Starting phenix.real_space_refine on Sun Jun 7 07:44:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o4c_70094/06_2026/9o4c_70094.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o4c_70094/06_2026/9o4c_70094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o4c_70094/06_2026/9o4c_70094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o4c_70094/06_2026/9o4c_70094.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o4c_70094/06_2026/9o4c_70094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o4c_70094/06_2026/9o4c_70094.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 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 176 5.16 5 C 22273 2.51 5 N 5995 2.21 5 O 6382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34826 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3320 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3328 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3336 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3340 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3340 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3340 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "G" Number of atoms: 3316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3316 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 403} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3332 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "J" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "K" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1018 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 113} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1018 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 113} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1021 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 113} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1021 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 113} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "P" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Time building chain proxies: 8.95, per 1000 atoms: 0.26 Number of scatterers: 34826 At special positions: 0 Unit cell: (142.31, 144.45, 126.26, 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 176 16.00 O 6382 8.00 N 5995 7.00 C 22273 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS B 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 247 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS D 247 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 247 " - pdb=" SG CYS H 247 " 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: 3.37 Conformation dependent library (CDL) restraints added in 1.6 seconds 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8032 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 32 sheets defined 45.3% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 49 through 63 removed outlier: 3.939A pdb=" N SER A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 153 through 163 removed outlier: 4.145A pdb=" N VAL A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.635A pdb=" N GLY A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.514A pdb=" N ARG A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.672A pdb=" N LEU A 314 " --> pdb=" O HIS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 412 through 433 Processing helix chain 'A' and resid 436 through 450 removed outlier: 6.297A pdb=" N ASN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 462 Processing helix chain 'B' and resid 49 through 61 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 112 through 122 Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.930A pdb=" N VAL B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 213 through 233 Processing helix chain 'B' and resid 246 through 261 Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 297 through 302 removed outlier: 4.215A pdb=" N ILE B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.635A pdb=" N LEU B 314 " --> pdb=" O HIS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 351 Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 412 through 433 Processing helix chain 'B' and resid 436 through 452 removed outlier: 7.096A pdb=" N ASN B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 462 Processing helix chain 'C' and resid 49 through 63 Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.518A pdb=" N PHE C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 122 Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 153 through 163 removed outlier: 4.109A pdb=" N VAL C 157 " --> pdb=" O HIS C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.621A pdb=" N GLY C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 Processing helix chain 'C' and resid 246 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 273 through 288 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 310 through 322 removed outlier: 3.757A pdb=" N LEU C 314 " --> pdb=" O HIS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 351 Processing helix chain 'C' and resid 383 through 385 No H-bonds generated for 'chain 'C' and resid 383 through 385' Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 412 through 433 Processing helix chain 'C' and resid 436 through 450 removed outlier: 6.804A pdb=" N ASN C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 462 Processing helix chain 'D' and resid 49 through 63 Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 153 through 163 removed outlier: 4.133A pdb=" N VAL D 157 " --> pdb=" O HIS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.605A pdb=" N GLY D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 233 Processing helix chain 'D' and resid 246 through 261 Processing helix chain 'D' and resid 268 through 273 Processing helix chain 'D' and resid 273 through 288 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 310 through 322 removed outlier: 3.649A pdb=" N LEU D 314 " --> pdb=" O HIS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 351 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 386 through 394 Processing helix chain 'D' and resid 412 through 433 Processing helix chain 'D' and resid 436 through 450 removed outlier: 6.705A pdb=" N ASN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLU D 443 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 462 Processing helix chain 'E' and resid 49 through 63 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 112 through 122 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 141 through 146 Processing helix chain 'E' and resid 153 through 163 removed outlier: 4.136A pdb=" N VAL E 157 " --> pdb=" O HIS E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 213 through 233 Processing helix chain 'E' and resid 246 through 261 Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 298 through 303 removed outlier: 3.553A pdb=" N ARG E 303 " --> pdb=" O ALA E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 322 removed outlier: 3.659A pdb=" N LEU E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 351 Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 383 through 385 No H-bonds generated for 'chain 'E' and resid 383 through 385' Processing helix chain 'E' and resid 386 through 395 Processing helix chain 'E' and resid 412 through 433 Processing helix chain 'E' and resid 436 through 450 removed outlier: 7.163A pdb=" N ASN E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU E 443 " --> pdb=" O VAL E 439 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS E 450 " --> pdb=" O ARG E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 463 Processing helix chain 'F' and resid 49 through 63 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 112 through 121 Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 153 through 163 removed outlier: 4.214A pdb=" N VAL F 157 " --> pdb=" O HIS F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 195 removed outlier: 3.621A pdb=" N GLY F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 Processing helix chain 'F' and resid 246 through 261 Processing helix chain 'F' and resid 268 through 273 Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 310 through 322 removed outlier: 3.724A pdb=" N LEU F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 351 Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 386 through 394 Processing helix chain 'F' and resid 412 through 434 Processing helix chain 'F' and resid 436 through 450 removed outlier: 6.766A pdb=" N ASN F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLU F 443 " --> pdb=" O VAL F 439 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS F 450 " --> pdb=" O ARG F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 462 Processing helix chain 'G' and resid 49 through 63 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'G' and resid 112 through 121 Processing helix chain 'G' and resid 123 through 127 Processing helix chain 'G' and resid 141 through 146 Processing helix chain 'G' and resid 153 through 163 removed outlier: 4.167A pdb=" N VAL G 157 " --> pdb=" O HIS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 195 removed outlier: 3.592A pdb=" N GLY G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 233 Processing helix chain 'G' and resid 246 through 261 Processing helix chain 'G' and resid 268 through 273 Processing helix chain 'G' and resid 273 through 288 Processing helix chain 'G' and resid 298 through 303 removed outlier: 3.610A pdb=" N ARG G 303 " --> pdb=" O ALA G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.710A pdb=" N LEU G 314 " --> pdb=" O HIS G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 351 Processing helix chain 'G' and resid 383 through 385 No H-bonds generated for 'chain 'G' and resid 383 through 385' Processing helix chain 'G' and resid 386 through 394 Processing helix chain 'G' and resid 412 through 434 removed outlier: 3.631A pdb=" N GLY G 416 " --> pdb=" O GLY G 412 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 452 removed outlier: 6.860A pdb=" N ASN G 442 " --> pdb=" O ALA G 438 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLU G 443 " --> pdb=" O VAL G 439 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TRP G 451 " --> pdb=" O GLU G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 462 Processing helix chain 'H' and resid 49 through 63 Processing helix chain 'H' and resid 104 through 108 Processing helix chain 'H' and resid 112 through 122 Processing helix chain 'H' and resid 141 through 146 Processing helix chain 'H' and resid 153 through 163 removed outlier: 4.142A pdb=" N VAL H 157 " --> pdb=" O HIS H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 195 removed outlier: 3.661A pdb=" N GLY H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 233 Processing helix chain 'H' and resid 246 through 261 Processing helix chain 'H' and resid 268 through 273 Processing helix chain 'H' and resid 273 through 288 Processing helix chain 'H' and resid 298 through 303 removed outlier: 3.579A pdb=" N ARG H 303 " --> pdb=" O ALA H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 322 removed outlier: 3.768A pdb=" N LEU H 314 " --> pdb=" O HIS H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 351 Processing helix chain 'H' and resid 357 through 361 Processing helix chain 'H' and resid 383 through 385 No H-bonds generated for 'chain 'H' and resid 383 through 385' Processing helix chain 'H' and resid 386 through 395 Processing helix chain 'H' and resid 412 through 433 Processing helix chain 'H' and resid 436 through 450 removed outlier: 7.095A pdb=" N ASN H 442 " --> pdb=" O ALA H 438 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLU H 443 " --> pdb=" O VAL H 439 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS