Starting phenix.real_space_refine on Thu Mar 5 01:55:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vwz_65403/03_2026/9vwz_65403.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vwz_65403/03_2026/9vwz_65403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vwz_65403/03_2026/9vwz_65403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vwz_65403/03_2026/9vwz_65403.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vwz_65403/03_2026/9vwz_65403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vwz_65403/03_2026/9vwz_65403.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 11235 2.51 5 N 2955 2.21 5 O 3385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17690 Number of models: 1 Model: "" Number of chains: 7 Chain: "L" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 701 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 96} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'TYR:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "H" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 872 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 118} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3171 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 380} Chain breaks: 4 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3177 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 377} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3196 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 380} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3268 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 387} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3305 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 3.55, per 1000 atoms: 0.20 Number of scatterers: 17690 At special positions: 0 Unit cell: (126, 124, 130, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 3385 8.00 N 2955 7.00 C 11235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 747.4 milliseconds 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 30 sheets defined 12.2% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.559A pdb=" N LEU A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 240 Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.768A pdb=" N TYR A 277 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 388 through 399 Processing helix chain 'A' and resid 399 through 406 removed outlier: 4.263A pdb=" N LEU A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 removed outlier: 3.612A pdb=" N GLN A 465 " --> pdb=" O ASP A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.557A pdb=" N LYS A 471 " --> pdb=" O PRO A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 388 through 399 Processing helix chain 'B' and resid 400 through 405 removed outlier: 3.504A pdb=" N ASN B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 465 Processing helix chain 'B' and resid 466 through 476 Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 234 through 240 Processing helix chain 'E' and resid 360 through 362 No H-bonds generated for 'chain 'E' and resid 360 through 362' Processing helix chain 'E' and resid 388 through 399 Processing helix chain 'E' and resid 399 through 406 removed outlier: 4.523A pdb=" N LEU E 403 " --> pdb=" O ASN E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 477 removed outlier: 3.535A pdb=" N LYS E 471 " --> pdb=" O PRO E 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.698A pdb=" N LEU C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 210 through 215' Processing helix chain 'C' and resid 234 through 240 Processing helix chain 'C' and resid 327 through 329 No H-bonds generated for 'chain 'C' and resid 327 through 329' Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 390 through 399 Processing helix chain 'C' and resid 399 through 406 removed outlier: 4.349A pdb=" N LEU C 403 " --> pdb=" O ASN C 399 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 404 " --> pdb=" O SER C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 465 Processing helix chain 'C' and resid 466 through 477 Processing helix chain 'D' and resid 58 through 62 Processing helix chain 'D' and resid 210 through 215 removed outlier: 3.601A pdb=" N GLN D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 240 Processing helix chain 'D' and resid 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' Processing helix chain 'D' and resid 388 through 406 removed outlier: 7.854A pdb=" N SER D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE D 402 " --> pdb=" O MET D 398 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU D 403 " --> pdb=" O ASN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 465 removed outlier: 3.767A pdb=" N GLN D 465 " --> pdb=" O ASP D 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 462 through 465' Processing helix chain 'D' and resid 466 through 477 Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.530A pdb=" N ILE L 21 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.697A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR L 84 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 88 through 89 removed outlier: 4.070A pdb=" N GLN L 89 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.789A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.678A pdb=" N VAL H 12 " --> pdb=" O THR H 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 45 through 52 removed outlier: 6.931A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 28 through 38 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 28 through 38 current: chain 'A' and resid 314 through 315 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 314 through 315 current: chain 'A' and resid 364 through 386 removed outlier: 6.253A pdb=" N PHE A 364 " --> pdb=" O VAL E 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 72 through 77 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 72 through 77 current: chain 'A' and resid 250 through 262 removed outlier: 6.551A pdb=" N SER A 297 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE A 261 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER A 295 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 119 through 124 removed outlier: 3.595A pdb=" N PHE A 123 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP A 146 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 189 through 195 removed outlier: 6.027A pdb=" N TRP A 170 " --> pdb=" O CYS A 230 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N CYS A 230 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N MET A 201 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 267 through 268 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 267 through 268 current: chain 'B' and resid 314 through 315 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 314 through 315 current: chain 'B' and resid 364 through 386 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 303 through 304 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 