Starting phenix.real_space_refine on Sun Dec 29 09:12:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sqn_40711/12_2024/8sqn_40711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sqn_40711/12_2024/8sqn_40711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sqn_40711/12_2024/8sqn_40711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sqn_40711/12_2024/8sqn_40711.map" model { file = "/net/cci-nas-00/data/ceres_data/8sqn_40711/12_2024/8sqn_40711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sqn_40711/12_2024/8sqn_40711.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 176 5.16 5 C 18053 2.51 5 N 4916 2.21 5 O 5352 1.98 5 H 27807 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 56304 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4190 Classifications: {'peptide': 265} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 257} Chain: "B" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6568 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 410} Chain: "D" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6429 Classifications: {'peptide': 415} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "F" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6568 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 410} Chain: "H" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6429 Classifications: {'peptide': 415} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "J" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6568 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "L" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6429 Classifications: {'peptide': 415} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "N" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6568 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 410} Chain: "P" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6429 Classifications: {'peptide': 415} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 20.15, per 1000 atoms: 0.36 Number of scatterers: 56304 At special positions: 0 Unit cell: (194.4, 163.2, 210, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 176 16.00 O 5352 8.00 N 4916 7.00 C 18053 6.00 H 27807 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.04 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.04 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.06 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 28 " distance=2.03 Simple disulfide: pdb=" SG CYS D 94 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 269 " distance=2.03 Simple disulfide: pdb=" SG CYS D 204 " - pdb=" SG CYS D 229 " distance=2.03 Simple disulfide: pdb=" SG CYS D 206 " - pdb=" SG CYS D 223 " distance=2.04 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 68 " - pdb=" SG CYS F 78 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.03 Simple disulfide: pdb=" SG CYS F 301 " - pdb=" SG CYS F 376 " distance=2.03 Simple disulfide: pdb=" SG CYS F 306 " - pdb=" SG CYS F 380 " distance=2.03 Simple disulfide: pdb=" SG CYS F 328 " - pdb=" SG CYS F 370 " distance=2.04 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 127 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 28 " distance=2.03 Simple disulfide: pdb=" SG CYS H 94 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 269 " distance=2.03 Simple disulfide: pdb=" SG CYS H 204 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS H 206 " - pdb=" SG CYS H 223 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.04 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.04 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.03 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.04 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 127 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 28 " distance=2.03 Simple disulfide: pdb=" SG CYS L 94 " - pdb=" SG CYS L 108 " distance=2.03 Simple disulfide: pdb=" SG CYS L 155 " - pdb=" SG CYS L 269 " distance=2.03 Simple disulfide: pdb=" SG CYS L 204 " - pdb=" SG CYS L 229 " distance=2.04 Simple disulfide: pdb=" SG CYS L 206 " - pdb=" SG CYS L 223 " distance=2.04 Simple disulfide: pdb=" SG CYS N 49 " - pdb=" SG CYS N 114 " distance=2.03 Simple disulfide: pdb=" SG CYS N 62 " - pdb=" SG CYS N 94 " distance=2.03 Simple disulfide: pdb=" SG CYS N 63 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 68 " - pdb=" SG CYS N 78 " distance=2.03 Simple disulfide: pdb=" SG CYS N 259 " - pdb=" SG CYS N 271 " distance=2.04 Simple disulfide: pdb=" SG CYS N 301 " - pdb=" SG CYS N 376 " distance=2.04 Simple disulfide: pdb=" SG CYS N 306 " - pdb=" SG CYS N 380 " distance=2.03 Simple disulfide: pdb=" SG CYS N 328 " - pdb=" SG CYS N 370 " distance=2.03 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 127 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 28 " distance=2.05 Simple disulfide: pdb=" SG CYS P 94 " - pdb=" SG CYS P 108 " distance=2.03 Simple disulfide: pdb=" SG CYS P 155 " - pdb=" SG CYS P 269 " distance=2.03 Simple disulfide: pdb=" SG CYS P 204 " - pdb=" SG CYS P 229 " distance=2.03 Simple disulfide: pdb=" SG CYS P 206 " - pdb=" SG CYS P 223 " 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 Links applied NAG-ASN " NAG B 501 " - " ASN B 139 " " NAG D 501 " - " ASN D 199 " " NAG F 501 " - " ASN F 139 " " NAG H 501 " - " ASN H 199 " " NAG J 501 " - " ASN J 139 " " NAG L 501 " - " ASN L 199 " " NAG N 501 " - " ASN N 139 " " NAG P 501 " - " ASN P 199 " Time building additional restraints: 11.13 Conformation dependent library (CDL) restraints added in 3.7 seconds 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6860 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 82 sheets defined 14.1% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.38 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.528A pdb=" N ALA A 164 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 237 through 243 Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.538A pdb=" N GLU A 268 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.827A pdb=" N GLY B 258 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 259' Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 403 through 414 Processing helix chain 'B' and resid 416 through 438 removed outlier: 3.596A pdb=" N LEU B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 357 through 365 removed outlier: 4.363A pdb=" N HIS D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 400 removed outlier: 3.570A pdb=" N VAL D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 372 " --> pdb=" O VAL D 368 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 373 " --> pdb=" O TYR D 369 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 374 " --> pdb=" O THR D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 419 Processing helix chain 'F' and resid 113 through 118 Processing helix chain 'F' and resid 238 through 247 removed outlier: 3.602A pdb=" N MET F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 254 removed outlier: 3.648A pdb=" N GLU F 253 " --> pdb=" O PRO F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.830A pdb=" N GLY F 258 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS F 259 " --> pdb=" O PRO F 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 255 through 259' Processing helix chain 'F' and resid 283 through 287 Processing helix chain 'F' and resid 403 through 414 Processing helix chain 'F' and resid 416 through 438 Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 225 through 227 No H-bonds generated for 'chain 'H' and resid 225 through 227' Processing