Starting phenix.real_space_refine on Sat May 17 13:47:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sik_40508/05_2025/8sik_40508.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sik_40508/05_2025/8sik_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sik_40508/05_2025/8sik_40508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sik_40508/05_2025/8sik_40508.map" model { file = "/net/cci-nas-00/data/ceres_data/8sik_40508/05_2025/8sik_40508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sik_40508/05_2025/8sik_40508.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.043 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.50, per 1000 atoms: 0.60 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: 4.28 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.44 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: 4.71 Time building geometry restraints manager: 4.84 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 149 or resid 201)) selection = (chain 'D' and (resid 6 through 149 or resid 201)) selection = chain 'F' selection = (chain 'H' and (resid 6 through 149 or resid 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: 3.070 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: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 35.560 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.023 0.002 TRP G 323 HIS 0.005 0.001 HIS E 363 PHE 0.013 0.001 PHE E 332 TYR 0.017 0.001 TYR D 139 ARG 0.013 0.001 ARG G 507 Details of bonding type rmsd hydrogen bonds : bond 0.09180 ( 1112) hydrogen bonds : angle 4.47777 ( 3306) covalent geometry : bond 0.00278 (16152) covalent geometry : angle 0.50590 (21824) *********************** 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 : 1.642 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: 1.4397 time to fit residues: 339.5143 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 : 1.722 ------------------------------------------------------------------------------- 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 165 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 153 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4037 r_free = 0.4037 target = 0.182331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.147734 restraints weight = 15605.030| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.85 r_work: 0.3462 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16152 Z= 0.153 Angle : 0.476 7.676 21824 Z= 0.263 Chirality : 0.039 0.214 2444 Planarity : 0.004 0.046 2752 Dihedral : 4.000 37.967 2182 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.43 % Allowed : 16.57 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.19), residues: 1952 helix: 2.12 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.15 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 323 HIS 0.003 0.001 HIS C 240 PHE 0.014 0.001 PHE C 332 TYR 0.013 0.002 TYR C 545 ARG 0.006 0.000 ARG G 507 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 1112) hydrogen bonds : angle 3.83067 ( 3306) covalent geometry : bond 0.00365 (16152) covalent geometry : angle 0.47591 (21824) *********************** 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 259 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 1.858 Fit side-chains REVERT: B 131 ILE cc_start: 0.4381 (OUTLIER) cc_final: 0.4103 (pp) REVERT: A 191 LEU cc_start: 0.7097 (mp) cc_final: 0.6769 (mm) REVERT: D 112 ASN cc_start: 0.8626 (m-40) cc_final: 0.8405 (m-40) REVERT: F 42 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.6834 (mp10) REVERT: F 68 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7123 (mt-10) REVERT: F 140 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6234 (mp0) REVERT: H 112 ASN cc_start: 0.8633 (m-40) cc_final: 0.8420 (m-40) REVERT: H 141 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6989 (pp20) REVERT: G 195 ARG cc_start: 0.7248 (mtp180) cc_final: 0.6855 (mtm110) REVERT: C 191 LEU cc_start: 0.7156 (mp) cc_final: 0.6806 (mm) outliers start: 57 outliers final: 21 residues processed: 242 average time/residue: 1.4286 time to fit residues: 377.1682 Evaluate side-chains 222 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 175 LEU 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 42 GLN 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 172 VAL 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 102 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 149 optimal weight: 0.4980 chunk 165 optimal weight: 6.9990 chunk 150 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4052 r_free = 0.4052 target = 0.184026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.149413 restraints weight = 15609.027| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.85 r_work: 0.3492 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16152 Z= 0.113 Angle : 0.436 6.917 21824 Z= 0.239 Chirality : 0.037 0.225 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.454 23.792 2170 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.83 % Allowed : 17.11 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.19), residues: 1952 helix: 2.28 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.10 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 379 HIS 0.003 0.001 HIS G 363 PHE 0.012 0.001 PHE E 332 TYR 0.011 0.001 TYR C 545 ARG 0.006 0.000 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 