303 through 304 current: chain 'E' and resid 250 through 263 removed outlier: 5.402A pdb=" N ALA E 258 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER E 299 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HIS E 260 " --> pdb=" O SER E 297 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 250 through 255 removed outlier: 3.539A pdb=" N GLN B 154 " --> pdb=" O GLN B 255 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 334 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 73 " --> pdb=" O TRP B 451 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL B 453 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ARG B 75 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.517A pdb=" N SER B 119 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 148 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 123 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASP B 146 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 189 through 195 removed outlier: 3.598A pdb=" N LYS B 192 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS B 169 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TRP B 170 " --> pdb=" O CYS B 230 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N CYS B 230 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET B 201 " --> pdb=" O LYS B 231 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 257 through 261 removed outlier: 5.479A pdb=" N ALA B 258 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER B 299 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS B 260 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 267 through 268 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 267 through 268 current: chain 'C' and resid 314 through 315 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 314 through 315 current: chain 'C' and resid 364 through 386 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 29 through 38 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 29 through 38 current: chain 'E' and resid 314 through 315 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 314 through 315 current: chain 'E' and resid 364 through 386 No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 119 through 124 removed outlier: 4.856A pdb=" N GLY E 120 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL E 150 " --> pdb=" O GLY E 120 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL E 148 " --> pdb=" O PRO E 122 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP E 146 " --> pdb=" O TYR E 124 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 189 through 195 removed outlier: 5.915A pdb=" N TRP E 170 " --> pdb=" O CYS E 230 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N CYS E 230 " --> pdb=" O TRP E 170 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET E 201 " --> pdb=" O LYS E 231 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 250 through 255 removed outlier: 3.529A pdb=" N GLN C 154 " --> pdb=" O GLN C 255 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 73 " --> pdb=" O TRP C 451 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL C 453 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG C 75 " --> pdb=" O VAL C 453 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 119 through 124 removed outlier: 3.556A pdb=" N SER C 119 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 148 " --> pdb=" O HIS C 121 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE C 123 " --> pdb=" O ASP C 146 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP C 146 " --> pdb=" O PHE C 123 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 189 through 195 removed outlier: 3.510A pdb=" N LYS C 192 " --> pdb=" O HIS C 169 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TRP C 170 " --> pdb=" O CYS C 230 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N CYS C 230 " --> pdb=" O TRP C 170 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET C 201 " --> pdb=" O LYS C 231 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 257 through 263 removed outlier: 6.642A pdb=" N SER C 297 " --> pdb=" O ARG C 259 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N PHE C 261 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N SER C 295 " --> pdb=" O PHE C 261 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 267 through 268 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 267 through 268 current: chain 'D' and resid 313 through 315 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 313 through 315 current: chain 'D' and resid 364 through 386 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 250 through 255 removed outlier: 3.564A pdb=" N GLN D 154 " --> pdb=" O GLN D 255 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL D 73 " --> pdb=" O TRP D 451 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL D 453 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG D 75 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 119 through 121 Processing sheet with id=AD2, first strand: chain 'D' and resid 128 through 129 removed outlier: 4.030A pdb=" N ASP D 128 " --> pdb=" O ASN D 263 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN D 263 " --> pdb=" O ASP D 128 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALA D 258 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER D 299 " --> pdb=" O ALA D 258 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N HIS D 260 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 189 through 195 removed outlier: 5.634A pdb=" N TRP D 170 " --> pdb=" O CYS D 230 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N CYS D 230 " --> pdb=" O TRP D 170 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N MET D 201 " --> pdb=" O LYS D 231 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5679 1.34 - 1.46: 4353 1.46 - 1.58: 7956 1.58 - 1.71: 1 1.71 - 1.83: 162 Bond restraints: 18151 Sorted by residual: bond pdb=" N GLY H 111 " pdb=" CA GLY H 111 " ideal model delta sigma weight residual 1.444 1.475 -0.031 1.02e-02 9.61e+03 9.40e+00 bond pdb=" N VAL L 3 " pdb=" CA VAL L 3 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.15e-02 7.56e+03 9.06e+00 bond pdb=" N VAL D 53 " pdb=" CA VAL D 53 " ideal model delta sigma weight residual 1.460 1.487 -0.028 9.30e-03 1.16e+04 8.80e+00 bond pdb=" CB PRO H 14 " pdb=" CG PRO H 14 " ideal model delta sigma weight residual 1.492 1.640 -0.148 5.00e-02 4.00e+02 8.75e+00 bond pdb=" N ILE L 2 " pdb=" CA ILE L 2 " ideal model delta sigma weight residual 1.458 1.492 -0.033 1.17e-02 7.31e+03 8.14e+00 ... (remaining 18146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 24593 3.06 - 6.11: 123 6.11 - 9.17: 13 9.17 - 12.22: 0 12.22 - 15.28: 1 Bond angle restraints: 24730 Sorted by residual: angle pdb=" CA PRO H 14 " pdb=" N PRO H 14 " pdb=" CD PRO H 14 " ideal model delta sigma weight residual 112.00 96.72 15.28 1.40e+00 5.10e-01 1.19e+02 angle pdb=" CA PRO L 94 " pdb=" C PRO