helix chain 'H' and resid 357 through 365 removed outlier: 4.322A pdb=" N HIS H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 401 removed outlier: 3.565A pdb=" N VAL H 371 " --> pdb=" O PRO H 367 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE H 372 " --> pdb=" O VAL H 368 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL H 373 " --> pdb=" O TYR H 369 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 374 " --> pdb=" O THR H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 419 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 238 through 246 Processing helix chain 'J' and resid 255 through 259 removed outlier: 3.635A pdb=" N GLY J 258 " --> pdb=" O ALA J 255 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS J 259 " --> pdb=" O PRO J 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 255 through 259' Processing helix chain 'J' and resid 403 through 414 removed outlier: 3.579A pdb=" N PHE J 414 " --> pdb=" O LEU J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 438 Processing helix chain 'L' and resid 358 through 365 removed outlier: 3.639A pdb=" N TYR L 362 " --> pdb=" O ILE L 358 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 401 removed outlier: 3.710A pdb=" N VAL L 371 " --> pdb=" O PRO L 367 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE L 372 " --> pdb=" O VAL L 368 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL L 373 " --> pdb=" O TYR L 369 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU L 374 " --> pdb=" O THR L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 419 Processing helix chain 'N' and resid 113 through 118 Processing helix chain 'N' and resid 238 through 246 Processing helix chain 'N' and resid 250 through 254 removed outlier: 3.804A pdb=" N GLU N 253 " --> pdb=" O PRO N 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 255 through 259 removed outlier: 3.733A pdb=" N GLY N 258 " --> pdb=" O ALA N 255 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS N 259 " --> pdb=" O PRO N 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 255 through 259' Processing helix chain 'N' and resid 283 through 287 Processing helix chain 'N' and resid 403 through 414 removed outlier: 3.555A pdb=" N PHE N 414 " --> pdb=" O LEU N 410 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 438 removed outlier: 3.910A pdb=" N LEU N 420 " --> pdb=" O GLY N 416 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 84 No H-bonds generated for 'chain 'P' and resid 82 through 84' Processing helix chain 'P' and resid 225 through 227 No H-bonds generated for 'chain 'P' and resid 225 through 227' Processing helix chain 'P' and resid 357 through 365 removed outlier: 4.314A pdb=" N HIS P 361 " --> pdb=" O GLU P 357 " (cutoff:3.500A) Processing helix chain 'P' and resid 366 through 400 removed outlier: 3.577A pdb=" N VAL P 371 " --> pdb=" O PRO P 367 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE P 372 " --> pdb=" O VAL P 368 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL P 373 " --> pdb=" O TYR P 369 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU P 374 " --> pdb=" O THR P 370 " (cutoff:3.500A) Processing helix chain 'P' and resid 411 through 419 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 44 removed outlier: 6.780A pdb=" N VAL A 206 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP A 225 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP A 208 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP A 221 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 93 removed outlier: 6.805A pdb=" N TRP A 74 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASP A 91 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 72 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR A 93 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG A 70 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 10.678A pdb=" N ALA A 173 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LYS A 152 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ILE A 175 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN A 154 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA A 177 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP A 156 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 8 removed outlier: 3.687A pdb=" N ILE B 162 " --> pdb=" O SER B 279 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 17 removed outlier: 5.571A pdb=" N ILE B 31 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL B 136 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL B 33 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG B 134 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B 35 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 41 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N THR B 126 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASN B 43 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL B 124 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU B 45 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU B 122 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 47 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 120 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 140 through 147 removed outlier: 6.750A pdb=" N VAL B 120 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 47 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU B 122 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU B 45 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL B 124 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASN B 43 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N THR B 126 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 41 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B 35 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG B 134 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL B 33 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL B 136 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE B 31 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AB3, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AB4, first strand: chain 'B' and resid 296 through 302 removed outlier: 4.186A pdb=" N VAL B 299 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN B 319 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS B 301 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 317 " --> pdb=" O CYS B 301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 343 through 346 removed outlier: 3.673A pdb=" N GLY B 326 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 387 through 388 removed outlier: 5.865A pdb=" N GLU D 337 " --> pdb=" O TRP D 333 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TRP D 333 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 17 through 19 Processing sheet with id=AB8, first strand: chain 'D' and resid 34 through 38 removed outlier: 4.343A pdb=" N ASN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.203A pdb=" N TYR D 69 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 86 through 89 Processing sheet with id=AC2, first strand: chain 'D' and resid 151 through 158 Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 171 Processing sheet with id=AC4, first strand: chain 'D' and resid 183 through 184 Processing sheet with id=AC5, first strand: chain 'D' and resid 210 through 215 Processing sheet with id=AC6, first strand: chain 'D' and resid 278 through 279 removed outlier: 3.897A pdb=" N THR D 278 " --> pdb=" O HIS D 289 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 