H 450 " --> pdb=" O ARG H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 462 Processing helix chain 'I' and resid 77 through 91 Processing helix chain 'I' and resid 134 through 149 removed outlier: 4.109A pdb=" N VAL I 138 " --> pdb=" O ASP I 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 91 Processing helix chain 'J' and resid 134 through 149 removed outlier: 3.998A pdb=" N VAL J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 91 Processing helix chain 'K' and resid 134 through 149 removed outlier: 4.086A pdb=" N VAL K 138 " --> pdb=" O ASP K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 91 Processing helix chain 'L' and resid 134 through 149 removed outlier: 4.051A pdb=" N VAL L 138 " --> pdb=" O ASP L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 91 Processing helix chain 'M' and resid 134 through 149 removed outlier: 4.093A pdb=" N VAL M 138 " --> pdb=" O ASP M 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 91 Processing helix chain 'N' and resid 134 through 149 removed outlier: 4.171A pdb=" N VAL N 138 " --> pdb=" O ASP N 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 91 Processing helix chain 'O' and resid 134 through 149 removed outlier: 4.175A pdb=" N VAL O 138 " --> pdb=" O ASP O 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 91 Processing helix chain 'P' and resid 134 through 149 removed outlier: 3.971A pdb=" N VAL P 138 " --> pdb=" O ASP P 134 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 5.756A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 137 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 41 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU A 135 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR A 43 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU A 133 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 174 removed outlier: 6.156A pdb=" N ASN A 241 " --> pdb=" O ASP A 202 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N HIS A 238 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N MET A 266 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU A 240 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N HIS A 325 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A 377 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N HIS A 327 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER A 379 " --> pdb=" O HIS A 327 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLY A 329 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU A 169 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.015A pdb=" N CYS B 84 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ALA B 102 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS B 86 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 37 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU B 138 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA B 39 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N GLY B 308 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU B 133 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 174 removed outlier: 7.529A pdb=" N THR B 200 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ASN B 241 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N ASP B 202 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N HIS B 238 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N MET B 266 " --> pdb=" O HIS B 238 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU B 240 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL B 265 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU B 375 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N HIS B 327 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL B 377 " --> pdb=" O HIS B 327 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 329 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY B 380 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 169 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AA7, first strand: chain 'C' and resid 83 through 89 removed outlier: 5.907A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU C 37 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 169 through 174 removed outlier: 7.550A pdb=" N THR C 200 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ASN C 241 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ASP C 202 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N HIS C 238 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N MET C 266 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 240 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASP C 268 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER C 379 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR C 330 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLY C 381 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL C 332 " --> pdb=" O GLY C 381 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY C 380 " --> pdb=" O GLN C 401 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 169 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AB1, first strand: chain 'D' and resid 83 through 89 removed outlier: 5.736A pdb=" N CYS D 84 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA D 102 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS D 86 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU D 37 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU D 138 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA D 39 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 290 through 293 removed outlier: 5.120A pdb=" N HIS D 238 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N MET D 266 " --> pdb=" O HIS D 238 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU D 240 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR D 200 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN D 241 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ASP D 202 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU D 169 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY D 380 " --> pdb=" O GLN D 401 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU D 375 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N HIS D 327 " --> pdb=" O LEU D 375 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL D 377 " --> pdb=" O HIS D 327 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY D 329 " --> pdb=" O VAL D 377 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AB4, first strand: chain 'E' and resid 83 through 89 removed outlier: 6.869A pdb=" N TYR E 100 " --> pdb=" O TYR E 85 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE E 87 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE E 98 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU E 37 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU E 138 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA E 39 " --> pdb=" O GLU E 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 169 through 174 removed outlier: 7.532A pdb=" N THR E 200 " --> pdb=" O TYR E 239 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASN E 241 " --> pdb=" O THR E 200 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASP E 202 " --> pdb=" O ASN E 241 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N HIS E 238 " --> pdb=" O ILE E 264 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N MET E 266 " --> pdb=" O HIS E 238 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU E 240 " --> pdb=" O MET E 266 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ASP E 268 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL E 265 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N HIS E 294 " --> pdb=" O VAL E 265 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N HIS E 267 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS E 325 " --> pdb=" O LEU E 375 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL E 377 " --> pdb=" O HIS E 325 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N HIS E 327 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N SER E 379 " --> pdb=" O HIS E 327 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY E 329 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLY E 381 " --> pdb=" O GLY E 329 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL E 331 " --> pdb=" O GLY E 381 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY E 380 " --> pdb=" O GLN E 401 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU E 169 " --> pdb=" O LEU E 400 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AB7, first strand: chain 'F' and resid 83 through 89 removed outlier: 5.861A pdb=" N CYS F 84 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA F 102 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS F 86 " --> pdb=" O TYR F 100 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU F 37 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU F 138 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA F 39 " --> pdb=" O GLU F 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 169 through 174 removed outlier: 7.446A pdb=" N THR F 200 " --> pdb=" O TYR F 239 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASN F 241 " --> pdb=" O THR F 200 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ASP F 202 " --> pdb=" O ASN F 241 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N HIS F 238 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N MET F 266 " --> pdb=" O HIS F 238 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU F 240 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N HIS F 325 " --> pdb=" O LEU F 375 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL F 377 " --> pdb=" O HIS F 325 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N HIS F 327 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N SER F 379 " --> pdb=" O HIS F 327 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY F 329 " --> pdb=" O SER F 379 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N GLY F 381 " --> pdb=" O GLY F 329 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL F 331 " --> pdb=" O GLY F 381 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLN F 401 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA F 378 " --> pdb=" O GLN F 401 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU F 169 " --> pdb=" O LEU F 400 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AC1, first strand: chain 'G' and resid 83 through 89 removed outlier: 6.681A pdb=" N TYR G 100 " --> pdb=" O TYR G 85 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE G 87 " --> pdb=" O ILE G 98 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE G 98 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP G 137 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG G 41 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU G 135 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR G 43 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU G 133 " --> pdb=" O THR G 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 169 through 174 removed outlier: 7.533A pdb=" N THR G 200 " --> pdb=" O TYR G 239 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ASN G 241 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ASP G 202 " --> pdb=" O ASN G 241 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N HIS G 238 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N MET G 266 " --> pdb=" O HIS G 238 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU G 240 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL G 265 " --> pdb=" O HIS G 292 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER G 379 " --> pdb=" O ALA G 328 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR G 330 " --> pdb=" O SER G 379 