L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 117.93 122.95 -5.02 1.20e+00 6.94e-01 1.75e+01 angle pdb=" CA MET D 285 " pdb=" CB MET D 285 " pdb=" CG MET D 285 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 angle pdb=" N PRO H 14 " pdb=" CA PRO H 14 " pdb=" C PRO H 14 " ideal model delta sigma weight residual 111.41 117.32 -5.91 1.50e+00 4.44e-01 1.55e+01 angle pdb=" N PRO H 14 " pdb=" CD PRO H 14 " pdb=" CG PRO H 14 " ideal model delta sigma weight residual 103.20 97.38 5.82 1.50e+00 4.44e-01 1.50e+01 ... (remaining 24725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9316 17.98 - 35.96: 1079 35.96 - 53.93: 249 53.93 - 71.91: 37 71.91 - 89.89: 31 Dihedral angle restraints: 10712 sinusoidal: 4093 harmonic: 6619 Sorted by residual: dihedral pdb=" CA MET C 209 " pdb=" C MET C 209 " pdb=" N ASP C 210 " pdb=" CA ASP C 210 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CD ARG H 98 " pdb=" NE ARG H 98 " pdb=" CZ ARG H 98 " pdb=" NH1 ARG H 98 " ideal model delta sinusoidal sigma weight residual 0.00 50.38 -50.38 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CA MET D 209 " pdb=" C MET D 209 " pdb=" N ASP D 210 " pdb=" CA ASP D 210 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 10709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2186 0.054 - 0.108: 412 0.108 - 0.163: 115 0.163 - 0.217: 5 0.217 - 0.271: 6 Chirality restraints: 2724 Sorted by residual: chirality pdb=" CA PRO H 14 " pdb=" N PRO H 14 " pdb=" C PRO H 14 " pdb=" CB PRO H 14 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA MET C 398 " pdb=" N MET C 398 " pdb=" C MET C 398 " pdb=" CB MET C 398 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA TYR H 100 " pdb=" N TYR H 100 " pdb=" C TYR H 100 " pdb=" CB TYR H 100 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2721 not shown) Planarity restraints: 3194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 98 " 0.862 9.50e-02 1.11e+02 3.87e-01 9.18e+01 pdb=" NE ARG H 98 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG H 98 " -0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG H 98 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 98 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG H 13 " 0.110 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO H 14 " -0.262 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 57 " 0.046 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO L 58 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO L 58 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO L 58 " 0.039 5.00e-02 4.00e+02 ... (remaining 3191 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2302 2.75 - 3.29: 16041 3.29 - 3.83: 27041 3.83 - 4.36: 30351 4.36 - 4.90: 54999 Nonbonded interactions: 130734 Sorted by model distance: nonbonded pdb=" O SER D 342 " pdb=" OG SER D 342 " model vdw 2.214 3.040 nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 114 " model vdw 2.260 3.040 nonbonded pdb=" N GLU H 89 " pdb=" OE1 GLU H 89 " model vdw 2.278 3.120 nonbonded pdb=" OE2 GLU C 131 " pdb=" NE2 HIS D 260 " model vdw 2.287 3.120 nonbonded pdb=" OD2 ASP B 200 " pdb=" NZ LYS B 231 " model vdw 2.289 3.120 ... (remaining 130729 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 53 or resid 62 through 83 or resid \ 93 through 115 or (resid 116 and (name N or name CA or name C or name O or name \ CB )) or resid 117 through 130 or resid 141 through 174 or (resid 175 and (name \ N or name CA or name C or name O or name CB )) or resid 176 or resid 183 throug \ h 219 or (resid 220 and (name N or name CA or name C or name O or name CB )) or \ resid 221 through 251 or (resid 252 and (name N or name CA or name C or name O o \ r name CB )) or resid 253 through 278 or resid 287 through 305 or (resid 306 and \ (name N or name CA or name C or name O or name CB )) or resid 307 through 397 o \ r (resid 398 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 99 through 404 or (resid 405 and (name N or name CA or name C or name O or name \ CB )) or resid 406 or (resid 407 through 408 and (name N or name CA or name C or \ name O or name CB )) or resid 444 through 445 or (resid 446 through 447 and (na \ me N or name CA or name C or name O or name CB )) or resid 448 through 476)) selection = (chain 'B' and (resid 19 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 83 or resid 93 through 115 or (res \ id 116 and (name N or name CA or name C or name O or name CB )) or resid 117 thr \ ough 130 or resid 141 through 165 or (resid 166 and (name N or name CA or name C \ or name O or name CB )) or resid 167 through 171 or (resid 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 174 or (resid 175 \ and (name N or name CA or name C or name O or name CB )) or resid 176 through 21 \ 9 or (resid 220 and (name N or name CA or name C or name O or name CB )) or resi \ d 221 through 251 or (resid 252 and (name N or name CA or name C or name O or na \ me CB )) or resid 253 through 311 or (resid 312 and (name N or name CA or name C \ or name O or name CB )) or resid 313 through 389 or (resid 390 and (name N or n \ ame CA or name C or name O or name CB )) or resid 391 or (resid 392 and (name N \ or name CA or name C or name O or name CB )) or resid 393 through 403 or (resid \ 404 through 405 and (name N or name CA or name C or name O or name CB )) or resi \ d 406 through 407 or (resid 408 and (name N or name CA or name C or name O or na \ me CB )) or resid 444 through 445 or (resid 446 through 447 and (name N or name \ CA or name C or name O or name CB )) or resid 448 or (resid 449 and (name N or n \ ame CA or name C or name O or name CB )) or resid 450 through 470 or (resid 471 \ and (name N or name CA or name C or name O or name CB )) or resid 472 through 47 \ 6)) selection = (chain 'C' and (resid 19 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 53 or resid 62 through 83 or resid \ 93 through 115 or (resid 116 and (name N or name CA or name C or name O or name \ CB )) or resid 117 through 130 or resid 141 through 165 or (resid 166 and (name \ N or name CA or name C or name O or name CB )) or resid 167 through 171 or (res \ id 172 and (name N or name CA or name C or name O or name CB )) or resid 173 thr \ ough 174 or (resid 175 and (name N or name CA or name C or name O or name CB )) \ or resid 176 or resid 183 through 219 or (resid 220 and (name N or name CA or na \ me C or name O or name CB )) or resid 221 through 278 or resid 287 through 305 o \ r (resid 306 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 07 through 311 or (resid 312 and (name N or name CA or name C or name O or name \ CB )) or resid 313 through 389 or (resid 390 and (name N or name CA or name C or \ name O or name CB )) or resid 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 397 or (resid 398 and (name N or \ name CA or name C or name O or name CB )) or resid 399 through 403 or (resid 404 \ through 405 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 