1112) hydrogen bonds : angle 3.65329 ( 3306) covalent geometry : bond 0.00249 (16152) covalent geometry : angle 0.43600 (21824) *********************** 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 254 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 1.615 Fit side-chains REVERT: A 557 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7330 (mtpt) REVERT: D 12 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: D 68 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6920 (mt-10) REVERT: D 112 ASN cc_start: 0.8558 (m-40) cc_final: 0.8306 (m-40) REVERT: F 68 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7094 (mt-10) REVERT: F 140 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6161 (mp0) REVERT: H 112 ASN cc_start: 0.8597 (m-40) cc_final: 0.8343 (m-40) REVERT: H 141 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6951 (pp20) REVERT: G 195 ARG cc_start: 0.7200 (mtp180) cc_final: 0.6793 (mtm110) REVERT: G 508 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: C 533 ARG cc_start: 0.7923 (mtp85) cc_final: 0.7583 (mtm180) outliers start: 47 outliers final: 18 residues processed: 241 average time/residue: 1.4485 time to fit residues: 380.4906 Evaluate side-chains 222 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 1.742 ------------------------------------------------------------------------------- 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 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 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 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 163 LEU 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 49 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 92 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 178 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 155 optimal weight: 0.0270 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4069 r_free = 0.4069 target = 0.185565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151390 restraints weight = 15619.266| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.81 r_work: 0.3508 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16152 Z= 0.103 Angle : 0.421 6.319 21824 Z= 0.231 Chirality : 0.037 0.244 2444 Planarity : 0.003 0.028 2752 Dihedral : 3.294 17.570 2168 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.71 % Allowed : 17.23 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.19), residues: 1952 helix: 2.28 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.25 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 323 HIS 0.003 0.001 HIS G 363 PHE 0.011 0.001 PHE E 332 TYR 0.010 0.001 TYR C 545 ARG 0.002 0.000 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 1112) hydrogen bonds : angle 3.55817 ( 3306) covalent geometry : bond 0.00220 (16152) covalent geometry : angle 0.42089 (21824) *********************** 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 253 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 208 time to evaluate : 1.748 Fit side-chains REVERT: B 141 GLU cc_start: 0.7394 (pt0) cc_final: 0.6934 (pp20) REVERT: A 557 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7329 (mtpt) REVERT: D 12 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6887 (pm20) REVERT: D 68 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6969 (mt-10) REVERT: D 112 ASN cc_start: 0.8518 (m-40) cc_final: 0.8275 (m-40) REVERT: F 68 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: F 112 ASN cc_start: 0.8334 (m-40) cc_final: 0.7907 (m-40) REVERT: F 140 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6029 (mp0) REVERT: H 112 ASN cc_start: 0.8535 (m-40) cc_final: 0.8297 (m-40) REVERT: H 141 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6964 (pp20) REVERT: G 195 ARG cc_start: 0.7134 (mtp180) cc_final: 0.6731 (mtm110) REVERT: C 533 ARG cc_start: 0.7873 (mtp85) cc_final: 0.7523 (mtm180) REVERT: E 560 GLN cc_start: 0.7324 (tp-100) cc_final: 0.6634 (mt0) outliers start: 45 outliers final: 22 residues processed: 244 average time/residue: 1.4671 time to fit residues: 390.6005 Evaluate side-chains 232 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain A residue 163 LEU 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 125 MET 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 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 310 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 142 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 29 optimal weight: 0.1980 chunk 104 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4065 r_free = 0.4065 target = 0.185167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.150819 restraints weight = 15785.769| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.83 r_work: 0.3503 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- 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 = 0.21 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 = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16152 Z= 0.111 Angle : 0.430 6.752 21824 Z= 0.235 Chirality : 0.037 0.257 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.294 17.282 2168 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.89 % Allowed : 17.29 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.19), residues: 1952 helix: 2.27 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.23 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 