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLN G 401 " --> pdb=" O PRO G 376 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ALA G 378 " --> pdb=" O GLN G 401 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY G 403 " --> pdb=" O ALA G 378 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLY G 380 " --> pdb=" O GLY G 403 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU G 169 " --> pdb=" O LEU G 400 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N PHE G 402 " --> pdb=" O LEU G 169 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLY G 171 " --> pdb=" O PHE G 402 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 353 through 354 Processing sheet with id=AC4, first strand: chain 'H' and resid 83 through 89 removed outlier: 5.696A pdb=" N CYS H 84 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA H 102 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS H 86 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP H 137 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG H 41 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU H 135 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR H 43 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU H 133 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N GLY H 308 " --> pdb=" O ALA H 131 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU H 133 " --> pdb=" O GLY H 308 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 169 through 174 removed outlier: 7.598A pdb=" N THR H 200 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASN H 241 " --> pdb=" O THR H 200 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ASP H 202 " --> pdb=" O ASN H 241 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N HIS H 238 " --> pdb=" O ILE H 264 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N MET H 266 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU H 240 " --> pdb=" O MET H 266 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU H 291 " --> pdb=" O HIS H 325 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N HIS H 327 " --> pdb=" O LEU H 291 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE H 293 " --> pdb=" O HIS H 327 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N GLY H 329 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N SER H 379 " --> pdb=" O ALA H 328 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR H 330 " --> pdb=" O SER H 379 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU H 169 " --> pdb=" O LEU H 400 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 353 through 354 Processing sheet with id=AC7, first strand: chain 'I' and resid 123 through 124 removed outlier: 7.707A pdb=" N ILE I 154 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE I 171 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE I 156 " --> pdb=" O SER I 169 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER I 169 " --> pdb=" O ILE I 156 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY I 158 " --> pdb=" O CYS I 167 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 123 through 125 removed outlier: 4.807A pdb=" N VAL J 97 " --> pdb=" O TRP J 125 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE J 154 " --> pdb=" O ILE J 171 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE J 171 " --> pdb=" O ILE J 154 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE J 156 " --> pdb=" O SER J 169 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER J 169 " --> pdb=" O ILE J 156 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY J 158 " --> pdb=" O CYS J 167 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 123 through 125 removed outlier: 4.742A pdb=" N VAL K 97 " --> pdb=" O TRP K 125 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE K 154 " --> pdb=" O ILE K 171 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE K 171 " --> pdb=" O ILE K 154 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE K 156 " --> pdb=" O SER K 169 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER K 169 " --> pdb=" O ILE K 156 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY K 158 " --> pdb=" O CYS K 167 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 123 through 125 removed outlier: 4.742A pdb=" N VAL L 97 " --> pdb=" O TRP L 125 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE L 154 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE L 171 " --> pdb=" O ILE L 154 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE L 156 " --> pdb=" O SER L 169 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER L 169 " --> pdb=" O ILE L 156 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY L 158 " --> pdb=" O CYS L 167 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 123 through 125 removed outlier: 4.764A pdb=" N VAL M 97 " --> pdb=" O TRP M 125 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE M 154 " --> pdb=" O ILE M 171 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE M 171 " --> pdb=" O ILE M 154 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE M 156 " --> pdb=" O SER M 169 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER M 169 " --> pdb=" O ILE M 156 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY M 158 " --> pdb=" O CYS M 167 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 123 through 125 removed outlier: 4.685A pdb=" N VAL N 97 " --> pdb=" O TRP N 125 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE N 154 " --> pdb=" O ALA N 172 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE N 168 " --> pdb=" O GLY N 158 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASP N 160 " --> pdb=" O GLN N 166 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLN N 166 " --> pdb=" O ASP N 160 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 123 through 125 removed outlier: 4.772A pdb=" N VAL O 97 " --> pdb=" O TRP O 125 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE O 154 " --> pdb=" O ILE O 171 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ILE O 171 " --> pdb=" O ILE O 154 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE O 156 " --> pdb=" O SER O 169 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER O 169 " --> pdb=" O ILE O 156 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY O 158 " --> pdb=" O CYS O 167 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 123 through 125 removed outlier: 4.740A pdb=" N VAL P 97 " --> pdb=" O TRP P 125 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE P 154 " --> pdb=" O ILE P 171 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE P 171 " --> pdb=" O ILE P 154 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE P 156 " --> pdb=" O SER P 169 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER P 169 " --> pdb=" O ILE P 156 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY P 158 " --> pdb=" O CYS P 167 " (cutoff:3.500A) 1659 hydrogen bonds defined for protein. 4635 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: 8.34 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11449 1.34 - 1.46: 8279 1.46 - 1.58: 15774 1.58 - 1.70: 0 1.70 - 1.81: 248 Bond restraints: 35750 Sorted by residual: bond pdb=" N MET G 387 " pdb=" CA MET G 387 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.49e+00 bond pdb=" N VAL G 399 " pdb=" CA VAL G 399 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.95e+00 bond pdb=" N VAL G 384 " pdb=" CA VAL G 384 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.36e+00 bond pdb=" N LEU G 170 " pdb=" CA LEU G 170 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.15e-02 7.56e+03 8.32e+00 bond pdb=" N ILE F 235 " pdb=" CA ILE F 235 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.27e-02 6.20e+03 8.10e+00 ... (remaining 35745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 46292 1.12 - 2.25: 1649 2.25 - 3.37: 438 3.37 - 4.49: 73 4.49 - 5.62: 36 Bond angle restraints: 48488 Sorted by residual: angle pdb=" C GLU N 68 " pdb=" CA GLU N 68 " pdb=" CB GLU N 68 " ideal model delta sigma weight residual 116.63 111.01 5.62 1.16e+00 7.43e-01 2.34e+01 angle pdb=" N ASN I 91 " pdb=" CA ASN I 91 " pdb=" C ASN I 91 " ideal model delta sigma weight residual 113.15 108.39 4.76 1.19e+00 7.06e-01 1.60e+01 angle pdb=" N SER N 71 " pdb=" CA SER N 71 " pdb=" C SER N 71 " ideal model delta sigma weight residual 114.12 109.08 5.04 1.39e+00 5.18e-01 1.31e+01 angle pdb=" N TYR N 72 " pdb=" CA TYR N 72 " pdb=" C TYR N 72 " ideal model delta sigma weight residual 113.17 108.69 4.48 1.26e+00 6.30e-01 1.26e+01 angle pdb=" CA GLY G 380 " pdb=" C GLY G 380 " pdb=" O GLY G 380 " ideal model delta sigma weight residual 122.59 118.21 4.38 1.27e+00 6.20e-01 1.19e+01 ... (remaining 48483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 19898 17.83 - 35.67: 976 35.67 - 53.50: 129 53.50 - 71.34: 25 71.34 - 89.17: 8 Dihedral angle restraints: 21036 sinusoidal: 8422 harmonic: 12614 Sorted by residual: dihedral pdb=" CD ARG F 421 " pdb=" NE ARG F 421 " pdb=" CZ ARG F 421 " pdb=" NH1 ARG F 421 " ideal model delta sinusoidal sigma weight residual 0.00 -34.06 34.06 1 1.00e+01 1.00e-02 1.65e+01 dihedral pdb=" CA TYR N 149 " pdb=" C TYR N 149 " pdb=" N PRO N 150 " pdb=" CA PRO N 150 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PHE C 199 " pdb=" C PHE C 199 " pdb=" N THR C 200 " pdb=" CA THR C 200 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 21033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3854 0.045 - 0.091: 961 0.091 - 0.136: 305 0.136 - 0.182: 15 0.182 - 0.227: 6 Chirality restraints: 5141 Sorted by residual: chirality pdb=" CA ILE G 382 " pdb=" N ILE G 382 " pdb=" C ILE G 382 " pdb=" CB ILE G 382 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ILE G 174 " pdb=" N ILE G 174 " pdb=" C ILE G 174 " pdb=" CB ILE G 174 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL B 189 " pdb=" N VAL B 189 " pdb=" C VAL B 189 " pdb=" CB VAL B 189 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.83e-01 ... (remaining 5138 not shown) Planarity restraints: 6321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 421 " -0.600 9.50e-02 1.11e+02 2.69e-01 4.43e+01 pdb=" NE ARG F 421 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG F 421 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG F 421 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 421 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 421 " -0.490 9.50e-02 1.11e+02 2.20e-01 2.96e+01 pdb=" NE ARG G 421 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG G 421 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG G 421 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG G 421 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 167 " -0.413 9.50e-02 1.11e+02 1.85e-01 2.11e+01 pdb=" NE ARG F 167 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG F 167 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG F 167 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 167 " -0.013 2.00e-02 2.50e+03 ... (remaining 6318 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3457 2.74 - 3.28: 34963 3.28 - 3.82: 61934 3.82 - 4.36: 78089 4.36 - 4.90: 132079 Nonbonded interactions: 310522 Sorted by model distance: nonbonded pdb=" OH TYR H 29 " pdb=" OD2 ASP H 35 " model vdw 2.202 3.040 nonbonded pdb=" OE2 GLU A 158 " pdb=" NE2 HIS A 325 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASP D 202 " pdb=" NE2 HIS D 238 " model vdw 2.225 3.120 nonbonded pdb=" O LEU G 138 " pdb=" NZ LYS G 316 " model vdw 2.226 3.120 nonbonded pdb=" OD1 ASP B 202 " pdb=" NE2 HIS B 238 " model vdw 2.227 3.120 ... (remaining 310517 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 21 through 178 or resid 180 through 331 or resid 334 throu \ gh 335 or resid 338 through 463)) selection = (chain 'B' and ((resid 21 and (name