06 or (resid 407 through 408 and (name N or name CA or name C or name O or name \ CB )) or resid 444 through 448 or (resid 449 and (name N or name CA or name C or \ name O or name CB )) or resid 450 through 470 or (resid 471 and (name N or name \ CA or name C or name O or name CB )) or resid 472 through 476)) selection = (chain 'D' and (resid 19 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 53 or resid 62 through 83 or resid \ 93 through 115 or (resid 116 and (name N or name CA or name C or name O or name \ CB )) or resid 117 through 130 or resid 141 through 165 or (resid 166 and (name \ N or name CA or name C or name O or name CB )) or resid 167 through 171 or (res \ id 172 and (name N or name CA or name C or name O or name CB )) or resid 173 thr \ ough 176 or resid 183 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB )) or resid 221 through 251 or (resid 252 and (name N or n \ ame CA or name C or name O or name CB )) or resid 253 through 278 or resid 287 t \ hrough 305 or (resid 306 and (name N or name CA or name C or name O or name CB ) \ ) or resid 307 through 311 or (resid 312 and (name N or name CA or name C or nam \ e O or name CB )) or resid 313 through 389 or (resid 390 and (name N or name CA \ or name C or name O or name CB )) or resid 391 or (resid 392 and (name N or name \ CA or name C or name O or name CB )) or resid 393 through 397 or (resid 398 and \ (name N or name CA or name C or name O or name CB )) or resid 399 through 403 o \ r (resid 404 through 405 and (name N or name CA or name C or name O or name CB ) \ ) or resid 406 or (resid 407 through 408 and (name N or name CA or name C or nam \ e O or name CB )) or resid 444 through 445 or (resid 446 through 447 and (name N \ or name CA or name C or name O or name CB )) or resid 448 or (resid 449 and (na \ me N or name CA or name C or name O or name CB )) or resid 450 through 470 or (r \ esid 471 and (name N or name CA or name C or name O or name CB )) or resid 472 t \ hrough 476)) selection = (chain 'E' and (resid 19 through 53 or resid 62 through 83 or resid 93 through 1 \ 30 or resid 141 through 165 or (resid 166 and (name N or name CA or name C or na \ me O or name CB )) or resid 167 through 171 or (resid 172 and (name N or name CA \ or name C or name O or name CB )) or resid 173 through 174 or (resid 175 and (n \ ame N or name CA or name C or name O or name CB )) or resid 176 or resid 183 thr \ ough 251 or (resid 252 and (name N or name CA or name C or name O or name CB )) \ or resid 253 through 278 or resid 287 through 305 or (resid 306 and (name N or n \ ame CA or name C or name O or name CB )) or resid 307 through 311 or (resid 312 \ and (name N or name CA or name C or name O or name CB )) or resid 313 through 38 \ 9 or (resid 390 and (name N or name CA or name C or name O or name CB )) or resi \ d 391 or (resid 392 and (name N or name CA or name C or name O or name CB )) or \ resid 393 through 397 or (resid 398 and (name N or name CA or name C or name O o \ r name CB )) or resid 399 through 403 or (resid 404 through 405 and (name N or n \ ame CA or name C or name O or name CB )) or resid 406 or (resid 407 through 408 \ and (name N or name CA or name C or name O or name CB )) or resid 444 through 44 \ 5 or (resid 446 through 447 and (name N or name CA or name C or name O or name C \ B )) or resid 448 or (resid 449 and (name N or name CA or name C or name O or na \ me CB )) or resid 450 through 470 or (resid 471 and (name N or name CA or name C \ or name O or name CB )) or resid 472 through 476)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.610 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.200 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 18152 Z= 0.249 Angle : 0.633 15.281 24732 Z= 0.369 Chirality : 0.048 0.271 2724 Planarity : 0.009 0.387 3194 Dihedral : 16.506 89.888 6461 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.46 % Allowed : 26.47 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.17), residues: 2227 helix: 1.35 (0.40), residues: 175 sheet: -0.36 (0.20), residues: 674 loop : -0.94 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG H 99 TYR 0.015 0.001 TYR A 359 PHE 0.015 0.001 PHE C 408 TRP 0.024 0.001 TRP L 34 HIS 0.007 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00455 (18151) covalent geometry : angle 0.63346 (24730) SS BOND : bond 0.00582 ( 1) SS BOND : angle 1.02577 ( 2) hydrogen bonds : bond 0.26925 ( 272) hydrogen bonds : angle 7.89267 ( 738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 265 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: L 34 TRP cc_start: 0.6128 (m-10) cc_final: 0.5802 (m-10) REVERT: H 14 PRO cc_start: 0.8672 (Cg_endo) cc_final: 0.8403 (Cg_exo) REVERT: A 204 THR cc_start: 0.9135 (p) cc_final: 0.8884 (p) REVERT: A 228 SER cc_start: 0.9301 (t) cc_final: 0.8940 (t) REVERT: A 268 MET cc_start: 0.7512 (ttt) cc_final: 0.6780 (mtp) REVERT: A 408 PHE cc_start: 0.7962 (t80) cc_final: 0.7605 (t80) REVERT: B 201 MET cc_start: 0.9282 (mmm) cc_final: 0.9055 (mmm) REVERT: B 220 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7966 (mm-30) REVERT: E 209 MET cc_start: 0.9301 (ptm) cc_final: 0.9030 (ptm) REVERT: C 329 HIS cc_start: 0.7632 (m90) cc_final: 0.7115 (m90) REVERT: D 83 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8914 (tppp) REVERT: D 209 MET cc_start: 0.7601 (mtt) cc_final: 0.7322 (mtt) REVERT: D 218 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8243 (mmtp) REVERT: D 254 GLU cc_start: 0.9010 (pm20) cc_final: 0.8664 (pm20) REVERT: D 392 MET cc_start: 0.8528 (tpp) cc_final: 0.8250 (tpp) REVERT: D 398 MET cc_start: 0.8969 (ttt) cc_final: 0.8615 (ttm) outliers start: 9 outliers final: 4 residues processed: 270 average time/residue: 0.1093 time to fit residues: 47.8351 Evaluate side-chains 227 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 222 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 358 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN B 70 GLN B 154 GLN E 169 HIS C 255 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.094558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.074225 restraints weight = 32212.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.076235 restraints weight = 19374.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.077573 restraints weight = 13801.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.078451 restraints weight = 11023.