323 HIS 0.004 0.001 HIS G 363 PHE 0.012 0.001 PHE E 332 TYR 0.012 0.001 TYR C 545 ARG 0.003 0.000 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 1112) hydrogen bonds : angle 3.55912 ( 3306) covalent geometry : bond 0.00248 (16152) covalent geometry : angle 0.42959 (21824) *********************** 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 257 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 1.778 Fit side-chains REVERT: B 141 GLU cc_start: 0.7514 (pt0) cc_final: 0.7090 (pp20) REVERT: A 557 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7313 (mtpt) REVERT: D 12 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6902 (pm20) REVERT: D 68 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6879 (mt-10) REVERT: D 112 ASN cc_start: 0.8527 (m-40) cc_final: 0.8285 (m-40) REVERT: F 42 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.6854 (mp10) REVERT: F 68 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: F 140 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6066 (mp0) REVERT: H 112 ASN cc_start: 0.8539 (m-40) cc_final: 0.8286 (m-40) REVERT: H 141 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6967 (pp20) REVERT: G 195 ARG cc_start: 0.7125 (mtp180) cc_final: 0.6710 (mtm110) REVERT: C 533 ARG cc_start: 0.7837 (mtp85) cc_final: 0.7277 (mtm110) REVERT: E 560 GLN cc_start: 0.7326 (tp-100) cc_final: 0.6685 (mt0) outliers start: 48 outliers final: 24 residues processed: 246 average time/residue: 1.4129 time to fit residues: 379.9198 Evaluate side-chains 236 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 1.702 ------------------------------------------------------------------------------- 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 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 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 310 VAL Chi-restraints excluded: chain E residue 312 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 155 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.0010 chunk 24 optimal weight: 0.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.186426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.152010 restraints weight = 15695.546| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.83 r_work: 0.3517 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16152 Z= 0.099 Angle : 0.420 7.824 21824 Z= 0.228 Chirality : 0.037 0.247 2444 Planarity : 0.003 0.028 2752 Dihedral : 3.225 17.048 2168 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.83 % Allowed : 17.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.19), residues: 1952 helix: 2.36 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.12 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.004 0.001 HIS G 363 PHE 0.011 0.001 PHE E 332 TYR 0.010 0.001 TYR E 125 ARG 0.004 0.000 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 1112) hydrogen bonds : angle 3.48175 ( 3306) covalent geometry : bond 0.00209 (16152) covalent geometry : angle 0.41978 (21824) *********************** 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 259 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 1.706 Fit side-chains REVERT: B 141 GLU cc_start: 0.7515 (pt0) cc_final: 0.7081 (pp20) REVERT: A 557 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7334 (mtpt) REVERT: D 12 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6900 (pm20) REVERT: D 68 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7068 (mt-10) REVERT: D 112 ASN cc_start: 0.8492 (m-40) cc_final: 0.8273 (m-40) REVERT: D 145 MET cc_start: 0.7600 (pp-130) cc_final: 0.7317 (pp-130) REVERT: F 39 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.8216 (p) REVERT: F 68 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: F 140 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6014 (mp0) REVERT: H 112 ASN cc_start: 0.8504 (m-40) cc_final: 0.8284 (m-40) REVERT: H 141 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6954 (pp20) REVERT: G 195 ARG cc_start: 0.7095 (mtp180) cc_final: 0.6761 (mtm110) outliers start: 47 outliers final: 22 residues processed: 254 average time/residue: 1.3637 time to fit residues: 379.5493 Evaluate side-chains 238 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 1.938 ------------------------------------------------------------------------------- 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 366 ARG Chi-restraints excluded: chain A residue 557 LYS 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 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 513 THR 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 310 VAL 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 32 optimal weight: 0.0970 chunk 88 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN D 42 GLN G 234 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.185157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.150932 restraints weight = 15677.005| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.83 r_work: 0.3498 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 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 = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16152 Z= 0.114 Angle : 0.443 7.935 21824 Z= 0.240 Chirality : 0.037 0.252 2444 Planarity : 0.003 0.028 2752 Dihedral : 3.278 16.792 2168 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.59 % Allowed : 18.25 