N or name CA or name C or name O or name CB \ )) or resid 22 through 93 or (resid 94 and (name N or name CA or name C or name \ O or name CB )) or resid 95 through 331 or (resid 334 and (name N or name CA or \ name C or name O or name CB )) or resid 335 or resid 338 through 463)) selection = (chain 'C' and ((resid 21 and (name N or name CA or name C or name O or name CB \ )) or resid 22 through 93 or (resid 94 and (name N or name CA or name C or name \ O or name CB )) or resid 95 through 174 or (resid 175 and (name N or name CA or \ name C or name O or name CB )) or resid 176 through 178 or resid 180 through 331 \ or (resid 334 and (name N or name CA or name C or name O or name CB )) or resid \ 335 or resid 338 through 463)) selection = (chain 'D' and ((resid 21 and (name N or name CA or name C or name O or name CB \ )) or resid 22 through 93 or (resid 94 and (name N or name CA or name C or name \ O or name CB )) or resid 95 through 174 or (resid 175 and (name N or name CA or \ name C or name O or name CB )) or resid 176 through 178 or resid 180 through 331 \ or (resid 334 and (name N or name CA or name C or name O or name CB )) or resid \ 335 or resid 338 through 463)) selection = (chain 'E' and ((resid 21 and (name N or name CA or name C or name O or name CB \ )) or resid 22 through 93 or (resid 94 and (name N or name CA or name C or name \ O or name CB )) or resid 95 through 174 or (resid 175 and (name N or name CA or \ name C or name O or name CB )) or resid 176 through 178 or resid 180 through 331 \ or (resid 334 and (name N or name CA or name C or name O or name CB )) or resid \ 335 or resid 338 through 463)) selection = (chain 'F' and ((resid 21 and (name N or name CA or name C or name O or name CB \ )) or resid 22 through 93 or (resid 94 and (name N or name CA or name C or name \ O or name CB )) or resid 95 through 174 or (resid 175 and (name N or name CA or \ name C or name O or name CB )) or resid 176 through 178 or resid 180 through 331 \ or (resid 334 and (name N or name CA or name C or name O or name CB )) or resid \ 335 or resid 338 through 463)) selection = (chain 'G' and ((resid 21 and (name N or name CA or name C or name O or name CB \ )) or resid 22 through 93 or (resid 94 and (name N or name CA or name C or name \ O or name CB )) or resid 95 through 174 or (resid 175 and (name N or name CA or \ name C or name O or name CB )) or resid 176 through 178 or resid 180 through 331 \ or (resid 334 and (name N or name CA or name C or name O or name CB )) or resid \ 335 through 463)) selection = (chain 'H' and ((resid 21 and (name N or name CA or name C or name O or name CB \ )) or resid 22 through 93 or (resid 94 and (name N or name CA or name C or name \ O or name CB )) or resid 95 through 174 or (resid 175 and (name N or name CA or \ name C or name O or name CB )) or resid 176 through 178 or resid 180 through 331 \ or resid 334 through 335 or resid 338 through 463)) } ncs_group { reference = (chain 'I' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 162 or \ (resid 163 and (name N or name CA or name C or name O or name CB )) or resid 164 \ through 178)) selection = (chain 'J' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 162 or \ (resid 163 and (name N or name CA or name C or name O or name CB )) or resid 164 \ through 178)) selection = (chain 'K' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 178)) selection = (chain 'L' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 178)) selection = (chain 'M' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 178)) selection = (chain 'N' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 178)) selection = (chain 'O' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 162 or \ (resid 163 and (name N or name CA or name C or name O or name CB )) or resid 164 \ through 178)) selection = (chain 'P' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 162 or \ (resid 163 and (name N or name CA or name C or name O or name CB )) or resid 164 \ through 178)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 35.540 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 : 0.004 0.036 35754 Z= 0.211 Angle : 0.550 5.616 48496 Z= 0.324 Chirality : 0.044 0.227 5141 Planarity : 0.006 0.269 6321 Dihedral : 10.537 89.174 12992 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.79 % Allowed : 3.92 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.13), residues: 4362 helix: 1.86 (0.12), residues: 1701 sheet: -0.05 (0.19), residues: 721 loop : -0.14 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 421 TYR 0.010 0.001 TYR F 283 PHE 0.028 0.001 PHE D 345 TRP 0.009 0.001 TRP N 122 HIS 0.006 0.001 HIS H 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.21 (35750) covalent geometry : angle 0.54962 / 0.32 (48488) SS BOND : bond 0.00622 / 0.31 ( 4) SS BOND : angle 1.07033 / 0.62 ( 8) hydrogen bonds : bond 0.12157 / 8.14 ( 1659) hydrogen bonds : angle 6.06025 / 4.44 ( 4635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 899 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.7077 (m) cc_final: 0.6847 (m) REVERT: H 63 THR cc_start: 0.6462 (OUTLIER) cc_final: 0.5896 (t) REVERT: H 302 ASP cc_start: 0.7800 (p0) cc_final: 0.7533 (p0) REVERT: O 157 ILE cc_start: 0.8483 (pt) cc_final: 0.8150 (pt) outliers start: 65 outliers final: 21 residues processed: 938 average time/residue: 0.7484 time to fit residues: 839.1419 Evaluate side-chains 618 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 596 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 198 ASP Chi-restraints excluded: chain G residue 442 ASN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 269 TYR Chi-restraints excluded: chain H residue 449 CYS Chi-restraints excluded: chain I residue 161 ASN Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain P residue 134 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 0.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 3.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 HIS B 86 HIS B 277 ASN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN B 366 GLN C 86 HIS C 366 GLN C 429 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN D 304 GLN D 366 GLN D 420 ASN ** E 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 HIS ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN F 277 ASN F 366 GLN G 413 ASN H 96 GLN ** H 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 GLN H 325 HIS I 91 ASN I 103 HIS I 110 HIS I 166 GLN J 161 ASN J 166 GLN K 91 ASN K 110 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 HIS L 166 GLN M 110 HIS M 161 ASN M 166 GLN N 91 ASN N 166 GLN O 110 HIS O 166 GLN P 166 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.084718 restraints weight = 59401.406| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.37 r_work: 0.2901 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 35754 Z= 0.250 Angle : 0.614 7.643 48496 Z= 0.318 Chirality : 0.046 0.296 5141 Planarity : 0.004 0.038 6321 Dihedral : 4.968 54.651 4872 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.83 % Allowed : 13.54 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.13), residues: 4362 helix: 1.85 (0.12), residues: 1731 sheet: -0.20 (0.19), residues: 693 loop : -0.06 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 155 TYR 0.018 0.002 TYR M 173 PHE 0.027 0.002 PHE B 345 TRP 0.020 0.001 TRP G 462 HIS 0.007 0.001 HIS H 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.25 (35750) covalent geometry : angle 0.61315 / 0.32 (48488) SS BOND : bond 0.00759 / 0.38 ( 4) SS BOND : angle 1.75533 / 1.02 ( 8) hydrogen bonds : bond 0.04017 / 2.67 ( 1659) hydrogen bonds : angle 5.19418 / 3.79 ( 4635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 619 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8232 (tp30) REVERT: B 88 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8116 (mm-30) REVERT: B 106 ASP cc_start: 0.9040 (m-30) cc_final: 0.8754 (m-30) REVERT: B 128 LYS cc_start: 0.8662 (tmtt) cc_final: 0.8334 (tmmt) REVERT: B 268 ASP cc_start: 0.9085 (m-30) cc_final: 0.8883 (m-30) REVERT: B 295 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8303 (ptt-90) REVERT: B 347 ASP cc_start: 0.8604 (m-30) cc_final: 0.8334 (m-30) REVERT: C 96 GLN cc_start: 0.8720 (mt0) cc_final: 0.8515 (tt0) REVERT: D 163 ASN cc_start: 0.9145 (t0) cc_final: 0.8939 (t0) REVERT: E 269 TYR cc_start: 0.9352 (OUTLIER) cc_final: 0.8849 (p90) REVERT: E 305 LYS cc_start: 0.8860 (mptt) cc_final: 0.8625 (tptt) REVERT: E 339 ARG cc_start: 0.8664 (mtp-110) cc_final: 0.7760 (ttp80) REVERT: E 392 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8271 (tm-30) REVERT: F 204 GLU cc_start: 0.8422 (pm20) cc_final: 0.8180 (pm20) REVERT: F 211 PHE cc_start: 0.8769 (m-80) cc_final: 0.8559 (m-80) REVERT: G 334 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7418 (pmtt) REVERT: H 52 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: H 63 THR cc_start: 0.7701 (OUTLIER) cc_final: 0.7399 (t) REVERT: H 128 LYS cc_start: 0.8194 (pmtt) cc_final: 0.7687 (pttp) REVERT: H 248 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8472 (mp0) REVERT: I 155 ARG cc_start: 0.8748 (ptt-90) cc_final: 0.8126 (ptt-90) REVERT: J 68 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8651 (mm-30) REVERT: M 139 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8687 (mp) REVERT: N 68 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7594 (mm-30) REVERT: N 100 GLU cc_start: 0.8780 (tp30) cc_final: 0.8559 (tp30) REVERT: N 112 ASN cc_start: 0.8571 (t0) cc_final: 0.8341 (t0) REVERT: N 140 LYS cc_start: 0.9125 (ttpt) cc_final: 0.8545 (tptp) REVERT: N 174 LYS cc_start: 0.9274 (mttt) cc_final: 0.9015 (mtmm) REVERT: O 100 GLU cc_start: 0.8976 (tp30) cc_final: 0.8713 (tp30) REVERT: O 157 ILE cc_start: 0.9445 (pt) cc_final: 0.9154 (pt) REVERT: P 57 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8687 (ptmm) outliers start: 139 outliers final: 51 residues processed: 690 average time/residue: 0.6653 time to fit residues: 560.2734 Evaluate side-chains 616 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 555 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 269 TYR Chi-restraints excluded: chain F residue 459 CYS Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain G residue 334 LYS Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 269 TYR Chi-restraints excluded: chain H residue 309 MET Chi-restraints excluded: chain H residue 449 CYS Chi-restraints excluded: chain H residue 462 TRP Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 112 ASN Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 167 CYS Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain P residue 57 LYS Chi-restraints excluded: chain P residue 112 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 211 optimal weight: 4.9990 chunk 385 optimal weight: 5.9990 chunk 350 optimal weight: 6.9990 chunk 368 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 184 optimal weight: 0.7980 chunk 231 optimal weight: 7.