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.079048 restraints weight = 9515.662| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.052 18152 Z= 0.371 Angle : 0.710 10.165 24732 Z= 0.370 Chirality : 0.049 0.173 2724 Planarity : 0.006 0.062 3194 Dihedral : 5.077 37.960 2466 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 5.93 % Allowed : 23.89 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.17), residues: 2227 helix: 0.87 (0.38), residues: 188 sheet: -0.76 (0.19), residues: 705 loop : -1.14 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 286 TYR 0.019 0.002 TYR E 152 PHE 0.026 0.002 PHE A 257 TRP 0.026 0.002 TRP L 34 HIS 0.010 0.002 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00888 (18151) covalent geometry : angle 0.71029 (24730) SS BOND : bond 0.00446 ( 1) SS BOND : angle 0.39502 ( 2) hydrogen bonds : bond 0.04708 ( 272) hydrogen bonds : angle 5.92849 ( 738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 225 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 193 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8799 (m-40) REVERT: A 204 THR cc_start: 0.9129 (p) cc_final: 0.8835 (p) REVERT: A 408 PHE cc_start: 0.8143 (t80) cc_final: 0.7727 (t80) REVERT: B 190 GLU cc_start: 0.4717 (OUTLIER) cc_final: 0.2498 (mt-10) REVERT: B 220 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7672 (mm-30) REVERT: B 245 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8642 (t0) REVERT: B 268 MET cc_start: 0.7518 (mmm) cc_final: 0.7113 (ttt) REVERT: B 386 THR cc_start: 0.8880 (m) cc_final: 0.8650 (p) REVERT: E 24 THR cc_start: 0.9411 (p) cc_final: 0.9149 (t) REVERT: E 460 SER cc_start: 0.9395 (t) cc_final: 0.9096 (p) REVERT: C 71 TYR cc_start: 0.9365 (m-80) cc_final: 0.8846 (m-80) REVERT: C 459 PHE cc_start: 0.9465 (OUTLIER) cc_final: 0.8969 (m-10) REVERT: D 392 MET cc_start: 0.8700 (tpp) cc_final: 0.8433 (tpp) outliers start: 115 outliers final: 77 residues processed: 315 average time/residue: 0.0988 time to fit residues: 51.8069 Evaluate side-chains 288 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 207 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 36 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 383 CYS Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 384 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 106 optimal weight: 0.7980 chunk 187 optimal weight: 6.9990 chunk 177 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 36 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 ASN D 322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.098418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.077714 restraints weight = 31351.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.079958 restraints weight = 18213.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.081449 restraints weight = 12616.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.082438 restraints weight = 9900.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.083028 restraints weight = 8439.204| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18152 Z= 0.099 Angle : 0.513 8.010 24732 Z= 0.260 Chirality : 0.044 0.158 2724 Planarity : 0.004 0.048 3194 Dihedral : 4.156 37.066 2460 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.37 % Allowed : 26.93 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.17), residues: 2227 helix: 1.25 (0.39), residues: 189 sheet: -0.45 (0.19), residues: 693 loop : -0.93 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.015 0.001 TYR E 152 PHE 0.010 0.001 PHE C 333 TRP 0.016 0.001 TRP L 34 HIS 0.004 0.001 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00233 (18151) covalent geometry : angle 0.51257 (24730) SS BOND : bond 0.00551 ( 1) SS BOND : angle 0.57929 ( 2) hydrogen bonds : bond 0.03157 ( 272) hydrogen bonds : angle 5.00551 ( 738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 247 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7633 (p0) REVERT: A 193 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8811 (m-40) REVERT: A 204 THR cc_start: 0.9042 (p) cc_final: 0.8761 (p) REVERT: A 228 SER cc_start: 0.9302 (t) cc_final: 0.9034 (t) REVERT: A 375 ASP cc_start: 0.8972 (t70) cc_final: 0.8640 (t0) REVERT: A 397 SER cc_start: 0.9039 (t) cc_final: 0.8559 (p) REVERT: B 245 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8485 (t0) REVERT: B 268 MET cc_start: 0.7147 (mmm) cc_final: 0.6907 (ttt) REVERT: B 386 THR cc_start: 0.8689 (m) cc_final: 0.8427 (p) REVERT: E 106 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8219 (ptt) REVERT: E 127 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9104 (tt) REVERT: E 253 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7669 (ttm-80) REVERT: E 460 SER cc_start: 0.9318 (t) cc_final: 0.9047 (p) REVERT: C 83 LYS cc_start: 0.8699 (tmmt) cc_final: 0.8471 (tmtt) REVERT: C 197 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8307 (mm-30) REVERT: C 215 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8774 (mm110) REVERT: C 459 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.8819 (m-10) REVERT: D 392 MET cc_start: 0.8517 (tpp) cc_final: 0.8245 (tpp) outliers start: 46 outliers final: 25 residues processed: 279 average time/residue: 0.1010 time to fit residues: 46.5693 Evaluate side-chains 252 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 348 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 163 optimal weight: 0.4980 chunk 25 optimal weight: 0.0040 chunk 176 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN A 308 GLN B 154 GLN E 82 ASN D 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.098385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.077655 restraints weight = 31246.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.079870 restraints weight = 18291.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.081355 restraints weight = 12743.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.082334 restraints weight = 10007.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.082880 restraints weight = 8558.015| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18152 Z= 0.112 Angle : 0.506 8.974 24732 Z= 0.256 Chirality : 0.044 0.136 2724 Planarity : 0.004 0.044 3194 Dihedral : 3.968 33.810 2460 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.87 % Allowed : 26.32 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.17), residues: 2227 helix: 1.40 (0.39), residues: 189 sheet: -0.38 (0.19), residues: 672 loop : -0.88 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.019 0.001 TYR C 92 PHE 0.010 0.001 PHE A 257 TRP 0.012 0.001 TRP L 34 HIS 0.004 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00271 (18151) covalent geometry : angle 0.50558 (24730) SS BOND : bond 0.00457 ( 1) SS BOND : angle 0.63853 ( 2) hydrogen bonds : bond 0.02907 ( 272) hydrogen bonds : angle 4.75201 ( 738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 236 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 193 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8830 (m-40) REVERT: A 204 THR cc_start: 0.9047 (p) cc_final: 0.8777 (p) REVERT: A 228 SER cc_start: 0.9327 (t) cc_final: 0.9061 (t) REVERT: A 375 ASP cc_start: 0.8972 (t70) cc_final: 0.8609 (t0) REVERT: A 408 PHE cc_start: 0.8137 (t80) cc_final: 0.7658 (t80) REVERT: B 212 SER cc_start: 0.8686 (p) cc_final: 0.8424 (p) REVERT: B 220 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7216 (mm-30) REVERT: B 245 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8491 (t0) REVERT: B 386 THR cc_start: 0.8729 (m) cc_final: 0.8488 (p) REVERT: E 106 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8190 (ptt) REVERT: E 127 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9090 (tt) REVERT: E 253 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7459 (ttt90) REVERT: E 460 SER cc_start: 0.9297 (t) cc_final: 0.9061 (p) REVERT: C 83 LYS cc_start: 0.8721 (tmmt) cc_final: 0.8479 (tmtt) REVERT: C 197 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7956 (mm-30) REVERT: C 459 PHE cc_start: 0.9396 (OUTLIER) cc_final: 0.8798 (m-10) REVERT: D 121 HIS cc_start: 0.8767 (OUTLIER) cc_final: 0.7566 (t-90) REVERT: D 392 MET cc_start: 0.8506 (tpp) cc_final: 0.8208 (tpp) outliers start: 75 outliers final: 49 residues processed: 296 average time/residue: 0.0966 time to fit residues: 47.6990 Evaluate side-chains 275 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 HIS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 406 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 101 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN E 134 HIS C 399 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.095106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.074316 restraints weight = 31836.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.076443 restraints weight = 18869.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.077872 restraints weight = 13312.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.078736 restraints weight = 10566.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.079387 restraints weight = 9130.582| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 18152 Z= 0.248 Angle : 0.599 12.944 24732 Z= 0.307 Chirality : 0.046 0.144 2724 Planarity : 0.004 0.048 3194 Dihedral : 4.404 35.961 2460 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.68 % Allowed : 25.23 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.17), residues: 2227 helix: 1.41 (0.40), residues: 188 sheet: -0.49 (0.19), residues: 694 loop : -1.06 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.022 0.001 TYR E 152 PHE 0.017 0.002 PHE A 257 TRP 0.011 0.001 TRP A 328 HIS 0.006 0.001 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00594 (18151) covalent geometry : angle 0.59918 (24730) SS BOND : bond 0.00344 ( 1) SS BOND : angle 0.37672 ( 2) hydrogen bonds : bond 0.03716 ( 272) hydrogen bonds : angle 5.07991 ( 738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 219 time to evaluate : 0.635 Fit side-chains REVERT: A 41 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7818 (mtm180) REVERT: A 193 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8853 (m-40) REVERT: A 204 THR cc_start: 0.9080 (p) cc_final: 0.8797 (p) REVERT: A 210 ASP cc_start: 0.7734 (p0) cc_final: 0.7487 (p0) REVERT: A 228 SER cc_start: 0.9382 (t) cc_final: 0.9080 (t) REVERT: B 97 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8835 (mm-40) REVERT: B 245 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8596 (t0) REVERT: B 386 THR cc_start: 0.8800 (m) cc_final: 0.8543 (p) REVERT: E 460 SER cc_start: 0.9336 (t) cc_final: 0.9052 (p) REVERT: C 83 LYS cc_start: 0.8705 (tmmt) cc_final: 0.8479 (tmtt) REVERT: C 197 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8563 (mm-30) REVERT: C 459 PHE cc_start: 0.9451 (OUTLIER) cc_final: 0.8870 (m-10) REVERT: D 121 HIS cc_start: 0.8788 (OUTLIER) cc_final: 0.7663 (t-90) REVERT: D 375 ASP cc_start: 0.9096 (t0) cc_final: 0.8886 (t0) REVERT: D 392 MET cc_start: 0.8635 (tpp) cc_final: 0.8346 (tpp) outliers start: 110 outliers final: 86 residues processed: 305 average time/residue: 0.1024 time to fit residues: 51.7525 Evaluate side-chains 301 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 208 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 385 ILE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 406 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 75 optimal weight: 1.9990 chunk 159 optimal weight: 0.0980 chunk 223 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 199 optimal weight: 0.1980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.098671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.078038 restraints weight = 30931.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.080221 restraints weight = 18146.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.081573 restraints weight = 12703.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.082637 restraints weight = 10121.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.083161 restraints weight = 8610.442| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18152 Z= 0.102 Angle : 0.520 13.383 24732 Z= 0.262 Chirality : 0.043 0.143 2724 Planarity : 0.004 0.042 3194 Dihedral : 4.006 34.267 2460 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.18 % Allowed : 27.04 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.17), residues: 2227 helix: 1.44 (0.39), residues: 188 sheet: -0.35 (0.20), residues: 644 loop : -0.94 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.018 0.001 TYR E 152 PHE 0.014 0.001 PHE H 29 TRP 0.010 0.001 TRP L 34 HIS 0.003 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00243 (18151) covalent geometry : angle 0.52013 (24730) SS BOND : bond 0.00574 ( 1) SS BOND : angle 0.58142 ( 2) hydrogen bonds : bond 0.02766 ( 272) hydrogen bonds : angle 4.68502 ( 738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 234 time to evaluate : 0.599 Fit side-chains REVERT: A 41 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7813 (mtm180) REVERT: A 185 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7609 (p0) REVERT: A 193 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8814 (m-40) REVERT: A 204 THR cc_start: 0.9021 (p) cc_final: 0.8726 (p) REVERT: A 210 ASP cc_start: 0.7696 (p0) cc_final: 0.7480 (p0) REVERT: A 228 SER cc_start: 0.9354 (t) cc_final: 0.9074 (t) REVERT: A 375 ASP cc_start: 0.8901 (t70) cc_final: 0.8566 (t0) REVERT: A 408 PHE cc_start: 0.8236 (t80) cc_final: 0.7718 (t80) REVERT: B 212 SER cc_start: 0.8657 (p) cc_final: 0.8387 (p) REVERT: B 220 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7354 (mm-30) REVERT: B 245 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8481 (t0) REVERT: E 106 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8268 (ptt) REVERT: E 127 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9084 (tt) REVERT: E 460 SER cc_start: 0.9267 (t) cc_final: 0.9030 (p) REVERT: C 197 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: C 459 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.8821 (m-10) REVERT: D 121 HIS cc_start: 0.8741 (OUTLIER) cc_final: 0.7610 (t-90) REVERT: D 220 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8121 (mm-30) REVERT: D 392 MET cc_start: 0.8464 (tpp) cc_final: 0.8215 (tpp) outliers start: 81 outliers final: 60 residues processed: 295 average time/residue: 0.1023 time to fit residues: 49.6320 Evaluate side-chains 287 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 218 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 HIS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 406 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 116 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 159 optimal weight: 0.3980 chunk 212 optimal weight: 4.9990 chunk 30 optimal weight: 0.0020 chunk 205 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 222 optimal weight: 0.2980 chunk 167 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN D 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.099226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.078609 restraints weight = 31170.