2 through 8 Processing sheet with id=AC8, first strand: chain 'F' and resid 15 through 21 removed outlier: 3.622A pdb=" N VAL F 19 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 27 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG F 21 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ALA F 25 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLU F 30 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR F 137 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR F 32 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE F 135 " --> pdb=" O THR F 32 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL F 34 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU F 133 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N SER F 36 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL F 131 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU F 38 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 129 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA F 127 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR F 42 " --> pdb=" O HIS F 125 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS F 125 " --> pdb=" O THR F 42 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS F 44 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS F 123 " --> pdb=" O LYS F 44 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR F 46 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 140 through 147 removed outlier: 3.629A pdb=" N TYR F 46 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS F 123 " --> pdb=" O LYS F 44 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS F 44 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS F 125 " --> pdb=" O THR F 42 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR F 42 " --> pdb=" O HIS F 125 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA F 127 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 129 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU F 38 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL F 131 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N SER F 36 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU F 133 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL F 34 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE F 135 " --> pdb=" O THR F 32 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR F 32 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR F 137 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLU F 30 " --> pdb=" O TYR F 137 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AD2, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AD3, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AD4, first strand: chain 'F' and resid 219 through 221 Processing sheet with id=AD5, first strand: chain 'F' and resid 296 through 302 removed outlier: 4.115A pdb=" N VAL F 299 " --> pdb=" O GLN F 319 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN F 319 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS F 301 " --> pdb=" O THR F 317 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR F 317 " --> pdb=" O CYS F 301 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 343 through 346 removed outlier: 3.748A pdb=" N GLY F 326 " --> pdb=" O VAL F 346 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 387 through 388 Processing sheet with id=AD8, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=AD9, first strand: chain 'H' and resid 34 through 38 removed outlier: 4.309A pdb=" N ASN H 36 " --> pdb=" O GLN H 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN H 49 " --> pdb=" O ASN H 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.692A pdb=" N GLY H 55 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR H 69 " --> pdb=" O GLY H 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 86 through 89 Processing sheet with id=AE3, first strand: chain 'H' and resid 151 through 158 Processing sheet with id=AE4, first strand: chain 'H' and resid 240 through 241 Processing sheet with id=AE5, first strand: chain 'H' and resid 183 through 184 Processing sheet with id=AE6, first strand: chain 'H' and resid 210 through 215 Processing sheet with id=AE7, first strand: chain 'H' and resid 286 through 291 Processing sheet with id=AE8, first strand: chain 'H' and resid 296 through 300 Processing sheet with id=AE9, first strand: chain 'J' and resid 2 through 8 removed outlier: 3.581A pdb=" N ILE J 162 " --> pdb=" O SER J 279 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP J 281 " --> pdb=" O LYS J 160 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LYS J 160 " --> pdb=" O ASP J 281 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 15 through 17 removed outlier: 5.591A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER J 35 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU J 45 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL J 47 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 140 through 147 removed outlier: 6.672A pdb=" N VAL J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL J 47 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU J 45 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER J 35 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 51 through 54 Processing sheet with id=AF4, first strand: chain 'J' and resid 51 through 54 Processing sheet with id=AF5, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AF6, first strand: chain 'J' and resid 220 through 221 Processing sheet with id=AF7, first strand: chain 'J' and resid 296 through 302 removed outlier: 4.064A pdb=" N VAL J 299 " --> pdb=" O GLN J 319 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN J 319 " --> pdb=" O VAL J 299 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N CYS J 301 " --> pdb=" O THR J 317 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR J 317 " --> pdb=" O CYS J 301 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 343 through 346 removed outlier: 3.628A pdb=" N GLY J 326 " --> pdb=" O VAL J 346 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 387 through 388 removed outlier: 5.823A pdb=" N GLU L 337 " --> pdb=" O TRP L 333 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TRP L 333 " --> pdb=" O GLU L 337 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 17 through 19 Processing sheet with id=AG2, first strand: chain 'L' and resid 34 through 38 removed outlier: 4.273A pdb=" N ASN L 36 " --> pdb=" O GLN L 49 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN L 107 " --> pdb=" O ARG L 96 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ARG L 96 " --> pdb=" O GLN L 107 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AG4, first strand: chain 'L' and resid 86 through 89 Processing sheet with id=AG5, first strand: chain 'L' and resid 151 through 158 Processing sheet with id=AG6, first strand: chain 'L' and resid 169 through 171 Processing sheet with id=AG7, first strand: chain 'L' and resid 183 through 184 Processing sheet with id=AG8, first strand: chain 'L' and resid 210 through 215 Processing sheet with id=AG9, first strand: chain 'L' and resid 278 through 279 removed outlier: 3.821A pdb=" N THR L 278 " --> pdb=" O HIS L 289 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 2 through 8 removed outlier: 4.474A pdb=" N ASP N 281 " --> pdb=" O LYS N 160 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS N 160 " --> pdb=" O ASP N 281 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL N 161 " --> pdb=" O GLY N 154 