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.19), residues: 1952 helix: 2.31 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.15 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 323 HIS 0.005 0.001 HIS G 363 PHE 0.012 0.001 PHE G 332 TYR 0.013 0.001 TYR C 545 ARG 0.004 0.000 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 1112) hydrogen bonds : angle 3.52806 ( 3306) covalent geometry : bond 0.00257 (16152) covalent geometry : angle 0.44264 (21824) *********************** 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 253 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 1.685 Fit side-chains REVERT: B 141 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7058 (pp20) REVERT: A 557 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7368 (mtpt) REVERT: D 12 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6788 (pm20) REVERT: D 68 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.7021 (mt-10) REVERT: D 112 ASN cc_start: 0.8517 (m-40) cc_final: 0.8267 (m-40) REVERT: F 39 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8216 (p) REVERT: F 68 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: F 140 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6072 (mp0) REVERT: H 112 ASN cc_start: 0.8530 (m-40) cc_final: 0.8276 (m-40) REVERT: H 141 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6992 (pp20) REVERT: G 195 ARG cc_start: 0.7160 (mtp180) cc_final: 0.6803 (mtm110) REVERT: E 191 LEU cc_start: 0.7476 (mm) cc_final: 0.7273 (mp) outliers start: 43 outliers final: 28 residues processed: 243 average time/residue: 1.3870 time to fit residues: 368.7642 Evaluate side-chains 244 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR 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 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 513 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 111 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 39 optimal weight: 0.0170 chunk 129 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 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 = 0.4075 r_free = 0.4075 target = 0.186396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.151925 restraints weight = 15607.262| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.85 r_work: 0.3515 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16152 Z= 0.102 Angle : 0.435 7.947 21824 Z= 0.234 Chirality : 0.037 0.241 2444 Planarity : 0.003 0.027 2752 Dihedral : 3.230 16.909 2168 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.65 % Allowed : 18.31 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.19), residues: 1952 helix: 2.36 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.10 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.005 0.001 HIS G 363 PHE 0.011 0.001 PHE E 332 TYR 0.010 0.001 TYR C 545 ARG 0.004 0.000 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 1112) hydrogen bonds : angle 3.46740 ( 3306) covalent geometry : bond 0.00219 (16152) covalent geometry : angle 0.43451 (21824) *********************** 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 261 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 1.670 Fit side-chains REVERT: B 141 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7102 (pp20) REVERT: A 359 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8265 (pt0) REVERT: A 557 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7321 (mtpt) REVERT: D 12 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: D 68 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7063 (mt-10) REVERT: D 112 ASN cc_start: 0.8483 (m-40) cc_final: 0.8247 (m-40) REVERT: F 39 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8205 (p) REVERT: F 68 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: F 112 ASN cc_start: 0.8322 (m-40) cc_final: 0.7928 (m-40) REVERT: F 140 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6029 (mp0) REVERT: H 112 ASN cc_start: 0.8507 (m-40) cc_final: 0.8271 (m-40) REVERT: H 141 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6971 (pp20) REVERT: G 191 LEU cc_start: 0.7487 (mm) cc_final: 0.7213 (mp) outliers start: 44 outliers final: 27 residues processed: 251 average time/residue: 1.4226 time to fit residues: 392.2567 Evaluate side-chains 247 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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 310 VAL Chi-restraints excluded: chain A residue 359 GLN 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 513 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 95 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN A 359 GLN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4038 r_free = 0.4038 target = 0.182383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.147859 restraints weight = 15626.326| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.88 r_work: 0.3457 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16152 Z= 0.158 Angle : 0.503 8.274 21824 Z= 0.271 Chirality : 0.039 0.257 2444 Planarity : 0.003 0.028 2752 Dihedral : 3.447 16.780 2168 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.59 % Allowed : 18.19 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.19), residues: 1952 helix: 2.13 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.27 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 323 HIS 0.007 0.001 HIS G 363 PHE 0.014 0.001 PHE C 332 TYR 0.017 0.002 TYR C 545 ARG 