.523 Fit side-chains REVERT: B 141 GLU cc_start: 0.7514 (pt0) cc_final: 0.7065 (pp20) REVERT: A 557 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7362 (mtpt) REVERT: D 12 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: D 68 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6946 (mt-10) REVERT: D 112 ASN cc_start: 0.8535 (m-40) cc_final: 0.8274 (m-40) REVERT: F 42 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.6891 (mp10) REVERT: F 68 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: H 112 ASN cc_start: 0.8551 (m-40) cc_final: 0.8290 (m-40) REVERT: H 141 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6974 (pp20) REVERT: G 195 ARG cc_start: 0.7136 (mtp180) cc_final: 0.6794 (mtm110) REVERT: G 508 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6305 (mp0) REVERT: C 533 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7402 (mtm110) outliers start: 51 outliers final: 28 residues processed: 247 average time/residue: 0.6789 time to fit residues: 183.3308 Evaluate side-chains 239 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 508 GLU Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 390 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 24 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 138 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 132 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 GLN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.184088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149737 restraints weight = 15656.673| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.83 r_work: 0.3488 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16152 Z= 0.123 Angle : 0.450 7.918 21824 Z= 0.245 Chirality : 0.038 0.247 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.349 17.572 2168 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.13 % Allowed : 17.53 % Favored : 79.34 % 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: 2.59 (0.19), residues: 1952 helix: 2.22 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.21 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 109 TYR 0.013 0.001 TYR C 545 PHE 0.012 0.001 PHE C 332 TRP 0.018 0.001 TRP G 323 HIS 0.005 0.001 HIS G 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (16152) covalent geometry : angle 0.45025 / 0.24 (21824) hydrogen bonds : bond 0.03934 / 2.67 ( 1112) hydrogen bonds : angle 3.59319 / 2.57 ( 3306) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 0.512 Fit side-chains REVERT: B 141 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7049 (pp20) REVERT: A 557 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7356 (mtpt) REVERT: D 12 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: D 68 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6988 (mt-10) REVERT: D 112 ASN cc_start: 0.8515 (m-40) cc_final: 0.8244 (m-40) REVERT: F 42 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.6902 (mp10) REVERT: F 68 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: F 140 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6117 (mp0) REVERT: H 112 ASN cc_start: 0.8522 (m-40) cc_final: 0.8250 (m-40) REVERT: H 141 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6979 (pp20) REVERT: G 195 ARG cc_start: 0.7135 (mtp180) cc_final: 0.6792 (mtm110) REVERT: G 508 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: C 533 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7409 (mtm110) REVERT: E 191 LEU cc_start: 0.7473 (mm) cc_final: 0.7260 (mp) outliers start: 52 outliers final: 34 residues processed: 246 average time/residue: 0.6693 time to fit residues: 180.2465 Evaluate side-chains 254 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 508 GLU Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 567 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 92 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 182 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 42 GLN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.185565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151391 restraints weight = 15692.424| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.82 r_work: 0.3508 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16152 Z= 0.109 Angle : 0.446 7.935 21824 Z= 0.241 Chirality : 0.037 0.247 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.304 17.746 2168 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.71 % Allowed : 17.71 % Favored : 79.58 % 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: 2.68 (0.19), residues: 1952 helix: 2.28 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.17 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 109 TYR 0.011 0.001 TYR C 545 PHE 0.012 0.001 PHE E 332 TRP 0.019 0.001 TRP G 323 HIS 0.005 0.001 HIS G 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (16152) covalent geometry : angle 0.44585 / 0.24 (21824) hydrogen bonds : bond 0.03731 / 2.53 ( 1112) hydrogen bonds : angle 3.52916 / 2.52 ( 3306) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.608 Fit side-chains REVERT: B 141 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7084 (pp20) REVERT: A 557 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7375 (mtpt) REVERT: D 12 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6865 (pm20) REVERT: D 68 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.7013 (mt-10) REVERT: D 112 ASN cc_start: 0.8496 (m-40) cc_final: 0.8253 (m-40) REVERT: F 39 SER cc_start: 0.8489 (OUTLIER) cc_final: 0.8211 (p) REVERT: F 68 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: F 140 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6030 (mp0) REVERT: H 112 ASN cc_start: 0.8520 (m-40) cc_final: 0.8276 (m-40) REVERT: H 141 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7000 (pp20) REVERT: G 191 LEU cc_start: 0.7590 (mm) cc_final: 0.7202 (mp) REVERT: G 195 ARG cc_start: 0.7125 (mtp180) cc_final: 0.6780 (mtm110) REVERT: C 533 ARG cc_start: 0.7793 (mtp85) cc_final: 0.7368 (mtm110) outliers start: 45 outliers final: 27 residues processed: 244 average time/residue: 0.6941 time to fit residues: 184.8573 Evaluate side-chains 243 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 390 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 