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.080823 restraints weight = 18191.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.082182 restraints weight = 12673.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.083251 restraints weight = 10079.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.083796 restraints weight = 8564.237| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18152 Z= 0.119 Angle : 0.529 14.290 24732 Z= 0.266 Chirality : 0.044 0.139 2724 Planarity : 0.004 0.042 3194 Dihedral : 3.938 32.347 2460 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.59 % Allowed : 27.19 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.18), residues: 2227 helix: 1.55 (0.39), residues: 188 sheet: -0.31 (0.20), residues: 648 loop : -0.90 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 145 TYR 0.025 0.001 TYR E 152 PHE 0.010 0.001 PHE H 29 TRP 0.009 0.001 TRP B 262 HIS 0.005 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00288 (18151) covalent geometry : angle 0.52896 (24730) SS BOND : bond 0.00473 ( 1) SS BOND : angle 0.51604 ( 2) hydrogen bonds : bond 0.02786 ( 272) hydrogen bonds : angle 4.60109 ( 738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 225 time to evaluate : 0.715 Fit side-chains REVERT: A 41 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7823 (mtm180) REVERT: A 185 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7641 (p0) REVERT: A 204 THR cc_start: 0.9031 (p) cc_final: 0.8752 (p) REVERT: A 228 SER cc_start: 0.9327 (t) cc_final: 0.9051 (t) REVERT: A 268 MET cc_start: 0.7190 (ttt) cc_final: 0.6986 (mtt) REVERT: B 212 SER cc_start: 0.8670 (p) cc_final: 0.8402 (p) REVERT: B 220 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7418 (mm-30) REVERT: B 245 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8455 (t0) REVERT: E 106 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8203 (ptt) REVERT: E 127 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9098 (tt) REVERT: E 460 SER cc_start: 0.9256 (t) cc_final: 0.9021 (p) REVERT: C 197 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8018 (mm-30) REVERT: C 459 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.8809 (m-10) REVERT: D 121 HIS cc_start: 0.8743 (OUTLIER) cc_final: 0.7623 (t-90) REVERT: D 220 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8090 (mm-30) REVERT: D 392 MET cc_start: 0.8532 (tpp) cc_final: 0.8253 (tpp) REVERT: D 398 MET cc_start: 0.8733 (ttt) cc_final: 0.8461 (ttm) outliers start: 89 outliers final: 72 residues processed: 294 average time/residue: 0.1030 time to fit residues: 50.5592 Evaluate side-chains 300 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 220 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 406 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 104 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN C 255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.096338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.075852 restraints weight = 31515.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.077950 restraints weight = 18594.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.079359 restraints weight = 13105.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.080173 restraints weight = 10387.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.080852 restraints weight = 8998.533| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18152 Z= 0.219 Angle : 0.604 15.210 24732 Z= 0.307 Chirality : 0.045 0.141 2724 Planarity : 0.004 0.046 3194 Dihedral : 4.335 35.002 2460 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.88 % Allowed : 26.01 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.17), residues: 2227 helix: 1.50 (0.40), residues: 188 sheet: -0.52 (0.19), residues: 690 loop : -1.01 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.024 0.001 TYR E 152 PHE 0.015 0.001 PHE A 257 TRP 0.011 0.001 TRP A 328 HIS 0.006 0.001 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00526 (18151) covalent geometry : angle 0.60422 (24730) SS BOND : bond 0.00382 ( 1) SS BOND : angle 0.36348 ( 2) hydrogen bonds : bond 0.03437 ( 272) hydrogen bonds : angle 4.89640 ( 738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 217 time to evaluate : 0.493 Fit side-chains REVERT: A 41 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7808 (mtm180) REVERT: A 193 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8855 (m-40) REVERT: A 228 SER cc_start: 0.9388 (t) cc_final: 0.9088 (t) REVERT: B 245 ASP cc_start: 0.8996 (OUTLIER) cc_final: 0.8598 (t0) REVERT: B 386 THR cc_start: 0.8751 (m) cc_final: 0.8460 (p) REVERT: E 33 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8899 (tp) REVERT: E 127 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9092 (tt) REVERT: E 460 SER cc_start: 0.9290 (t) cc_final: 0.9020 (p) REVERT: C 71 TYR cc_start: 0.9382 (m-80) cc_final: 0.8881 (m-80) REVERT: C 197 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8588 (mm-30) REVERT: C 459 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.8852 (m-10) REVERT: D 121 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.7614 (t-90) REVERT: D 220 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8166 (mm-30) REVERT: D 392 MET cc_start: 0.8546 (tpp) cc_final: 0.8299 (tpp) outliers start: 114 outliers final: 93 residues processed: 310 average time/residue: 0.0981 time to fit residues: 51.1552 Evaluate side-chains 313 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 212 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 36 HIS Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 385 ILE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 406 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 134 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 70 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 193 optimal weight: 0.5980 chunk 119 optimal weight: 0.0000 chunk 122 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN C 255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.099394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.078652 restraints weight = 30879.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.080876 restraints weight = 18030.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.082375 restraints weight = 12546.