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 15 through 21 removed outlier: 3.601A pdb=" N VAL N 19 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU N 27 " --> pdb=" O VAL N 19 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ARG N 21 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ALA N 25 " --> pdb=" O ARG N 21 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE N 31 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL N 136 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL N 33 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG N 134 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER N 35 " --> pdb=" O GLY N 132 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY N 132 " --> pdb=" O SER N 35 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER N 41 " --> pdb=" O THR N 126 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR N 126 " --> pdb=" O SER N 41 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASN N 43 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL N 124 " --> pdb=" O ASN N 43 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU N 45 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU N 122 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL N 47 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL N 120 " --> pdb=" O VAL N 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 140 through 147 removed outlier: 6.750A pdb=" N VAL N 120 " --> pdb=" O VAL N 47 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL N 47 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU N 122 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU N 45 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL N 124 " --> pdb=" O ASN N 43 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASN N 43 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR N 126 " --> pdb=" O SER N 41 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER N 41 " --> pdb=" O THR N 126 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY N 132 " --> pdb=" O SER N 35 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER N 35 " --> pdb=" O GLY N 132 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG N 134 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL N 33 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL N 136 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE N 31 " --> pdb=" O VAL N 136 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 51 through 54 removed outlier: 3.528A pdb=" N TYR N 107 " --> pdb=" O VAL N 54 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 51 through 54 removed outlier: 3.528A pdb=" N TYR N 107 " --> pdb=" O VAL N 54 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'N' and resid 203 through 204 removed outlier: 3.641A pdb=" N GLN N 204 " --> pdb=" O VAL N 214 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL N 214 " --> pdb=" O GLN N 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'N' and resid 220 through 221 Processing sheet with id=AH8, first strand: chain 'N' and resid 296 through 302 removed outlier: 4.099A pdb=" N VAL N 299 " --> pdb=" O GLN N 319 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN N 319 " --> pdb=" O VAL N 299 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS N 301 " --> pdb=" O THR N 317 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR N 317 " --> pdb=" O CYS N 301 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 343 through 346 removed outlier: 3.714A pdb=" N GLY N 326 " --> pdb=" O VAL N 346 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'N' and resid 387 through 388 Processing sheet with id=AI2, first strand: chain 'P' and resid 17 through 19 Processing sheet with id=AI3, first strand: chain 'P' and resid 37 through 38 removed outlier: 10.563A pdb=" N SER P 51 " --> pdb=" O ASP P 73 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP P 73 " --> pdb=" O SER P 51 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N TYR P 69 " --> pdb=" O GLY P 55 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'P' and resid 37 through 38 removed outlier: 11.264A pdb=" N ILE P 48 " --> pdb=" O GLN P 107 " (cutoff:3.500A) removed outlier: 10.550A pdb=" N GLN P 107 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N VAL P 50 " --> pdb=" O LEU P 105 " (cutoff:3.500A) removed outlier: 10.471A pdb=" N LEU P 105 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N ALA P 52 " --> pdb=" O PHE P 103 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE P 103 " --> pdb=" O ALA P 52 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR P 56 " --> pdb=" O HIS P 99 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N HIS P 99 " --> pdb=" O TYR P 56 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE P 88 " --> pdb=" O CYS P 94 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG P 96 " --> pdb=" O LEU P 86 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N LEU P 86 " --> pdb=" O ARG P 96 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'P' and resid 151 through 158 Processing sheet with id=AI6, first strand: chain 'P' and resid 169 through 171 Processing sheet with id=AI7, first strand: chain 'P' and resid 183 through 184 Processing sheet with id=AI8, first strand: chain 'P' and resid 210 through 215 Processing sheet with id=AI9, first strand: chain 'P' and resid 286 through 290 Processing sheet with id=AJ1, first strand: chain 'P' and resid 296 through 300 1016 hydrogen bonds defined for protein. 2607 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: 21.48 Time building geometry restraints manager: 13.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 27806 1.04 - 1.24: 3885 1.24 - 1.45: 8859 1.45 - 1.65: 16287 1.65 - 1.85: 214 Bond restraints: 57051 Sorted by residual: bond pdb=" N PHE B 1 " pdb=" H3 PHE B 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N ILE L 5 " pdb=" H3 ILE L 5 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N ILE H 5 " pdb=" H2 ILE H 5 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N ILE P 5 " pdb=" H2 ILE P 5 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N PHE N 1 " pdb=" H3 PHE N 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 57046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.02: 103105 21.02 - 42.04: 17 42.04 - 63.05: 0 63.05 - 84.07: 0 84.07 - 105.09: 4 Bond angle restraints: 103126 Sorted by residual: angle pdb=" H1 ILE H 5 " pdb=" N ILE H 5 " pdb=" H2 ILE H 5 " ideal model delta sigma weight residual 109.47 4.38 105.09 3.00e+00 1.11e-01 1.23e+03 angle pdb=" H1 ILE L 5 " pdb=" N ILE L 5 " pdb=" H2 ILE L 5 " ideal model delta sigma weight residual 109.47 4.47 105.00 3.00e+00 1.11e-01 1.22e+03 angle pdb=" H1 ILE D 5 " pdb=" N ILE D 5 " pdb=" H2 ILE D 5 " ideal model delta sigma weight residual 109.47 7.85 101.62 3.00e+00 1.11e-01 1.15e+03 angle pdb=" H1 ILE P 5 " pdb=" N ILE P 5 " pdb=" H2 ILE P 5 " ideal model delta sigma weight residual 109.47 11.04 98.43 3.00e+00 1.11e-01 1.08e+03 angle pdb=" CB LEU H 405 " pdb=" CA LEU H 405 " pdb=" HA LEU H 405 " ideal model delta sigma weight residual 109.00 73.59 35.41 3.00e+00 1.11e-01 1.39e+02 ... (remaining 103121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 24069 17.99 - 35.98: 2425 35.98 - 53.98: 799 53.98 - 71.97: 149 71.97 - 89.96: 37 Dihedral angle restraints: 27479 sinusoidal: 14798 harmonic: 12681 Sorted by residual: dihedral pdb=" CB CYS H 155 " pdb=" SG CYS H 155 " pdb=" SG CYS H 269 " pdb=" CB CYS H 269 " ideal model delta sinusoidal sigma weight residual -86.00 -164.66 78.66 1 1.00e+01 