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN D 401 GLN E 156 GLN E 267 HIS ** E 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN G 149 GLN G 366 GLN H 294 HIS I 103 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN N 161 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.101338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.085623 restraints weight = 58985.658| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.33 r_work: 0.2912 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 35754 Z= 0.204 Angle : 0.562 7.196 48496 Z= 0.292 Chirality : 0.045 0.230 5141 Planarity : 0.004 0.033 6321 Dihedral : 4.710 54.030 4850 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.50 % Allowed : 14.92 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.13), residues: 4362 helix: 1.90 (0.12), residues: 1735 sheet: -0.04 (0.19), residues: 727 loop : -0.09 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 446 TYR 0.020 0.002 TYR M 149 PHE 0.034 0.002 PHE A 345 TRP 0.026 0.001 TRP G 462 HIS 0.009 0.001 HIS M 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (35750) covalent geometry : angle 0.56215 / 0.29 (48488) SS BOND : bond 0.00664 / 0.33 ( 4) SS BOND : angle 1.43587 / 0.83 ( 8) hydrogen bonds : bond 0.03740 / 2.49 ( 1659) hydrogen bonds : angle 4.99542 / 3.65 ( 4635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 613 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: A 156 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8101 (tp40) REVERT: A 192 CYS cc_start: 0.9309 (m) cc_final: 0.8877 (m) REVERT: A 248 GLU cc_start: 0.8900 (mp0) cc_final: 0.8597 (mp0) REVERT: A 327 HIS cc_start: 0.8899 (m170) cc_final: 0.8665 (m-70) REVERT: A 357 ASP cc_start: 0.8369 (t70) cc_final: 0.8021 (t70) REVERT: A 392 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8182 (tp30) REVERT: B 88 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8131 (mm-30) REVERT: B 106 ASP cc_start: 0.9058 (m-30) cc_final: 0.8802 (m-30) REVERT: B 128 LYS cc_start: 0.8675 (tmtt) cc_final: 0.8383 (tmmt) REVERT: B 200 THR cc_start: 0.9199 (p) cc_final: 0.8854 (p) REVERT: B 231 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8612 (tt0) REVERT: B 268 ASP cc_start: 0.9080 (m-30) cc_final: 0.8817 (m-30) REVERT: B 347 ASP cc_start: 0.8635 (m-30) cc_final: 0.8297 (m-30) REVERT: C 52 GLU cc_start: 0.8385 (tp30) cc_final: 0.8170 (tp30) REVERT: D 163 ASN cc_start: 0.9118 (t0) cc_final: 0.8911 (t0) REVERT: E 52 GLU cc_start: 0.7984 (tp30) cc_final: 0.7438 (tt0) REVERT: E 305 LYS cc_start: 0.8848 (mptt) cc_final: 0.8568 (tptt) REVERT: E 347 ASP cc_start: 0.9192 (m-30) cc_final: 0.8810 (m-30) REVERT: E 392 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8339 (tm-30) REVERT: F 88 GLU cc_start: 0.8536 (tt0) cc_final: 0.8194 (pt0) REVERT: F 211 PHE cc_start: 0.8797 (m-80) cc_final: 0.8554 (m-80) REVERT: G 334 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7378 (pmtt) REVERT: H 45 GLN cc_start: 0.7706 (mt0) cc_final: 0.7410 (mt0) REVERT: H 52 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: H 128 LYS cc_start: 0.8144 (pmtt) cc_final: 0.7608 (pttp) REVERT: H 248 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8472 (mp0) REVERT: H 357 ASP cc_start: 0.8647 (t0) cc_final: 0.8301 (t70) REVERT: H 366 GLN cc_start: 0.9136 (tp40) cc_final: 0.8807 (tp40) REVERT: H 379 SER cc_start: 0.9333 (t) cc_final: 0.9012 (p) REVERT: I 155 ARG cc_start: 0.8872 (ptt-90) cc_final: 0.8023 (ptt-90) REVERT: I 160 ASP cc_start: 0.8074 (t0) cc_final: 0.7752 (t0) REVERT: K 86 ASP cc_start: 0.8541 (m-30) cc_final: 0.8320 (m-30) REVERT: L 68 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8109 (mm-30) REVERT: M 139 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8670 (mp) REVERT: N 68 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7643 (mm-30) REVERT: N 100 GLU cc_start: 0.8835 (tp30) cc_final: 0.8595 (tp30) REVERT: N 112 ASN cc_start: 0.8592 (t0) cc_final: 0.8248 (t0) REVERT: N 140 LYS cc_start: 0.9114 (ttpt) cc_final: 0.8584 (tptp) REVERT: N 174 LYS cc_start: 0.9224 (mttt) cc_final: 0.8979 (mtmm) REVERT: O 91 ASN cc_start: 0.9205 (m110) cc_final: 0.8903 (m-40) REVERT: O 100 GLU cc_start: 0.8962 (tp30) cc_final: 0.8658 (tp30) REVERT: O 157 ILE cc_start: 0.9365 (pt) cc_final: 0.9105 (pt) REVERT: O 164 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7014 (mm-40) outliers start: 127 outliers final: 52 residues processed: 673 average time/residue: 0.6487 time to fit residues: 535.7511 Evaluate side-chains 623 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 564 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 459 CYS Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 334 LYS Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 269 TYR Chi-restraints excluded: chain H residue 309 MET Chi-restraints excluded: chain H residue 449 CYS Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 161 ASN Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 112 ASN Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 160 ASP Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain O residue 161 ASN Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain P residue 169 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 307 optimal weight: 4.9990 chunk 410 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 412 optimal weight: 0.8980 chunk 384 optimal weight: 0.0970 chunk 285 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 331 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 353 optimal weight: 0.6980 overall best weight: 2.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN A 401 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 HIS D 420 ASN E 156 GLN ** E 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 GLN G 366 GLN I 103 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN ** L 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 112 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.085646 restraints weight = 59039.226| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.31 r_work: 0.2929 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 35754 Z= 0.215 Angle : 0.564 7.128 48496 Z= 0.292 Chirality : 0.045 0.236 5141 Planarity : 0.004 0.036 6321 Dihedral : 4.654 54.050 4846 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.42 % Allowed : 16.13 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.13), residues: 4362 helix: 1.93 (0.12), residues: 1734 sheet: -0.04 (0.19), residues: 717 loop : -0.11 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 339 TYR 0.018 0.002 TYR M 149 PHE 0.028 0.002 PHE D 345 TRP 0.026 0.001 TRP G 462 HIS 0.008 0.001 HIS M 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (35750) covalent geometry : angle 0.56413 / 0.29 (48488) SS BOND : bond 0.00644 / 0.32 ( 4) SS BOND : angle 1.42841 / 0.83 ( 8) hydrogen bonds : bond 0.03682 / 2.45 ( 1659) hydrogen bonds : angle 4.92556 / 3.61 ( 4635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 583 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7374 (tp30) REVERT: A 156 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8243 (mm-40) REVERT: A 192 CYS cc_start: 0.9344 (m) cc_final: 0.8919 (m) REVERT: A 327 HIS cc_start: 0.8882 (m170) cc_final: 0.8465 (m90) REVERT: A 357 ASP cc_start: 0.8421 (t70) cc_final: 0.8058 (t0) REVERT: A 366 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.9044 (mm-40) REVERT: A 392 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8227 (tp30) REVERT: B 88 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8131 (mm-30) REVERT: B 106 ASP cc_start: 0.9064 (m-30) cc_final: 0.8747 (m-30) REVERT: B 128 LYS cc_start: 0.8627 (tmtt) cc_final: 0.8332 (tmmt) REVERT: B 200 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8813 (p) REVERT: B 231 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8554 (tt0) REVERT: B 268 ASP cc_start: 0.9069 (m-30) cc_final: 0.8793 (m-30) REVERT: B 347 ASP cc_start: 0.8703 (m-30) cc_final: 0.8354 (m-30) REVERT: C 52 GLU cc_start: 0.8386 (tp30) cc_final: 0.8159 (tp30) REVERT: C 117 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8556 (m-10) REVERT: E 106 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8828 (m-30) REVERT: E 305 LYS cc_start: 0.8867 (mptt) cc_final: 0.8562 (tptt) REVERT: E 339 ARG cc_start: 0.8590 (mtp-110) cc_final: 0.7704 (ttp80) REVERT: F 88 GLU cc_start: 0.8630 (tt0) cc_final: 0.8241 (pt0) REVERT: F 140 ILE cc_start: 0.9216 (mm) cc_final: 0.9013 (mp) REVERT: F 211 PHE cc_start: 0.8769 (m-80) cc_final: 0.8538 (m-80) REVERT: G 334 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7467 (pmtt) REVERT: H 45 GLN cc_start: 0.7610 (mt0) cc_final: 0.7369 (mt0) REVERT: H 52 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: H 239 TYR cc_start: 0.9311 (m-10) cc_final: 0.9049 (m-10) REVERT: H 248 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8441 (mp0) REVERT: H 295 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7795 (ptt180) REVERT: H 357 ASP cc_start: 0.8674 (t0) cc_final: 0.8322 (t70) REVERT: H 379 SER cc_start: 0.9362 (t) cc_final: 0.9059 (p) REVERT: I 155 ARG cc_start: 0.8861 (ptt-90) cc_final: 0.8012 (ptt-90) REVERT: I 160 ASP cc_start: 0.8181 (t0) cc_final: 0.7951 (t0) REVERT: J 141 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8100 (mm-30) REVERT: J 160 ASP cc_start: 0.8543 (t0) cc_final: 0.8126 (t0) REVERT: J 163 ARG cc_start: 0.8330 (mtp85) cc_final: 0.8077 (mtm-85) REVERT: K 86 ASP cc_start: 0.8561 (m-30) cc_final: 0.8350 (m-30) REVERT: K 102 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8362 (tp30) REVERT: L 68 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8147 (mm-30) REVERT: L 86 ASP cc_start: 0.8297 (m-30) cc_final: 0.8089 (m-30) REVERT: M 139 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8682 (mp) REVERT: N 68 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7673 (mm-30) REVERT: N 100 GLU cc_start: 0.8835 (tp30) cc_final: 0.8572 (tp30) REVERT: N 112 ASN cc_start: 0.8604 (t0) cc_final: 0.8229 (t0) REVERT: N 140 LYS cc_start: 0.9123 (ttpt) cc_final: 0.8543 (tptp) REVERT: N 147 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8593 (ttpp) REVERT: O 91 ASN cc_start: 0.9201 (m110) cc_final: 0.8915 (m-40) REVERT: O 100 GLU cc_start: 0.8980 (tp30) cc_final: 0.8671 (tp30) REVERT: O 157 ILE cc_start: 0.9335 (pt) cc_final: 0.9086 (pt) REVERT: O 164 GLN cc_start: 0.7865 (mm-40) cc_final: 0.6966 (mm-40) outliers start: 124 outliers final: 65 residues processed: 649 average time/residue: 0.6548 time to fit residues: 520.9821 Evaluate side-chains 635 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 558 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 459 CYS Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 334 LYS Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 269 TYR Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 309 MET Chi-restraints excluded: chain H residue 449 CYS Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 161 ASN Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 112 ASN Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 92 LYS Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 141 GLU Chi-restraints excluded: chain K residue 167 CYS Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 169 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 425 optimal weight: 4.9990 chunk 332 optimal weight: 0.9990 chunk 381 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 333 optimal weight: 0.7980 chunk 321 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN A 401 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN G 149 GLN G 366 GLN I 103 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.086753 restraints weight = 58558.693| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.34 r_work: 0.2959 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 35754 Z= 0.136 Angle : 0.528 5.897 48496 Z= 0.274 Chirality : 0.043 0.215 5141 Planarity : 0.003 0.033 6321 Dihedral : 4.541 51.616 4846 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.41 % Favored : 97.57 % Rotamer: Outliers : 3.28 % Allowed : 16.76 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.13), residues: 4362 helix: 2.04 (0.12), residues: 1740 sheet: -0.09 (0.18), residues: 723 loop : -0.05 (0.15), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 339 TYR 0.016 0.001 TYR G 24 PHE 0.032 0.001 PHE A 345 TRP 0.023 0.001 TRP G 462 HIS 0.008 0.001 HIS M 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (35750) covalent geometry : angle 