55 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 ASN G 234 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.184864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.150685 restraints weight = 15634.188| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.81 r_work: 0.3497 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16152 Z= 0.118 Angle : 0.460 8.576 21824 Z= 0.248 Chirality : 0.038 0.275 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.327 17.488 2168 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.59 % Allowed : 18.01 % Favored : 79.40 % 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: 2.63 (0.19), residues: 1952 helix: 2.24 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.20 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 109 TYR 0.012 0.001 TYR C 545 PHE 0.012 0.001 PHE E 332 TRP 0.020 0.001 TRP C 323 HIS 0.006 0.001 HIS G 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (16152) covalent geometry : angle 0.46028 / 0.25 (21824) hydrogen bonds : bond 0.03814 / 2.58 ( 1112) hydrogen bonds : angle 3.55685 / 2.54 ( 3306) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 0.612 Fit side-chains REVERT: B 141 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7082 (pp20) REVERT: A 557 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7364 (mtpt) REVERT: D 12 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6763 (pm20) REVERT: D 68 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6983 (mt-10) REVERT: D 112 ASN cc_start: 0.8493 (m-40) cc_final: 0.8243 (m-40) REVERT: F 39 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8217 (p) REVERT: F 68 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: F 140 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6080 (mp0) REVERT: H 112 ASN cc_start: 0.8537 (m-40) cc_final: 0.8283 (m-40) REVERT: H 141 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7027 (pp20) REVERT: G 195 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6753 (mtm110) REVERT: C 533 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7367 (mtm110) REVERT: E 191 LEU cc_start: 0.7455 (mm) cc_final: 0.7243 (mp) outliers start: 43 outliers final: 28 residues processed: 239 average time/residue: 0.6301 time to fit residues: 165.0190 Evaluate side-chains 245 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 567 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 28 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 179 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.184277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.150028 restraints weight = 15577.147| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.80 r_work: 0.3490 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16152 Z= 0.129 Angle : 0.476 7.930 21824 Z= 0.257 Chirality : 0.038 0.270 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.374 17.399 2168 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.41 % Allowed : 18.19 % Favored : 79.40 % 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: 2.54 (0.19), residues: 1952 helix: 2.18 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.24 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 109 TYR 0.013 0.001 TYR C 545 PHE 0.013 0.001 PHE E 332 TRP 0.024 0.002 TRP E 323 HIS 0.007 0.001 HIS G 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (16152) covalent geometry : angle 0.47555 / 0.26 (21824) hydrogen bonds : bond 0.03948 / 2.67 ( 1112) hydrogen bonds : angle 3.59998 / 2.58 ( 3306) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.527 Fit side-chains REVERT: B 141 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7089 (pp20) REVERT: A 557 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7360 (mtpt) REVERT: D 12 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6912 (pm20) REVERT: D 68 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6887 (mt-10) REVERT: D 112 ASN cc_start: 0.8496 (m-40) cc_final: 0.8227 (m-40) REVERT: F 39 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8211 (p) REVERT: F 68 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7276 (mt-10) REVERT: H 112 ASN cc_start: 0.8515 (m-40) cc_final: 0.8251 (m-40) REVERT: H 141 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7049 (pp20) REVERT: G 191 LEU cc_start: 0.7579 (mm) cc_final: 0.7181 (mp) REVERT: G 195 ARG cc_start: 0.7107 (mtp180) cc_final: 0.6759 (mtm110) REVERT: G 508 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: C 533 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7396 (mtm110) REVERT: E 191 LEU cc_start: 0.7469 (mm) cc_final: 0.7251 (mp) outliers start: 40 outliers final: 27 residues processed: 237 average time/residue: 0.6354 time to fit residues: 164.2782 Evaluate side-chains 241 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 508 GLU Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 567 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 7 optimal weight: 0.0470 chunk 25 optimal weight: 9.9990 chunk 180 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 42 GLN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.185782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151651 restraints weight = 15600.440| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.81 r_work: 0.3509 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16152 Z= 0.111 Angle : 0.462 8.053 21824 Z= 0.247 Chirality : 0.038 0.260 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.298 17.627 2168 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.11 % Allowed : 18.43 % Favored : 79.46 % 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: 2.66 (0.19), residues: 1952 helix: 2.27 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.20 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 109 TYR 0.011 0.001 TYR C 545 PHE 0.011 0.001 PHE E 332 TRP 0.023 0.002 TRP C 323 HIS 0.007 0.001 HIS G 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (16152) covalent geometry : angle 0.46158 / 0.25 (21824) hydrogen bonds : bond 0.03693 / 2.50 ( 1112) hydrogen bonds : angle 3.51616 / 2.51 ( 3306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5909.98 seconds wall clock time: 101 minutes 15.41 seconds (6075.41 seconds total)