1.00e-02 7.71e+01 dihedral pdb=" CB CYS B 328 " pdb=" SG CYS B 328 " pdb=" SG CYS B 370 " pdb=" CB CYS B 370 " ideal model delta sinusoidal sigma weight residual -86.00 -7.42 -78.58 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS P 22 " pdb=" SG CYS P 22 " pdb=" SG CYS P 28 " pdb=" CB CYS P 28 " ideal model delta sinusoidal sigma weight residual 93.00 17.82 75.18 1 1.00e+01 1.00e-02 7.14e+01 ... (remaining 27476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4073 0.078 - 0.156: 451 0.156 - 0.234: 1 0.234 - 0.312: 1 0.312 - 0.390: 4 Chirality restraints: 4530 Sorted by residual: chirality pdb=" CA LEU L 405 " pdb=" N LEU L 405 " pdb=" C LEU L 405 " pdb=" CB LEU L 405 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA LEU P 405 " pdb=" N LEU P 405 " pdb=" C LEU P 405 " pdb=" CB LEU P 405 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA LEU H 405 " pdb=" N LEU H 405 " pdb=" C LEU H 405 " pdb=" CB LEU H 405 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 4527 not shown) Planarity restraints: 8542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 264 " -0.116 5.00e-02 4.00e+02 1.67e-01 4.49e+01 pdb=" N PRO F 265 " 0.289 5.00e-02 4.00e+02 pdb=" CA PRO F 265 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO F 265 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 152 " -0.067 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO J 153 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO J 153 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO J 153 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 85 " -0.055 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO F 86 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO F 86 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 86 " -0.046 5.00e-02 4.00e+02 ... (remaining 8539 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 1865 2.13 - 2.75: 102550 2.75 - 3.37: 154288 3.37 - 3.98: 191789 3.98 - 4.60: 291620 Nonbonded interactions: 742112 Sorted by model distance: nonbonded pdb=" OE1 GLU F 264 " pdb=" H GLU F 264 " model vdw 1.518 2.450 nonbonded pdb=" OE1 GLU L 327 " pdb=" H GLU L 327 " model vdw 1.521 2.450 nonbonded pdb=" OE1 GLU J 390 " pdb=" H GLU J 390 " model vdw 1.522 2.450 nonbonded pdb="HH12 ARG D 47 " pdb=" O PRO D 261 " model vdw 1.536 2.450 nonbonded pdb=" O LEU A 240 " pdb=" H VAL A 244 " model vdw 1.555 2.450 ... (remaining 742107 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 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.770 Extract box with map and model: 1.530 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 92.090 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.170 29244 Z= 0.209 Angle : 0.605 14.629 39858 Z= 0.320 Chirality : 0.045 0.390 4530 Planarity : 0.005 0.167 5093 Dihedral : 15.801 88.657 10640 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.29 % Allowed : 23.09 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3659 helix: 2.32 (0.27), residues: 395 sheet: -0.92 (0.15), residues: 1210 loop : -1.06 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 282 HIS 0.008 0.001 HIS P 149 PHE 0.022 0.001 PHE J 95 TYR 0.019 0.001 TYR H 182 ARG 0.005 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 553 time to evaluate : 3.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 ASN cc_start: 0.8074 (p0) cc_final: 0.7794 (p0) REVERT: J 46 TYR cc_start: 0.8782 (p90) cc_final: 0.8347 (p90) REVERT: J 218 ASP cc_start: 0.7814 (t0) cc_final: 0.7527 (t0) REVERT: L 69 TYR cc_start: 0.6299 (m-10) cc_final: 0.5749 (m-10) REVERT: L 80 GLU cc_start: 0.5793 (tt0) cc_final: 0.5362 (tt0) outliers start: 9 outliers final: 7 residues processed: 559 average time/residue: 0.6871 time to fit residues: 611.5765 Evaluate side-chains 536 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 529 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain P residue 108 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 4.9990 chunk 274 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 93 optimal weight: 0.4980 chunk 185 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 328 optimal weight: 5.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 154 GLN ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS D 53 GLN D 74 HIS ** D 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 HIS H 74 HIS H 249 HIS ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 321 ASN J 9 ASN ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 275 HIS ** J 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 HIS L 249 HIS ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 335 ASN N 228 ASN ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 24 HIS P 149 HIS P 249 HIS ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 29244 Z= 0.368 Angle : 0.631 6.407 39858 Z= 0.337 Chirality : 0.047 0.394 4530 Planarity : 0.005 0.113 5093 Dihedral : 5.402 65.025 4190 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.27 % Allowed : 21.10 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3659 helix: 2.21 (0.25), residues: 414 sheet: -1.24 (0.15), residues: 1213 loop : -1.25 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 243 HIS 0.009 0.001 HIS D 172 PHE 0.017 0.002 PHE P 54 TYR 0.019 0.002 TYR H 21 ARG 0.005 0.000 ARG H 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 555 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.7343 (OUTLIER) cc_final: 0.7096 (p) REVERT: B 100 ASN cc_start: 0.8405 (p0) cc_final: 0.8158 (p0) REVERT: B 103 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7891 (tp) REVERT: B 377 ASN cc_start: 0.7923 (p0) cc_final: 0.7662 (p0) REVERT: D 220 MET cc_start: 0.5875 (mmp) cc_final: 0.5143 (mmt) REVERT: F 117 ASP cc_start: 0.8143 (t0) cc_final: 0.7886 (t0) REVERT: F 196 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.7971 (p0) REVERT: F 202 ASP cc_start: 0.7605 (p0) cc_final: 0.7163 (p0) REVERT: F 219 ILE cc_start: 0.8842 (mp) cc_final: 0.8630 (tt) REVERT: H 234 ARG cc_start: 0.7206 (ptt90) cc_final: 0.6885 (ptt90) REVERT: H 248 ARG cc_start: 0.7615 (mtp180) cc_final: 0.7150 (mtp180) REVERT: J 238 SER cc_start: 0.8400 (t) cc_final: 0.8041 (p) REVERT: J 352 ILE cc_start: 0.7704 (tt) cc_final: 0.7477 (mm) REVERT: L 69 TYR cc_start: 0.6738 (m-10) cc_final: 0.5990 (m-10) REVERT: L 80 GLU cc_start: 0.6134 (tt0) cc_final: 0.5817 (tt0) REVERT: N 99 GLU cc_start: 0.7567 (mp0) cc_final: 0.7349 (mp0) REVERT: N 387 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8079 (pt) outliers start: 102 outliers final: 64 residues processed: 617 average time/residue: 0.7640 time to fit residues: 759.7588 Evaluate side-chains 595 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 527 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 241 PHE Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 110 PHE Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 107 TYR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain N residue 367 VAL Chi-restraints excluded: chain N residue 387 ILE Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 149 HIS Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 317 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 182 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 273 optimal weight: 0.0970 chunk 223 optimal weight: 0.0980 chunk 90 optimal weight: 6.9990 chunk 329 optimal weight: 1.9990 chunk 355 optimal weight: 0.9980 chunk 293 optimal weight: 1.9990 chunk 326 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 264 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN D 99 HIS ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 HIS ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 HIS ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 335 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29244 Z= 0.171 Angle : 0.559 6.618 39858 Z= 0.292 Chirality : 0.046 0.385 4530 Planarity : 0.004 0.087 5093 Dihedral : 5.063 66.101 4186 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.37 % Allowed : 21.97 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3659 helix: 2.28 (0.25), residues: 413 sheet: -1.11 (0.15), residues: 1208 loop : -1.14 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 243 HIS 0.029 0.001 HIS P 149 PHE 0.013 0.001 PHE J 95 TYR 0.018 0.001 TYR L 21 ARG 0.006 0.000 ARG F 267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 554 time to evaluate : 3.