0.52804 / 0.27 (48488) SS BOND : bond 0.00675 / 0.34 ( 4) SS BOND : angle 1.32898 / 0.77 ( 8) hydrogen bonds : bond 0.03366 / 2.24 ( 1659) hydrogen bonds : angle 4.78668 / 3.51 ( 4635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 629 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 VAL cc_start: 0.8137 (t) cc_final: 0.7909 (m) REVERT: A 52 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7392 (tp30) REVERT: A 140 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9169 (mm) REVERT: A 192 CYS cc_start: 0.9292 (m) cc_final: 0.8847 (m) REVERT: A 327 HIS cc_start: 0.8874 (m170) cc_final: 0.8512 (m90) REVERT: A 357 ASP cc_start: 0.8398 (t70) cc_final: 0.8012 (t0) REVERT: A 370 SER cc_start: 0.9265 (m) cc_final: 0.9063 (p) REVERT: B 88 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8058 (mm-30) REVERT: B 128 LYS cc_start: 0.8587 (tmtt) cc_final: 0.8289 (tmmt) REVERT: B 200 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8809 (p) REVERT: B 347 ASP cc_start: 0.8706 (m-30) cc_final: 0.8421 (m-30) REVERT: C 117 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8610 (m-10) REVERT: E 52 GLU cc_start: 0.8537 (tp30) cc_final: 0.7916 (tt0) REVERT: E 106 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8792 (m-30) REVERT: E 305 LYS cc_start: 0.8875 (mptt) cc_final: 0.8557 (tptt) REVERT: E 339 ARG cc_start: 0.8585 (mtp-110) cc_final: 0.7759 (ttp80) REVERT: F 88 GLU cc_start: 0.8555 (tt0) cc_final: 0.8186 (pt0) REVERT: F 115 ASN cc_start: 0.9348 (t0) cc_final: 0.9006 (t0) REVERT: F 211 PHE cc_start: 0.8772 (m-80) cc_final: 0.8558 (m-80) REVERT: H 45 GLN cc_start: 0.7549 (mt0) cc_final: 0.7287 (mt0) REVERT: H 52 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: H 79 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7769 (mtp180) REVERT: H 128 LYS cc_start: 0.8174 (pmtt) cc_final: 0.7485 (pttp) REVERT: H 239 TYR cc_start: 0.9288 (m-10) cc_final: 0.9021 (m-10) REVERT: H 295 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7841 (ptt180) REVERT: H 357 ASP cc_start: 0.8606 (t0) cc_final: 0.8257 (t70) REVERT: H 379 SER cc_start: 0.9343 (t) cc_final: 0.9069 (p) REVERT: H 462 TRP cc_start: 0.6456 (OUTLIER) cc_final: 0.5999 (t-100) REVERT: I 68 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7888 (mm-30) REVERT: I 155 ARG cc_start: 0.8850 (ptt-90) cc_final: 0.7980 (ptt-90) REVERT: I 160 ASP cc_start: 0.8037 (t0) cc_final: 0.7658 (t0) REVERT: J 56 MET cc_start: 0.8312 (mtm) cc_final: 0.8062 (mtp) REVERT: J 141 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7925 (mt-10) REVERT: K 86 ASP cc_start: 0.8567 (m-30) cc_final: 0.8357 (m-30) REVERT: K 102 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8282 (tp30) REVERT: L 68 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8067 (mm-30) REVERT: L 86 ASP cc_start: 0.8286 (m-30) cc_final: 0.8031 (m-30) REVERT: L 148 GLU cc_start: 0.9103 (tp30) cc_final: 0.8899 (tp30) REVERT: M 139 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8657 (mp) REVERT: M 148 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: N 68 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7664 (mm-30) REVERT: N 112 ASN cc_start: 0.8596 (t0) cc_final: 0.8197 (t0) REVERT: N 140 LYS cc_start: 0.9122 (ttpt) cc_final: 0.8489 (tptp) REVERT: N 143 GLU cc_start: 0.8657 (tp30) cc_final: 0.8439 (tp30) REVERT: O 91 ASN cc_start: 0.9180 (m110) cc_final: 0.8960 (m-40) REVERT: O 100 GLU cc_start: 0.9011 (tp30) cc_final: 0.8730 (tp30) REVERT: O 157 ILE cc_start: 0.9297 (pt) cc_final: 0.9038 (pt) REVERT: O 164 GLN cc_start: 0.7772 (mm-40) cc_final: 0.6812 (tp40) outliers start: 119 outliers final: 51 residues processed: 687 average time/residue: 0.6504 time to fit residues: 547.4395 Evaluate side-chains 628 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 566 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 117 PHE Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 459 CYS Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 309 MET Chi-restraints excluded: chain H residue 356 LYS Chi-restraints excluded: chain H residue 449 CYS Chi-restraints excluded: chain H residue 462 TRP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain J residue 112 ASN Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 92 LYS Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 148 GLU Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain P residue 168 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 146 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 343 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN A 401 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 GLN C 401 GLN C 429 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN E 156 GLN ** E 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 366 GLN H 429 GLN I 103 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN O 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.085602 restraints weight = 59037.226| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.36 r_work: 0.2938 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35754 Z= 0.189 Angle : 0.557 7.858 48496 Z= 0.287 Chirality : 0.044 0.212 5141 Planarity : 0.004 0.045 6321 Dihedral : 4.518 51.766 4842 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.75 % Favored : 97.23 % Rotamer: Outliers : 3.42 % Allowed : 16.98 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.13), residues: 4362 helix: 2.02 (0.12), residues: 1740 sheet: -0.14 (0.18), residues: 722 loop : -0.05 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 446 TYR 0.017 0.002 TYR M 173 PHE 0.028 0.002 PHE A 345 TRP 0.024 0.001 TRP G 462 HIS 0.006 0.001 HIS M 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (35750) covalent geometry : angle 0.55669 / 0.29 (48488) SS BOND : bond 0.00607 / 0.31 ( 4) SS BOND : angle 1.30902 / 0.76 ( 8) hydrogen bonds : bond 0.03491 / 2.33 ( 1659) hydrogen bonds : angle 4.77195 / 3.50 ( 4635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 583 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 VAL cc_start: 0.8193 (t) cc_final: 0.7958 (m) REVERT: A 52 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: A 140 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9197 (mm) REVERT: A 327 HIS cc_start: 0.8881 (m170) cc_final: 0.8570 (m90) REVERT: A 357 ASP cc_start: 0.8448 (t70) cc_final: 0.8063 (t0) REVERT: A 370 SER cc_start: 0.9280 (m) cc_final: 0.9068 (p) REVERT: B 88 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8136 (mm-30) REVERT: B 128 LYS cc_start: 0.8632 (tmtt) cc_final: 0.8330 (tmmt) REVERT: B 347 ASP cc_start: 0.8677 (m-30) cc_final: 0.8315 (m-30) REVERT: C 21 LYS cc_start: 0.5519 (pptt) cc_final: 0.4664 (ttpt) REVERT: C 24 TYR cc_start: 0.8740 (m-80) cc_final: 0.8482 (m-10) REVERT: C 117 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8684 (m-10) REVERT: E 52 GLU cc_start: 0.8556 (tp30) cc_final: 0.8338 (tp30) REVERT: E 140 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.8973 (mm) REVERT: E 200 THR cc_start: 0.9317 (p) cc_final: 0.9117 (p) REVERT: E 305 LYS cc_start: 0.8895 (mptt) cc_final: 0.8605 (tptt) REVERT: E 339 ARG cc_start: 0.8596 (mtp-110) cc_final: 0.7808 (ttp80) REVERT: E 447 GLU cc_start: 0.8036 (pt0) cc_final: 0.7835 (pt0) REVERT: F 88 GLU cc_start: 0.8576 (tt0) cc_final: 0.8220 (pt0) REVERT: F 115 ASN cc_start: 0.9343 (t0) cc_final: 0.8975 (t0) REVERT: F 424 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8331 (tp) REVERT: G 334 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7460 (pmtt) REVERT: H 45 GLN cc_start: 0.7583 (mt0) cc_final: 0.7336 (mt0) REVERT: H 52 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: H 79 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7795 (mtp180) REVERT: H 128 LYS cc_start: 0.8172 (pmtt) cc_final: 0.7499 (pttp) REVERT: H 239 TYR cc_start: 0.9291 (m-10) cc_final: 0.9024 (m-10) REVERT: H 248 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8444 (mp0) REVERT: H 295 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7902 (ptt180) REVERT: H 357 ASP cc_start: 0.8615 (t0) cc_final: 0.8299 (t70) REVERT: H 379 SER cc_start: 0.9359 (t) cc_final: 0.9089 (p) REVERT: H 462 TRP cc_start: 0.6469 (OUTLIER) cc_final: 0.6009 (t-100) REVERT: I 68 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7801 (mm-30) REVERT: I 80 GLU cc_start: 0.8601 (mp0) cc_final: 0.7949 (mp0) REVERT: I 160 ASP cc_start: 0.8064 (t0) cc_final: 0.7847 (t0) REVERT: J 56 MET cc_start: 0.8380 (mtm) cc_final: 0.8142 (mtp) REVERT: J 141 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8031 (mm-30) REVERT: K 86 ASP cc_start: 0.8588 (m-30) cc_final: 0.8351 (m-30) REVERT: K 102 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8287 (tp30) REVERT: L 68 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8139 (mm-30) REVERT: L 86 ASP cc_start: 0.8347 (m-30) cc_final: 0.8106 (m-30) REVERT: L 148 GLU cc_start: 0.9096 (tp30) cc_final: 0.8877 (tp30) REVERT: M 139 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8667 (mp) REVERT: M 148 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: N 68 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7729 (mm-30) REVERT: N 100 GLU cc_start: 0.8818 (tp30) cc_final: 0.8614 (tp30) REVERT: N 112 ASN cc_start: 0.8628 (t0) cc_final: 0.8222 (t0) REVERT: N 140 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8548 (tptp) REVERT: N 147 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8643 (ttpp) REVERT: O 100 GLU cc_start: 0.9009 (tp30) cc_final: 0.8758 (tp30) REVERT: O 157 ILE cc_start: 0.9300 (pt) cc_final: 0.9034 (pt) REVERT: O 164 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7001 (mm-40) REVERT: P 57 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8701 (ptmm) REVERT: P 142 VAL cc_start: 0.8738 (t) cc_final: 0.8509 (p) outliers start: 124 outliers final: 67 residues processed: 652 average time/residue: 0.6402 time to fit residues: 512.7027 Evaluate side-chains 636 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 555 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 117 PHE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 424 LEU Chi-restraints excluded: chain F residue 459 CYS Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain G residue 334 LYS Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 309 MET Chi-restraints excluded: chain H residue 356 LYS Chi-restraints excluded: chain H residue 449 CYS Chi-restraints excluded: chain H residue 462 TRP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain J residue 112 ASN Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 92 LYS Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 167 CYS Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 148 GLU Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 57 GLN Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 57 LYS Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain P residue 168 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 214 optimal weight: 1.9990 chunk 325 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 432 optimal weight: 0.5980 chunk 216 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 384 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 366 GLN H 429 GLN I 103 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN O 91 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.102555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.086853 restraints weight = 58766.091| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.34 r_work: 0.2969 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35754 Z= 0.143 Angle : 0.539 7.944 48496 Z= 0.278 Chirality : 0.043 0.204 5141 Planarity : 0.004 0.055 6321 Dihedral : 4.434 43.768 4842 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 2.89 % Allowed : 17.59 