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.083233 restraints weight = 9854.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.083936 restraints weight = 8487.058| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 18152 Z= 0.098 Angle : 0.537 14.139 24732 Z= 0.270 Chirality : 0.044 0.146 2724 Planarity : 0.004 0.045 3194 Dihedral : 3.869 32.728 2460 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.33 % Allowed : 27.86 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.17), residues: 2227 helix: 1.48 (0.39), residues: 189 sheet: -0.27 (0.20), residues: 650 loop : -0.90 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 264 TYR 0.024 0.001 TYR E 152 PHE 0.009 0.001 PHE H 29 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00234 (18151) covalent geometry : angle 0.53682 (24730) SS BOND : bond 0.00492 ( 1) SS BOND : angle 0.45901 ( 2) hydrogen bonds : bond 0.02513 ( 272) hydrogen bonds : angle 4.50886 ( 738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 239 time to evaluate : 0.639 Fit side-chains REVERT: A 41 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7815 (mtm180) REVERT: A 185 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.7610 (p0) REVERT: A 228 SER cc_start: 0.9340 (t) cc_final: 0.9057 (t) REVERT: A 375 ASP cc_start: 0.8945 (t70) cc_final: 0.8600 (t0) REVERT: B 212 SER cc_start: 0.8772 (p) cc_final: 0.8511 (p) REVERT: B 220 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7393 (mm-30) REVERT: B 245 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8408 (t0) REVERT: B 256 LEU cc_start: 0.9114 (tp) cc_final: 0.8772 (tp) REVERT: B 366 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8563 (mm-40) REVERT: E 106 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8052 (ptt) REVERT: E 127 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9034 (tt) REVERT: C 197 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: C 459 PHE cc_start: 0.9389 (OUTLIER) cc_final: 0.8686 (m-10) REVERT: D 121 HIS cc_start: 0.8684 (OUTLIER) cc_final: 0.7574 (t-90) REVERT: D 392 MET cc_start: 0.8495 (tpp) cc_final: 0.8235 (tpp) REVERT: D 479 ARG cc_start: 0.4084 (mtt90) cc_final: 0.3449 (mtm180) outliers start: 84 outliers final: 70 residues processed: 303 average time/residue: 0.1019 time to fit residues: 51.2603 Evaluate side-chains 304 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 226 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 36 HIS Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 406 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 152 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 174 optimal weight: 0.2980 chunk 221 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 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 = 0.2995 r_free = 0.2995 target = 0.098320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.077809 restraints weight = 31158.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.079974 restraints weight = 18299.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.081397 restraints weight = 12802.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.082371 restraints weight = 10120.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.082901 restraints weight = 8672.779| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18152 Z= 0.158 Angle : 0.570 14.609 24732 Z= 0.288 Chirality : 0.044 0.178 2724 Planarity : 0.004 0.043 3194 Dihedral : 4.026 32.684 2460 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.49 % Allowed : 27.86 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.18), residues: 2227 helix: 1.37 (0.39), residues: 194 sheet: -0.35 (0.19), residues: 675 loop : -0.92 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 252 TYR 0.024 0.001 TYR E 152 PHE 0.011 0.001 PHE A 257 TRP 0.010 0.001 TRP B 262 HIS 0.004 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00381 (18151) covalent geometry : angle 0.57044 (24730) SS BOND : bond 0.00355 ( 1) SS BOND : angle 0.05371 ( 2) hydrogen bonds : bond 0.02931 ( 272) hydrogen bonds : angle 4.63144 ( 738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 226 time to evaluate : 0.691 Fit side-chains REVERT: A 41 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7819 (mtm180) REVERT: A 228 SER cc_start: 0.9342 (t) cc_final: 0.9057 (t) REVERT: B 212 SER cc_start: 0.8813 (p) cc_final: 0.8545 (p) REVERT: B 245 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8502 (t0) REVERT: B 268 MET cc_start: 0.7043 (mmm) cc_final: 0.6625 (ttt) REVERT: B 363 LYS cc_start: 0.8994 (mttt) cc_final: 0.8651 (mttp) REVERT: B 366 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8548 (mm-40) REVERT: E 127 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9075 (tt) REVERT: C 197 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8051 (mm-30) REVERT: C 459 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.8806 (m-10) REVERT: D 121 HIS cc_start: 0.8726 (OUTLIER) cc_final: 0.7586 (t-90) REVERT: D 392 MET cc_start: 0.8508 (tpp) cc_final: 0.8249 (tpp) outliers start: 87 outliers final: 78 residues processed: 294 average time/residue: 0.1017 time to fit residues: 49.9510 Evaluate side-chains 311 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 227 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 36 HIS Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 406 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 145 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 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 = 0.2981 r_free = 0.2981 target = 0.097273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.076848 restraints weight = 31533.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.079011 restraints weight = 18493.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.080336 restraints weight = 12914.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.081364 restraints weight = 10287.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.081939 restraints weight = 8771.178| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18152 Z= 0.186 Angle : 0.592 14.598 24732 Z= 0.300 Chirality : 0.045 0.151 2724 Planarity : 0.004 0.044 3194 Dihedral : 4.238 33.426 2460 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.70 % Allowed : 27.55 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.18), residues: 2227 helix: 1.35 (0.40), residues: 193 sheet: -0.47 (0.19), residues: 692 loop : -0.99 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.024 0.001 TYR E 152 PHE 0.013 0.001 PHE A 257 TRP 0.010 0.001 TRP L 34 HIS 0.006 0.001 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00448 (18151) covalent geometry : angle 0.59217 (24730) SS BOND : bond 0.00349 ( 1) SS BOND : angle 0.09316 ( 2) hydrogen bonds : bond 0.03177 ( 272) hydrogen bonds : angle 4.77301 ( 738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2388.62 seconds wall clock time: 42 minutes 42.40 seconds (2562.40 seconds total)