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 CYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6462 (p) REVERT: A 139 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.7126 (m-40) REVERT: D 220 MET cc_start: 0.5936 (mmp) cc_final: 0.5243 (mmt) REVERT: D 262 PHE cc_start: 0.7517 (m-80) cc_final: 0.6697 (m-10) REVERT: D 327 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: F 95 PHE cc_start: 0.6260 (p90) cc_final: 0.6057 (p90) REVERT: F 117 ASP cc_start: 0.8080 (t0) cc_final: 0.7839 (t0) REVERT: F 219 ILE cc_start: 0.8796 (mp) cc_final: 0.8579 (tt) REVERT: F 334 SER cc_start: 0.8217 (m) cc_final: 0.7826 (t) REVERT: H 169 ILE cc_start: 0.6210 (OUTLIER) cc_final: 0.5991 (tt) REVERT: H 234 ARG cc_start: 0.7274 (ptt90) cc_final: 0.6904 (ptt90) REVERT: H 248 ARG cc_start: 0.7252 (mtp180) cc_final: 0.6948 (mtp180) REVERT: J 144 LEU cc_start: 0.7534 (tp) cc_final: 0.7330 (tp) REVERT: J 373 LYS cc_start: 0.7318 (mttm) cc_final: 0.7055 (mttp) REVERT: L 69 TYR cc_start: 0.6695 (m-10) cc_final: 0.5896 (m-10) REVERT: L 80 GLU cc_start: 0.6077 (tt0) cc_final: 0.5778 (tt0) REVERT: N 87 PHE cc_start: 0.8088 (m-10) cc_final: 0.7787 (m-10) REVERT: P 149 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7684 (p-80) outliers start: 74 outliers final: 48 residues processed: 606 average time/residue: 0.6835 time to fit residues: 660.3646 Evaluate side-chains 588 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 535 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 346 VAL Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 149 HIS Chi-restraints excluded: chain P residue 227 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 325 optimal weight: 2.9990 chunk 247 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 330 optimal weight: 0.9990 chunk 349 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 313 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS D 53 GLN ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 HIS ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 149 HIS ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29244 Z= 0.213 Angle : 0.554 6.482 39858 Z= 0.290 Chirality : 0.045 0.386 4530 Planarity : 0.004 0.094 5093 Dihedral : 5.005 66.593 4185 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 3.04 % Allowed : 21.90 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3659 helix: 2.34 (0.25), residues: 413 sheet: -1.15 (0.15), residues: 1208 loop : -1.16 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 243 HIS 0.009 0.001 HIS P 149 PHE 0.012 0.001 PHE J 95 TYR 0.011 0.001 TYR H 182 ARG 0.003 0.000 ARG N 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 544 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7724 (tp) REVERT: B 241 GLU cc_start: 0.7626 (tp30) cc_final: 0.7353 (tp30) REVERT: D 43 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7326 (t0) REVERT: D 80 GLU cc_start: 0.7601 (pm20) cc_final: 0.7322 (pm20) REVERT: D 220 MET cc_start: 0.6020 (mmp) cc_final: 0.5378 (mmt) REVERT: D 327 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7468 (pm20) REVERT: F 95 PHE cc_start: 0.6464 (p90) cc_final: 0.6109 (p90) REVERT: F 117 ASP cc_start: 0.8161 (t0) cc_final: 0.7915 (t0) REVERT: F 196 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.7954 (p0) REVERT: F 334 SER cc_start: 0.8241 (m) cc_final: 0.7850 (t) REVERT: H 234 ARG cc_start: 0.7211 (ptt90) cc_final: 0.6849 (ptt90) REVERT: J 45 GLU cc_start: 0.8221 (tp30) cc_final: 0.7878 (tp30) REVERT: J 46 TYR cc_start: 0.8984 (p90) cc_final: 0.8560 (p90) REVERT: J 144 LEU cc_start: 0.7616 (tp) cc_final: 0.7361 (tp) REVERT: L 115 THR cc_start: 0.8616 (m) cc_final: 0.8404 (t) REVERT: N 87 PHE cc_start: 0.8085 (m-10) cc_final: 0.7848 (m-10) outliers start: 95 outliers final: 63 residues processed: 605 average time/residue: 0.7034 time to fit residues: 681.0287 Evaluate side-chains 596 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 529 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 110 PHE Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 321 LYS Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 78 CYS Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 149 HIS Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 265 THR Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 312 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 291 optimal weight: 0.4980 chunk 198 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 260 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 chunk 241 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN ** J 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29244 Z= 0.208 Angle : 0.552 6.499 39858 Z= 0.288 Chirality : 0.045 0.385 4530 Planarity : 0.004 0.081 5093 Dihedral : 4.931 67.224 4184 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.65 % Allowed : 21.04 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3659 helix: 2.40 (0.25), residues: 413 sheet: -1.19 (0.15), residues: 1216 loop : -1.12 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 243 HIS 0.017 0.001 HIS P 149 PHE 0.021 0.001 PHE F 95 TYR 0.016 0.001 TYR L 21 ARG 0.003 0.000 ARG H 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 544 time to evaluate : 3.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7678 (tp) REVERT: B 366 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8610 (mm) REVERT: B 368 SER cc_start: 0.8731 (t) cc_final: 0.8520 (t) REVERT: B 406 SER cc_start: 0.7527 (OUTLIER) cc_final: 0.7140 (t) REVERT: D 80 GLU cc_start: 0.7503 (pm20) cc_final: 0.7223 (pm20) REVERT: D 220 MET cc_start: 0.6028 (mmp) cc_final: 0.5426 (mmt) REVERT: D 262 PHE cc_start: 0.7630 (m-80) cc_final: 0.6543 (m-10) REVERT: D 327 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: F 117 ASP cc_start: 0.8174 (t0) cc_final: 0.7945 (t0) REVERT: F 196 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.7953 (p0) REVERT: F 334 SER cc_start: 0.8265 (m) cc_final: 0.7868 (t) REVERT: H 234 ARG cc_start: 0.7230 (ptt90) cc_final: 0.6855 (ptt90) REVERT: J 45 GLU cc_start: 0.8185 (tp30) cc_final: 0.7870 (tp30) REVERT: J 46 TYR cc_start: 0.8971 (p90) cc_final: 0.8553 (p90) outliers start: 114 outliers final: 85 residues processed: 619 average time/residue: 0.7176 time to fit residues: 709.7780 Evaluate side-chains 617 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 527 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 110 PHE Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 MET Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 265 THR Chi-restraints excluded: chain P residue 312 GLU Chi-restraints excluded: chain P residue 345 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 117 optimal weight: 3.9990 chunk 315 optimal weight: 1.9990 chunk 69 optimal weight: 0.0470 chunk 205 optimal weight: 2.9990 chunk 86 optimal weight: 0.0370 chunk 350 optimal weight: 0.9980 chunk 290 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 overall best weight: 0.