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.13), residues: 4362 helix: 2.07 (0.12), residues: 1739 sheet: -0.02 (0.18), residues: 712 loop : -0.05 (0.15), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 446 TYR 0.017 0.001 TYR M 173 PHE 0.028 0.001 PHE G 345 TRP 0.025 0.001 TRP G 462 HIS 0.008 0.001 HIS M 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (35750) covalent geometry : angle 0.53915 / 0.28 (48488) SS BOND : bond 0.00629 / 0.32 ( 4) SS BOND : angle 1.28442 / 0.75 ( 8) hydrogen bonds : bond 0.03335 / 2.22 ( 1659) hydrogen bonds : angle 4.70477 / 3.45 ( 4635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 598 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 VAL cc_start: 0.8176 (t) cc_final: 0.7937 (m) REVERT: A 52 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: A 140 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9162 (mm) REVERT: A 327 HIS cc_start: 0.8843 (m170) cc_final: 0.8518 (m90) REVERT: A 357 ASP cc_start: 0.8411 (t70) cc_final: 0.8003 (t0) REVERT: B 60 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7283 (mm-30) REVERT: B 88 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8111 (mm-30) REVERT: B 106 ASP cc_start: 0.9022 (m-30) cc_final: 0.8730 (m-30) REVERT: B 127 PHE cc_start: 0.8381 (t80) cc_final: 0.8169 (m-80) REVERT: B 128 LYS cc_start: 0.8632 (tmtt) cc_final: 0.8343 (tmmt) REVERT: B 295 ARG cc_start: 0.8579 (ppt-90) cc_final: 0.8284 (ptt90) REVERT: B 347 ASP cc_start: 0.8664 (m-30) cc_final: 0.8362 (m-30) REVERT: C 21 LYS cc_start: 0.5692 (pptt) cc_final: 0.4867 (ttpt) REVERT: C 24 TYR cc_start: 0.8747 (m-80) cc_final: 0.8516 (m-10) REVERT: C 117 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8649 (m-10) REVERT: E 52 GLU cc_start: 0.8513 (tp30) cc_final: 0.8122 (tp30) REVERT: E 200 THR cc_start: 0.9285 (p) cc_final: 0.9072 (p) REVERT: E 305 LYS cc_start: 0.8929 (mptt) cc_final: 0.8611 (tptt) REVERT: F 88 GLU cc_start: 0.8473 (tt0) cc_final: 0.8126 (pt0) REVERT: F 115 ASN cc_start: 0.9320 (t0) cc_final: 0.8821 (t0) REVERT: H 45 GLN cc_start: 0.7540 (mt0) cc_final: 0.7293 (mt0) REVERT: H 52 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: H 79 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7770 (mtp180) REVERT: H 128 LYS cc_start: 0.8127 (pmtt) cc_final: 0.7496 (pttp) REVERT: H 239 TYR cc_start: 0.9277 (m-10) cc_final: 0.9019 (m-10) REVERT: H 248 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8437 (mp0) REVERT: H 295 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7869 (ptt180) REVERT: H 357 ASP cc_start: 0.8521 (t0) cc_final: 0.8185 (t70) REVERT: H 379 SER cc_start: 0.9335 (t) cc_final: 0.9069 (p) REVERT: H 462 TRP cc_start: 0.6366 (OUTLIER) cc_final: 0.5955 (t-100) REVERT: I 80 GLU cc_start: 0.8608 (mp0) cc_final: 0.7931 (mp0) REVERT: I 155 ARG cc_start: 0.8721 (ptt-90) cc_final: 0.8481 (ptt-90) REVERT: I 160 ASP cc_start: 0.8030 (t0) cc_final: 0.7634 (t0) REVERT: J 56 MET cc_start: 0.8328 (mtm) cc_final: 0.8089 (mtp) REVERT: J 141 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8011 (mm-30) REVERT: K 86 ASP cc_start: 0.8632 (m-30) cc_final: 0.8402 (m-30) REVERT: K 102 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8289 (tp30) REVERT: L 86 ASP cc_start: 0.8365 (m-30) cc_final: 0.8149 (m-30) REVERT: L 148 GLU cc_start: 0.9162 (tp30) cc_final: 0.8931 (tp30) REVERT: M 148 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: N 68 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7716 (mm-30) REVERT: N 112 ASN cc_start: 0.8636 (t0) cc_final: 0.8237 (t0) REVERT: N 140 LYS cc_start: 0.9118 (ttpt) cc_final: 0.8526 (tptp) REVERT: N 147 LYS cc_start: 0.8881 (ttmm) cc_final: 0.8631 (ttpp) REVERT: O 100 GLU cc_start: 0.8982 (tp30) cc_final: 0.8734 (tp30) REVERT: O 157 ILE cc_start: 0.9262 (pt) cc_final: 0.8993 (pt) REVERT: O 164 GLN cc_start: 0.7711 (mm-40) cc_final: 0.6989 (mm-40) outliers start: 105 outliers final: 57 residues processed: 656 average time/residue: 0.6464 time to fit residues: 520.1902 Evaluate side-chains 625 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 559 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 117 PHE Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 459 CYS Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 309 MET Chi-restraints excluded: chain H residue 449 CYS Chi-restraints excluded: chain H residue 462 TRP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 112 ASN Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 92 LYS Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 167 CYS Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 148 GLU Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 57 GLN Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 160 ASP Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain P residue 168 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 354 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 314 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 370 optimal weight: 3.9990 chunk 416 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN ** E 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 366 GLN H 156 GLN H 429 GLN I 103 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.103233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.087442 restraints weight = 58353.153| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.37 r_work: 0.2950 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35754 Z= 0.135 Angle : 0.543 9.049 48496 Z= 0.279 Chirality : 0.043 0.208 5141 Planarity : 0.004 0.063 6321 Dihedral : 4.388 41.840 4842 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % Rotamer: Outliers : 2.70 % Allowed : 18.00 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.13), residues: 4362 helix: 2.09 (0.12), residues: 1739 sheet: 0.01 (0.18), residues: 712 loop : -0.02 (0.15), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 339 TYR 0.020 0.001 TYR M 173 PHE 0.032 0.001 PHE A 345 TRP 0.028 0.001 TRP G 462 HIS 0.006 0.001 HIS M 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (35750) covalent geometry : angle 0.54238 / 0.28 (48488) SS BOND : bond 0.00628 / 0.32 ( 4) SS BOND : angle 1.24004 / 0.72 ( 8) hydrogen bonds : bond 0.03267 / 2.17 ( 1659) hydrogen bonds : angle 4.66226 / 3.42 ( 4635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 591 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7354 (tp30) REVERT: A 140 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9150 (mm) REVERT: A 268 ASP cc_start: 0.8784 (m-30) cc_final: 0.8540 (m-30) REVERT: A 327 HIS cc_start: 0.8837 (m170) cc_final: 0.8539 (m90) REVERT: A 357 ASP cc_start: 0.8360 (t70) cc_final: 0.7931 (t0) REVERT: A 369 VAL cc_start: 0.9265 (OUTLIER) cc_final: 0.9034 (m) REVERT: B 88 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8055 (mm-30) REVERT: B 106 ASP cc_start: 0.9022 (m-30) cc_final: 0.8742 (m-30) REVERT: B 128 LYS cc_start: 0.8557 (tmtt) cc_final: 0.8265 (tmmt) REVERT: B 347 ASP cc_start: 0.8698 (m-30) cc_final: 0.8391 (m-30) REVERT: C 21 LYS cc_start: 0.5570 (pptt) cc_final: 0.4793 (ttpt) REVERT: C 117 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8647 (m-10) REVERT: E 200 THR cc_start: 0.9247 (p) cc_final: 0.9027 (p) REVERT: E 305 LYS cc_start: 0.8928 (mptt) cc_final: 0.8588 (tptt) REVERT: E 339 ARG cc_start: 0.8649 (mtp-110) cc_final: 0.7693 (ttp80) REVERT: F 88 GLU cc_start: 0.8468 (tt0) cc_final: 0.8110 (pt0) REVERT: G 392 GLU cc_start: 0.8250 (pt0) cc_final: 0.7904 (pm20) REVERT: H 52 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: H 79 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7691 (mtp180) REVERT: H 128 LYS cc_start: 0.8010 (pmtt) cc_final: 0.7350 (pttp) REVERT: H 239 TYR cc_start: 0.9264 (m-10) cc_final: 0.9007 (m-10) REVERT: H 248 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8434 (mp0) REVERT: H 295 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7864 (ptt180) REVERT: H 357 ASP cc_start: 0.8496 (t0) cc_final: 0.8141 (t70) REVERT: H 379 SER cc_start: 0.9334 (t) cc_final: 0.9078 (p) REVERT: H 462 TRP cc_start: 0.6371 (OUTLIER) cc_final: 0.5983 (t-100) REVERT: I 141 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: I 155 ARG cc_start: 0.8705 (ptt-90) cc_final: 0.8402 (ptt-90) REVERT: I 160 ASP cc_start: 0.8025 (t0) cc_final: 0.7593 (t0) REVERT: J 56 MET cc_start: 0.8286 (mtm) cc_final: 0.8060 (mtp) REVERT: J 141 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8006 (mm-30) REVERT: K 102 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8304 (tp30) REVERT: L 86 ASP cc_start: 0.8351 (m-30) cc_final: 0.8108 (m-30) REVERT: L 148 GLU cc_start: 0.9163 (tp30) cc_final: 0.8931 (tp30) REVERT: M 148 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: N 68 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7644 (mm-30) REVERT: N 112 ASN cc_start: 0.8612 (t0) cc_final: 0.8226 (t0) REVERT: N 116 TYR cc_start: 0.8987 (t80) cc_final: 0.8757 (t80) REVERT: N 140 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8529 (tptp) REVERT: O 100 GLU cc_start: 0.8981 (tp30) cc_final: 0.8728 (tp30) REVERT: O 157 ILE cc_start: 0.9263 (pt) cc_final: 0.8992 (pt) REVERT: O 164 GLN cc_start: 0.7599 (mm-40) cc_final: 0.6928 (mm-40) outliers start: 98 outliers final: 58 residues processed: 642 average time/residue: 0.6629 time to fit residues: 519.8331 Evaluate side-chains 624 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 555 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 117 PHE Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 459 CYS Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 309 MET Chi-restraints excluded: chain H residue 449 CYS Chi-restraints excluded: chain H residue 462 TRP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain J residue 112 ASN Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 92 LYS Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 167 CYS Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 148 GLU Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 57 GLN Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 160 ASP Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain P residue 168 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 265 optimal weight: 3.9990 chunk 312 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 415 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 357 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN ** E 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 GLN H 413 ASN H 429 GLN I 103 HIS J 164 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.087902 restraints weight = 58633.458| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.35 r_work: 0.2961 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35754 Z= 0.135 Angle : 0.548 9.526 48496 Z= 0.282 Chirality : 0.043 0.252 5141 Planarity : 0.004 0.056 6321 Dihedral : 4.347 39.767 4840 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 2.51 % Allowed : 18.75 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.13), residues: 4362 helix: 2.11 (0.12), residues: 1739 sheet: 0.01 (0.19), residues: 712 loop : -0.02 (0.15), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 339 TYR 0.020 0.001 TYR K 87 PHE 0.031 0.001 PHE G 345 TRP 0.031 0.001 TRP G 462 HIS 0.008 0.001 HIS M 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (35750) covalent geometry : angle 0.54818 / 0.28 (48488) SS BOND : bond 0.00615 / 0.31 ( 4) SS BOND : angle 1.22136 / 0.71 ( 8) hydrogen bonds : bond 0.03247 / 2.16 ( 1659) hydrogen bonds : angle 4.63495 / 3.40 ( 4635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 591 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7351 (tp30) REVERT: A 140 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9131 (mm) REVERT: A 248 GLU cc_start: 0.8902 (mp0) cc_final: 