0.004 0.000 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 1112) hydrogen bonds : angle 3.68037 ( 3306) covalent geometry : bond 0.00382 (16152) covalent geometry : angle 0.50319 (21824) *********************** 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 : 1.653 Fit side-chains REVERT: B 141 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7109 (pp20) REVERT: A 359 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8413 (pt0) REVERT: A 557 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7373 (mtpt) REVERT: D 12 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: D 68 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.7007 (mt-10) REVERT: D 112 ASN cc_start: 0.8542 (m-40) cc_final: 0.8276 (m-40) REVERT: F 68 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7180 (mt-10) REVERT: H 112 ASN cc_start: 0.8577 (m-40) cc_final: 0.8305 (m-40) REVERT: H 141 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7059 (pp20) REVERT: G 191 LEU cc_start: 0.7530 (mm) cc_final: 0.7235 (mp) REVERT: E 191 LEU cc_start: 0.7431 (mm) cc_final: 0.7223 (mp) outliers start: 43 outliers final: 28 residues processed: 240 average time/residue: 1.3612 time to fit residues: 358.4472 Evaluate side-chains 244 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 359 GLN 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 366 ARG 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 310 VAL Chi-restraints excluded: chain E residue 312 THR 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 119 optimal weight: 0.0370 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 0.0570 chunk 173 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** G 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 = 0.4083 r_free = 0.4083 target = 0.187245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.152833 restraints weight = 15686.391| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.84 r_work: 0.3520 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16152 Z= 0.100 Angle : 0.448 8.662 21824 Z= 0.241 Chirality : 0.037 0.249 2444 Planarity : 0.003 0.035 2752 Dihedral : 3.248 17.513 2168 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.69 % Allowed : 18.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.19), residues: 1952 helix: 2.34 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.11 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 323 HIS 0.006 0.001 HIS G 363 PHE 0.010 0.001 PHE E 332 TYR 0.010 0.001 TYR A 125 ARG 0.006 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 1112) hydrogen bonds : angle 3.45919 ( 3306) covalent geometry : bond 0.00201 (16152) covalent geometry : angle 0.44837 (21824) ********************** 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 242 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 1.735 Fit side-chains REVERT: B 141 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7085 (pp20) REVERT: A 557 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7306 (mtpt) REVERT: D 12 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7038 (pm20) REVERT: D 68 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: D 112 ASN cc_start: 0.8454 (m-40) cc_final: 0.8215 (m-40) REVERT: F 68 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: F 112 ASN cc_start: 0.8276 (m-40) cc_final: 0.7889 (m-40) REVERT: H 112 ASN cc_start: 0.8472 (m-40) cc_final: 0.8227 (m-40) REVERT: H 141 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7037 (pp20) REVERT: G 191 LEU cc_start: 0.7505 (mm) cc_final: 0.7224 (mp) REVERT: E 191 LEU cc_start: 0.7401 (mm) cc_final: 0.7185 (mp) outliers start: 28 outliers final: 15 residues processed: 239 average time/residue: 1.3955 time to fit residues: 364.9775 Evaluate side-chains 233 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain A residue 163 LEU 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 D residue 12 GLU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 131 ILE 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 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 C residue 163 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 111 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 171 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 182 optimal weight: 0.4980 chunk 96 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.185787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.151512 restraints weight = 15549.184| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.83 r_work: 0.3510 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16152 Z= 0.116 Angle : 0.474 8.011 21824 Z= 0.255 Chirality : 0.037 0.243 2444 Planarity : 0.003 0.028 2752 Dihedral : 3.284 17.030 2168 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.63 % Allowed : 18.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.19), residues: 1952 helix: 2.32 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.11 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 323 HIS 0.007 0.001 HIS G 363 PHE 0.012 0.001 PHE G 332 TYR 0.012 0.001 TYR C 545 ARG 0.004 0.000 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 1112) hydrogen bonds : angle 3.51079 ( 3306) covalent geometry : bond 0.00258 (16152) covalent geometry : angle 0.47418 (21824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12252.16 seconds wall clock time: 211 minutes 7.58 seconds (12667.58 seconds total)