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 HIS ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN ** J 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 HIS ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 149 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29244 Z= 0.168 Angle : 0.538 7.626 39858 Z= 0.279 Chirality : 0.045 0.383 4530 Planarity : 0.004 0.072 5093 Dihedral : 4.818 67.990 4184 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.17 % Allowed : 21.42 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3659 helix: 2.51 (0.25), residues: 414 sheet: -1.06 (0.15), residues: 1200 loop : -1.10 (0.14), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 243 HIS 0.009 0.001 HIS P 149 PHE 0.040 0.001 PHE F 95 TYR 0.012 0.001 TYR D 21 ARG 0.004 0.000 ARG H 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 545 time to evaluate : 3.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7568 (mt-10) REVERT: B 103 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7626 (tp) REVERT: B 241 GLU cc_start: 0.7586 (tp30) cc_final: 0.7297 (tp30) REVERT: B 368 SER cc_start: 0.8749 (t) cc_final: 0.8544 (t) REVERT: D 80 GLU cc_start: 0.7428 (pm20) cc_final: 0.7142 (pm20) REVERT: D 220 MET cc_start: 0.6061 (mmp) cc_final: 0.5472 (mmt) REVERT: D 262 PHE cc_start: 0.7551 (m-80) cc_final: 0.6400 (m-10) REVERT: D 327 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7550 (pm20) REVERT: F 117 ASP cc_start: 0.8143 (t0) cc_final: 0.7913 (t0) REVERT: F 196 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8026 (p0) REVERT: F 334 SER cc_start: 0.8276 (m) cc_final: 0.7901 (t) REVERT: H 13 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8614 (p) REVERT: H 257 LYS cc_start: 0.6881 (pptt) cc_final: 0.6253 (pttt) REVERT: J 45 GLU cc_start: 0.8145 (tp30) cc_final: 0.7888 (tp30) REVERT: J 46 TYR cc_start: 0.8928 (p90) cc_final: 0.8520 (p90) REVERT: L 248 ARG cc_start: 0.7945 (mtt-85) cc_final: 0.7520 (ttm-80) outliers start: 99 outliers final: 80 residues processed: 607 average time/residue: 0.7465 time to fit residues: 724.7707 Evaluate side-chains 604 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 520 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 MET Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 263 ARG Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 225 SER Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 265 THR Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 312 GLU Chi-restraints excluded: chain P residue 345 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 337 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 255 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 294 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 348 optimal weight: 0.7980 chunk 218 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN L 24 HIS ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29244 Z= 0.189 Angle : 0.542 6.703 39858 Z= 0.281 Chirality : 0.045 0.384 4530 Planarity : 0.004 0.066 5093 Dihedral : 4.800 68.495 4184 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.46 % Allowed : 21.17 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3659 helix: 2.59 (0.26), residues: 414 sheet: -1.04 (0.15), residues: 1200 loop : -1.10 (0.14), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 243 HIS 0.005 0.001 HIS H 275 PHE 0.023 0.001 PHE F 95 TYR 0.014 0.001 TYR L 21 ARG 0.004 0.000 ARG H 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 542 time to evaluate : 3.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7678 (tp) REVERT: B 368 SER cc_start: 0.8709 (t) cc_final: 0.8505 (t) REVERT: D 80 GLU cc_start: 0.7445 (pm20) cc_final: 0.7146 (pm20) REVERT: D 220 MET cc_start: 0.6080 (mmp) cc_final: 0.5502 (mmt) REVERT: D 262 PHE cc_start: 0.7701 (m-80) cc_final: 0.6545 (m-10) REVERT: D 327 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: F 117 ASP cc_start: 0.8160 (t0) cc_final: 0.7930 (t0) REVERT: F 196 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8058 (p0) REVERT: F 334 SER cc_start: 0.8287 (m) cc_final: 0.7916 (t) REVERT: H 234 ARG cc_start: 0.7218 (ptt90) cc_final: 0.6842 (ptt90) REVERT: H 257 LYS cc_start: 0.6835 (pptt) cc_final: 0.6211 (pttt) REVERT: J 45 GLU cc_start: 0.8144 (tp30) cc_final: 0.7874 (tp30) REVERT: J 46 TYR cc_start: 0.8935 (p90) cc_final: 0.8560 (p90) REVERT: J 218 ASP cc_start: 0.7948 (t0) cc_final: 0.7718 (t0) REVERT: L 248 ARG cc_start: 0.7970 (mtt-85) cc_final: 0.7536 (ttm-80) REVERT: N 99 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7349 (mp0) outliers start: 108 outliers final: 88 residues processed: 612 average time/residue: 0.7163 time to fit residues: 697.8204 Evaluate side-chains 619 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 528 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 110 PHE Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 MET Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 263 ARG Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 225 SER Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain N residue 428 LEU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 265 THR Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 312 GLU Chi-restraints excluded: chain P residue 345 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 215 optimal weight: 0.0270 chunk 139 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 221 optimal weight: 0.5980 chunk 237 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 274 optimal weight: 20.0000 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 HIS ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN N 364 ASN ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29244 Z= 0.165 Angle : 0.536 6.475 39858 Z= 0.277 Chirality : 0.045 0.383 4530 Planarity : 0.004 0.062 5093 Dihedral : 4.735 69.186 4182 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.17 % Allowed : 21.65 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3659 helix: 2.64 (0.26), residues: 414 sheet: -0.99 (0.15), residues: 1200 loop : -1.08 (0.14), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 282 HIS 0.006 0.001 HIS B 392 PHE 0.023 0.001 PHE F 95 TYR 0.012 0.001 TYR A 104 ARG 0.005 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 538 time to evaluate : 3.