0.8668 (mp0) REVERT: A 268 ASP cc_start: 0.8794 (m-30) cc_final: 0.8519 (m-30) REVERT: A 327 HIS cc_start: 0.8823 (m170) cc_final: 0.8508 (m90) REVERT: A 357 ASP cc_start: 0.8324 (t70) cc_final: 0.7890 (t0) REVERT: A 369 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.9018 (m) REVERT: B 88 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8065 (mm-30) REVERT: B 128 LYS cc_start: 0.8289 (tmtt) cc_final: 0.8055 (tmmt) REVERT: B 295 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8262 (ptt180) REVERT: B 347 ASP cc_start: 0.8693 (m-30) cc_final: 0.8367 (m-30) REVERT: C 21 LYS cc_start: 0.5607 (pptt) cc_final: 0.4914 (ttpt) REVERT: C 117 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8689 (m-10) REVERT: C 203 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8274 (m-30) REVERT: D 28 GLU cc_start: 0.8407 (pm20) cc_final: 0.8196 (pm20) REVERT: D 156 GLN cc_start: 0.8095 (tp40) cc_final: 0.7757 (tm-30) REVERT: E 200 THR cc_start: 0.9232 (p) cc_final: 0.9013 (p) REVERT: E 305 LYS cc_start: 0.8854 (mptt) cc_final: 0.8518 (tptt) REVERT: E 339 ARG cc_start: 0.8615 (mtp-110) cc_final: 0.7718 (ttp80) REVERT: F 88 GLU cc_start: 0.8460 (tt0) cc_final: 0.8100 (pt0) REVERT: F 387 MET cc_start: 0.9429 (tpp) cc_final: 0.9147 (tpp) REVERT: H 52 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: H 79 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7672 (mtp180) REVERT: H 128 LYS cc_start: 0.8000 (pmtt) cc_final: 0.7354 (pttp) REVERT: H 239 TYR cc_start: 0.9251 (m-10) cc_final: 0.8981 (m-10) REVERT: H 248 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: H 295 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7863 (ptt180) REVERT: H 357 ASP cc_start: 0.8489 (t0) cc_final: 0.8129 (t70) REVERT: H 379 SER cc_start: 0.9336 (t) cc_final: 0.9086 (p) REVERT: H 462 TRP cc_start: 0.6335 (OUTLIER) cc_final: 0.5967 (t-100) REVERT: I 141 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: I 155 ARG cc_start: 0.8711 (ptt-90) cc_final: 0.8399 (ptt-90) REVERT: I 160 ASP cc_start: 0.8083 (t0) cc_final: 0.7632 (t0) REVERT: J 56 MET cc_start: 0.8238 (mtm) cc_final: 0.8018 (mtp) REVERT: J 141 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7993 (mm-30) REVERT: K 102 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8302 (tp30) REVERT: L 86 ASP cc_start: 0.8395 (m-30) cc_final: 0.8157 (m-30) REVERT: L 148 GLU cc_start: 0.9139 (tp30) cc_final: 0.8917 (tp30) REVERT: M 148 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: N 68 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7612 (mm-30) REVERT: N 103 HIS cc_start: 0.9008 (m90) cc_final: 0.8743 (m90) REVERT: N 112 ASN cc_start: 0.8607 (t0) cc_final: 0.8218 (t0) REVERT: N 116 TYR cc_start: 0.9012 (t80) cc_final: 0.8790 (t80) REVERT: N 140 LYS cc_start: 0.9104 (ttpt) cc_final: 0.8518 (tptp) REVERT: N 147 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8495 (ttpp) REVERT: O 100 GLU cc_start: 0.8977 (tp30) cc_final: 0.8698 (tp30) REVERT: O 157 ILE cc_start: 0.9262 (pt) cc_final: 0.8987 (pt) REVERT: O 164 GLN cc_start: 0.7507 (mm-40) cc_final: 0.6920 (mm-40) outliers start: 91 outliers final: 60 residues processed: 638 average time/residue: 0.6610 time to fit residues: 515.4440 Evaluate side-chains 632 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 559 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 117 PHE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 459 CYS Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 309 MET Chi-restraints excluded: chain H residue 449 CYS Chi-restraints excluded: chain H residue 462 TRP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain J residue 112 ASN Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 92 LYS Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 141 GLU Chi-restraints excluded: chain K residue 167 CYS Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 148 GLU Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 57 GLN Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain P residue 57 LYS Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain P residue 168 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 281 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 375 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 191 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN H 156 GLN H 429 GLN I 103 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.104237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.088847 restraints weight = 58890.119| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.34 r_work: 0.2977 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35754 Z= 0.125 Angle : 0.554 11.211 48496 Z= 0.284 Chirality : 0.043 0.237 5141 Planarity : 0.004 0.063 6321 Dihedral : 4.281 36.679 4837 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 2.21 % Allowed : 19.52 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.13), residues: 4362 helix: 2.13 (0.12), residues: 1738 sheet: 0.02 (0.19), residues: 712 loop : 0.01 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 339 TYR 0.025 0.001 TYR K 87 PHE 0.032 0.001 PHE G 345 TRP 0.034 0.001 TRP G 462 HIS 0.010 0.001 HIS M 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (35750) covalent geometry : angle 0.55377 / 0.28 (48488) SS BOND : bond 0.00619 / 0.31 ( 4) SS BOND : angle 1.21158 / 0.71 ( 8) hydrogen bonds : bond 0.03196 / 2.13 ( 1659) hydrogen bonds : angle 4.61542 / 3.39 ( 4635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8724 Ramachandran restraints generated. 4362 Oldfield, 0 Emsley, 4362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 597 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7350 (tp30) REVERT: A 140 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9129 (mm) REVERT: A 248 GLU cc_start: 0.8887 (mp0) cc_final: 0.8670 (mp0) REVERT: A 327 HIS cc_start: 0.8799 (m170) cc_final: 0.8504 (m90) REVERT: A 357 ASP cc_start: 0.8319 (t70) cc_final: 0.7909 (t0) REVERT: A 369 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.9004 (m) REVERT: A 436 ASP cc_start: 0.8393 (t0) cc_final: 0.8047 (t0) REVERT: B 88 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8065 (mm-30) REVERT: B 106 ASP cc_start: 0.9107 (m-30) cc_final: 0.8875 (m-30) REVERT: B 128 LYS cc_start: 0.8290 (tmtt) cc_final: 0.8043 (tmmt) REVERT: B 295 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8261 (ptt180) REVERT: B 334 LYS cc_start: 0.6684 (ttpp) cc_final: 0.6250 (pmtt) REVERT: B 347 ASP cc_start: 0.8604 (m-30) cc_final: 0.8307 (m-30) REVERT: C 21 LYS cc_start: 0.5511 (pptt) cc_final: 0.4873 (ttpt) REVERT: C 117 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8662 (m-10) REVERT: C 203 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8236 (m-30) REVERT: D 28 GLU cc_start: 0.8440 (pm20) cc_final: 0.8234 (pm20) REVERT: D 156 GLN cc_start: 0.8098 (tp40) cc_final: 0.7894 (tm-30) REVERT: E 52 GLU cc_start: 0.8511 (tp30) cc_final: 0.7760 (tt0) REVERT: E 200 THR cc_start: 0.9225 (p) cc_final: 0.9007 (p) REVERT: E 305 LYS cc_start: 0.8846 (mptt) cc_final: 0.8539 (tptt) REVERT: E 339 ARG cc_start: 0.8603 (mtp-110) cc_final: 0.7723 (ttp80) REVERT: F 88 GLU cc_start: 0.8512 (tt0) cc_final: 0.8159 (pt0) REVERT: F 387 MET cc_start: 0.9410 (tpp) cc_final: 0.9123 (tpp) REVERT: G 392 GLU cc_start: 0.8097 (pt0) cc_final: 0.7832 (pm20) REVERT: H 52 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: H 79 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7684 (mtp180) REVERT: H 128 LYS cc_start: 0.7992 (pmtt) cc_final: 0.7359 (pttp) REVERT: H 239 TYR cc_start: 0.9224 (m-10) cc_final: 0.8963 (m-10) REVERT: H 248 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8423 (mp0) REVERT: H 295 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7900 (ptt180) REVERT: H 351 ASP cc_start: 0.8663 (m-30) cc_final: 0.8441 (m-30) REVERT: H 357 ASP cc_start: 0.8493 (t0) cc_final: 0.8132 (t0) REVERT: H 379 SER cc_start: 0.9329 (t) cc_final: 0.9110 (p) REVERT: I 80 GLU cc_start: 0.8535 (mp0) cc_final: 0.7777 (mp0) REVERT: I 141 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: I 155 ARG cc_start: 0.8707 (ptt-90) cc_final: 0.7739 (ptt90) REVERT: I 160 ASP cc_start: 0.8096 (t0) cc_final: 0.7641 (t0) REVERT: J 56 MET cc_start: 0.8221 (mtm) cc_final: 0.8020 (mtp) REVERT: J 141 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8008 (mm-30) REVERT: K 102 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8276 (tp30) REVERT: L 86 ASP cc_start: 0.8410 (m-30) cc_final: 0.8172 (m-30) REVERT: L 148 GLU cc_start: 0.9135 (tp30) cc_final: 0.8927 (tp30) REVERT: M 148 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: N 68 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7640 (mm-30) REVERT: N 112 ASN cc_start: 0.8607 (t0) cc_final: 0.8217 (t0) REVERT: N 116 TYR cc_start: 0.8967 (t80) cc_final: 0.8729 (t80) REVERT: N 140 LYS cc_start: 0.9119 (ttpt) cc_final: 0.8539 (tptp) REVERT: N 147 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8520 (ttpp) REVERT: O 100 GLU cc_start: 0.8917 (tp30) cc_final: 0.8644 (tp30) REVERT: O 157 ILE cc_start: 0.9248 (pt) cc_final: 0.8982 (pt) REVERT: O 164 GLN cc_start: 0.7483 (mm-40) cc_final: 0.6767 (tp40) outliers start: 80 outliers final: 53 residues processed: 639 average time/residue: 0.6508 time to fit residues: 508.8678 Evaluate side-chains 626 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 561 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 117 PHE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 459 CYS Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 149 GLN Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 309 MET Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain J residue 112 ASN Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 141 GLU Chi-restraints excluded: chain K residue 167 CYS Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 148 GLU Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 160 ASP Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain P residue 57 LYS Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain P residue 168 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 94 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 354 optimal weight: 5.9990 chunk 360 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 305 optimal weight: 2.9990 chunk 303 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 218 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN ** E 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 401 GLN H 429 GLN I 103 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.102471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.086938 restraints weight = 58867.555| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.34 r_work: 0.2971 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35754 Z= 0.203 Angle : 0.583 12.380 48496 Z= 0.300 Chirality : 0.045 0.228 5141 Planarity : 0.004 0.097 6321 Dihedral : 4.313 28.729 4836 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.23 % Rotamer: Outliers : 1.96 % Allowed : 20.07 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.13), residues: 4362 helix: 2.07 (0.12), residues: 1738 sheet: -0.01 (0.19), residues: 712 loop : -0.02 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 339 TYR 0.027 0.002 TYR K 87 PHE 0.034 0.002 PHE A 345 TRP 0.035 0.001 TRP A 451 HIS 0.011 0.001 HIS M 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (35750) covalent geometry : angle 0.58314 / 0.30 (48488) SS BOND : bond 0.00553 / 0.28 ( 4) SS BOND : angle 1.26718 / 0.73 ( 8) hydrogen bonds : bond 0.03427 / 2.28 ( 1659) hydrogen bonds : angle 4.66460 / 3.42 ( 4635) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12792.32 seconds wall clock time: 219 minutes 9.73 seconds (13149.73 seconds total)