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.5869 (tp40) REVERT: B 103 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7627 (tp) REVERT: B 241 GLU cc_start: 0.7631 (tp30) cc_final: 0.7171 (tm-30) REVERT: D 80 GLU cc_start: 0.7450 (pm20) cc_final: 0.7154 (pm20) REVERT: D 220 MET cc_start: 0.6058 (mmp) cc_final: 0.5475 (mmt) REVERT: D 262 PHE cc_start: 0.7746 (m-80) cc_final: 0.6667 (m-10) REVERT: D 327 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: F 117 ASP cc_start: 0.8131 (t0) cc_final: 0.7899 (t0) REVERT: F 196 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.8028 (p0) REVERT: F 334 SER cc_start: 0.8276 (m) cc_final: 0.7911 (t) REVERT: H 203 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6972 (mt-10) REVERT: H 234 ARG cc_start: 0.7273 (ptt90) cc_final: 0.6890 (ptt90) REVERT: H 257 LYS cc_start: 0.6874 (pptt) cc_final: 0.6255 (pttt) REVERT: J 45 GLU cc_start: 0.8110 (tp30) cc_final: 0.7881 (tp30) REVERT: J 46 TYR cc_start: 0.8872 (p90) cc_final: 0.8496 (p90) REVERT: J 218 ASP cc_start: 0.7949 (t0) cc_final: 0.7710 (t0) REVERT: L 128 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8230 (p) REVERT: L 248 ARG cc_start: 0.7936 (mtt-85) cc_final: 0.7521 (ttm-80) REVERT: N 99 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7324 (mp0) outliers start: 99 outliers final: 82 residues processed: 601 average time/residue: 0.7387 time to fit residues: 706.0817 Evaluate side-chains 609 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 522 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 MET Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 263 ARG Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 364 ASN Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain N residue 428 LEU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 265 THR Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 312 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 317 optimal weight: 1.9990 chunk 334 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 325 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 255 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 307 optimal weight: 3.9990 chunk 324 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN ** J 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29244 Z= 0.341 Angle : 0.598 6.532 39858 Z= 0.316 Chirality : 0.046 0.390 4530 Planarity : 0.005 0.064 5093 Dihedral : 4.958 69.090 4182 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.46 % Allowed : 21.52 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.14), residues: 3659 helix: 2.61 (0.26), residues: 414 sheet: -1.18 (0.15), residues: 1200 loop : -1.24 (0.14), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 282 HIS 0.009 0.001 HIS B 331 PHE 0.044 0.002 PHE N 365 TYR 0.019 0.002 TYR L 21 ARG 0.005 0.001 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 522 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7799 (tp) REVERT: B 406 SER cc_start: 0.7782 (OUTLIER) cc_final: 0.7447 (t) REVERT: D 80 GLU cc_start: 0.7545 (pm20) cc_final: 0.7237 (pm20) REVERT: D 220 MET cc_start: 0.6241 (mmp) cc_final: 0.5683 (mmt) REVERT: D 262 PHE cc_start: 0.8019 (m-80) cc_final: 0.6811 (m-10) REVERT: D 327 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7746 (pm20) REVERT: F 39 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7768 (p) REVERT: F 117 ASP cc_start: 0.8297 (t0) cc_final: 0.8011 (t0) REVERT: F 196 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8183 (p0) REVERT: F 334 SER cc_start: 0.8356 (m) cc_final: 0.7987 (t) REVERT: H 21 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.7088 (m-80) REVERT: H 257 LYS cc_start: 0.7020 (pptt) cc_final: 0.6400 (pttt) REVERT: J 93 GLN cc_start: 0.6662 (tm-30) cc_final: 0.6309 (tm-30) REVERT: L 115 THR cc_start: 0.8809 (m) cc_final: 0.8592 (p) REVERT: N 75 ASP cc_start: 0.8334 (t0) cc_final: 0.7691 (t0) outliers start: 108 outliers final: 89 residues processed: 593 average time/residue: 0.7187 time to fit residues: 670.6242 Evaluate side-chains 610 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 515 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 110 PHE Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 MET Chi-restraints excluded: chain L residue 263 ARG Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 225 SER Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 346 VAL Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain N residue 428 LEU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 265 THR Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 312 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 213 optimal weight: 0.9980 chunk 343 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 239 optimal weight: 0.0980 chunk 360 optimal weight: 0.9990 chunk 331 optimal weight: 0.9990 chunk 287 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN N 364 ASN ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 29244 Z= 0.191 Angle : 0.572 12.361 39858 Z= 0.297 Chirality : 0.045 0.385 4530 Planarity : 0.004 0.065 5093 Dihedral : 4.872 69.696 4182 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.75 % Rotamer: Outliers : 2.85 % Allowed : 22.51 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3659 helix: 2.65 (0.26), residues: 414 sheet: -1.04 (0.15), residues: 1192 loop : -1.17 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 243 HIS 0.005 0.001 HIS D 172 PHE 0.012 0.001 PHE F 95 TYR 0.013 0.001 TYR D 21 ARG 0.005 0.000 ARG H 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 517 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.5955 (tp40) REVERT: B 103 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7638 (tp) REVERT: B 241 GLU cc_start: 0.7665 (tp30) cc_final: 0.7288 (tp30) REVERT: D 80 GLU cc_start: 0.7470 (pm20) cc_final: 0.7177 (pm20) REVERT: D 220 MET cc_start: 0.6169 (mmp) cc_final: 0.5606 (mmt) REVERT: D 262 PHE cc_start: 0.7768 (m-80) cc_final: 0.6552 (m-10) REVERT: D 327 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: F 39 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7727 (p) REVERT: F 117 ASP cc_start: 0.8226 (t0) cc_final: 0.8009 (t0) REVERT: F 196 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8075 (p0) REVERT: F 334 SER cc_start: 0.8326 (m) cc_final: 0.7981 (t) REVERT: H 203 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7175 (mt-10) REVERT: H 234 ARG cc_start: 0.7260 (ptt90) cc_final: 0.6906 (ptt90) REVERT: H 257 LYS cc_start: 0.7009 (pptt) cc_final: 0.6394 (pttt) REVERT: J 46 TYR cc_start: 0.8903 (p90) cc_final: 0.8525 (p90) REVERT: L 248 ARG cc_start: 0.7964 (mtt-85) cc_final: 0.7504 (ttm-80) REVERT: N 75 ASP cc_start: 0.8231 (t0) cc_final: 0.7585 (t0) outliers start: 89 outliers final: 75 residues processed: 574 average time/residue: 0.7216 time to fit residues: 651.0612 Evaluate side-chains 596 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 516 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain H residue 232 TYR Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 MET Chi-restraints excluded: chain L residue 204 CYS Chi-restraints excluded: chain L residue 263 ARG Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain N residue 428 LEU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 312 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 228 optimal weight: 6.9990 chunk 305 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 264 optimal weight: 0.8980 chunk 42 optimal weight: 0.0770 chunk 79 optimal weight: 0.7980 chunk 287 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.185014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.145115 restraints weight = 104860.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.144438 restraints weight = 96385.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.147694 restraints weight = 78420.030| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 29244 Z= 0.194 Angle : 0.566 9.233 39858 Z= 0.293 Chirality : 0.045 0.385 4530 Planarity : 0.004 0.063 5093 Dihedral : 4.828 70.203 4182 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 2.75 % Allowed : 22.70 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3659 helix: 2.69 (0.26), residues: 414 sheet: -1.04 (0.15), residues: 1192 loop : -1.16 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 243 HIS 0.005 0.001 HIS D 172 PHE 0.020 0.001 PHE F 95 TYR 0.013 0.001 TYR H 232 ARG 0.005 0.000 ARG H 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11235.30 seconds wall clock time: 195 minutes 6.37 seconds (11706.37 seconds total)