Starting phenix.real_space_refine on Sun Aug 24 11:41:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dzf_27796/08_2025/8dzf_27796_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dzf_27796/08_2025/8dzf_27796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dzf_27796/08_2025/8dzf_27796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dzf_27796/08_2025/8dzf_27796.map" model { file = "/net/cci-nas-00/data/ceres_data/8dzf_27796/08_2025/8dzf_27796_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dzf_27796/08_2025/8dzf_27796_neut.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 18 5.49 5 S 84 5.16 5 C 12102 2.51 5 N 3390 2.21 5 O 3708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19308 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2171 SG CYS A 403 90.750 129.513 31.549 1.00158.25 S ATOM 2191 SG CYS A 406 94.003 131.502 31.911 1.00169.76 S ATOM 2475 SG CYS A 445 90.833 132.641 33.583 1.00185.26 S ATOM 2481 SG CYS A 446 92.703 129.447 34.824 1.00172.25 S Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.76, per 1000 atoms: 0.14 Number of scatterers: 19308 At special positions: 0 Unit cell: (147.96, 143.64, 82.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 84 16.00 P 18 15.00 O 3708 8.00 N 3390 7.00 C 12102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 943.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 403 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 406 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 445 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 446 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 406 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 403 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 445 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 446 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 406 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 403 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 445 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 446 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 403 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 406 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 445 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 446 " pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 406 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 403 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 445 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 446 " pdb=" ZN F 601 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 406 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 403 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 445 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 446 " Number of angles added : 36 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4668 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 43.6% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 238 through 250 removed outlier: 3.634A pdb=" N ASN A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 281 Processing helix chain 'A' and resid 312 through 327 removed outlier: 3.928A pdb=" N LEU A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 355 removed outlier: 3.865A pdb=" N GLY A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.100A pdb=" N ASP A 386 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.814A pdb=" N SER A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.581A pdb=" N ARG A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 477 through 485 Processing helix chain 'A' and resid 490 through 502 Processing helix chain 'A' and resid 505 through 513 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 520 through 534 Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 153 through 166 Processing helix chain 'B' and resid 238 through 250 removed outlier: 3.633A pdb=" N ASN B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 281 Processing helix chain 'B' and resid 312 through 327 removed outlier: 3.927A pdb=" N LEU B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 355 removed outlier: 3.865A pdb=" N GLY B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 378 Processing helix chain 'B' and resid 382 through 386 removed outlier: 4.100A pdb=" N ASP B 386 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 416 removed outlier: 3.815A pdb=" N SER B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 428 removed outlier: 3.580A pdb=" N ARG B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS B 426 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE B 427 " --> pdb=" O THR B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'B' and resid 490 through 502 Processing helix chain 'B' and resid 505 through 513 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 520 through 534 Processing helix chain 'C' and resid 108 through 120 Processing helix chain 'C' and resid 153 through 166 Processing helix chain 'C' and resid 238 through 250 removed outlier: 3.632A pdb=" N ASN C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 281 Processing helix chain 'C' and resid 312 through 327 removed outlier: 3.928A pdb=" N LEU C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 355 removed outlier: 3.866A pdb=" N GLY C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 382 through 386 removed outlier: 4.101A pdb=" N ASP C 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 416 removed outlier: 3.814A pdb=" N SER C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 428 removed outlier: 3.581A pdb=" N ARG C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 477 through 485 Processing helix chain 'C' and resid 490 through 502 Processing helix chain 'C' and resid 505 through 513 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 520 through 534 Processing helix chain 'D' and resid 108 through 120 Processing helix chain 'D' and resid 153 through 166 Processing helix chain 'D' and resid 238 through 250 removed outlier: 3.633A pdb=" N ASN D 250 " --> pdb=" O SER D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 281 Processing helix chain 'D' and resid 312 through 327 removed outlier: 3.928A pdb=" N LEU D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 355 removed outlier: 3.865A pdb=" N GLY D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 378 Processing helix chain 'D' and resid 382 through 386 removed outlier: 4.101A pdb=" N ASP D 386 " --> pdb=" O LYS D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 416 removed outlier: 3.815A pdb=" N SER D 416 " --> pdb=" O GLU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 428 removed outlier: 3.580A pdb=" N ARG D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS D 426 " --> pdb=" O ASP D 422 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE D 427 " --> pdb=" O THR D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 477 through 485 Processing helix chain 'D' and resid 490 through 502 Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 520 through 534 Processing helix chain 'E' and resid 108 through 120 Processing helix chain 'E' and resid 153 through 166 Processing helix chain 'E' and resid 238 through 250 removed outlier: 3.634A pdb=" N ASN E 250 " --> pdb=" O SER E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 281 Processing helix chain 'E' and resid 312 through 327 removed outlier: 3.927A pdb=" N LEU E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 355 removed outlier: 3.866A pdb=" N GLY E 355 " --> pdb=" O ALA E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 378 Processing helix chain 'E' and resid 382 through 386 removed outlier: 4.100A pdb=" N ASP E 386 " --> pdb=" O LYS E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 416 removed outlier: 3.814A pdb=" N SER E 416 " --> pdb=" O GLU E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 428 removed outlier: 3.580A pdb=" N ARG E 425 " --> pdb=" O SER E 421 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS E 426 " --> pdb=" O ASP E 422 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE E 427 " --> pdb=" O THR E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 477 through 485 Processing helix chain 'E' and resid 490 through 502 Processing helix chain 'E' and resid 505 through 513 Processing helix chain 'E' and resid 515 through 519 Processing helix chain 'E' and resid 520 through 534 Processing helix chain 'F' and resid 108 through 120 Processing helix chain 'F' and resid 153 through 166 Processing helix chain 'F' and resid 238 through 250 removed outlier: 3.633A pdb=" N ASN F 250 " --> pdb=" O SER F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 281 Processing helix chain 'F' and resid 312 through 327 removed outlier: 3.927A pdb=" N LEU F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 355 removed outlier: 3.866A pdb=" N GLY F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 378 Processing helix chain 'F' and resid 382 through 386 removed outlier: 4.102A pdb=" N ASP F 386 " --> pdb=" O LYS F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 416 removed outlier: 3.815A pdb=" N SER F 416 " --> pdb=" O GLU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 428 removed outlier: 3.580A pdb=" N ARG F 425 " --> pdb=" O SER F 421 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE F 427 " --> pdb=" O THR F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 477 through 485 Processing helix chain 'F' and resid 490 through 502 Processing helix chain 'F' and resid 505 through 513 Processing helix chain 'F' and resid 515 through 519 Processing helix chain 'F' and resid 520 through 534 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 152 removed outlier: 6.605A pdb=" N ILE A 137 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN A 150 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ALA A 135 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 212 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 357 through 362 removed outlier: 6.401A pdb=" N GLY A 254 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR A 360 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN A 256 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU A 362 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE A 258 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE A 255 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 392 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 401 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLY A 452 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 290 removed outlier: 6.771A pdb=" N SER A 289 " --> pdb=" O LEU A 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA5, first strand: chain 'B' and resid 144 through 152 removed outlier: 6.605A pdb=" N ILE B 137 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN B 150 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ALA B 135 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG B 212 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.401A pdb=" N GLY B 254 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR B 360 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN B 256 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU B 362 " --> pdb=" O ASN B 256 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE B 258 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE B 255 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY B 392 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 401 " --> pdb=" O GLY B 452 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLY B 452 " --> pdb=" O LYS B 401 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 288 through 290 removed outlier: 6.771A pdb=" N SER B 289 " --> pdb=" O LEU B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA9, first strand: chain 'C' and resid 144 through 152 removed outlier: 6.606A pdb=" N ILE C 137 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN C 150 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ALA C 135 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG C 212 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.401A pdb=" N GLY C 254 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR C 360 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASN C 256 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU C 362 " --> pdb=" O ASN C 256 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE C 258 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE C 255 " --> pdb=" O ILE C 390 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY C 392 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS C 401 " --> pdb=" O GLY C 452 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY C 452 " --> pdb=" O LYS C 401 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 288 through 290 removed outlier: 6.772A pdb=" N SER C 289 " --> pdb=" O LEU C 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'D' and resid 144 through 152 removed outlier: 6.606A pdb=" N ILE D 137 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN D 150 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ALA D 135 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG D 212 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.401A pdb=" N GLY D 254 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR D 360 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN D 256 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU D 362 " --> pdb=" O ASN D 256 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE D 258 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE D 255 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY D 392 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS D 401 " --> pdb=" O GLY D 452 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY D 452 " --> pdb=" O LYS D 401 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 288 through 290 removed outlier: 6.771A pdb=" N SER D 289 " --> pdb=" O LEU D 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'E' and resid 144 through 152 removed outlier: 6.605A pdb=" N ILE E 137 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN E 150 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ALA E 135 " --> pdb=" O GLN E 150 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG E 212 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 357 through 362 removed outlier: 6.401A pdb=" N GLY E 254 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR E 360 " --> pdb=" O GLY E 254 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASN E 256 " --> pdb=" O THR E 360 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU E 362 " --> pdb=" O ASN E 256 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE E 258 " --> pdb=" O LEU E 362 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE E 255 " --> pdb=" O ILE E 390 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY E 392 " --> pdb=" O ILE E 255 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS E 401 " --> pdb=" O GLY E 452 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY E 452 " --> pdb=" O LYS E 401 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 288 through 290 removed outlier: 6.772A pdb=" N SER E 289 " --> pdb=" O LEU E 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AC3, first strand: chain 'F' and resid 144 through 152 removed outlier: 6.606A pdb=" N ILE F 137 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN F 150 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ALA F 135 " --> pdb=" O GLN F 150 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG F 212 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 357 through 362 removed outlier: 6.402A pdb=" N GLY F 254 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR F 360 " --> pdb=" O GLY F 254 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASN F 256 " --> pdb=" O THR F 360 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU F 362 " --> pdb=" O ASN F 256 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE F 258 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE F 255 " --> pdb=" O ILE F 390 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY F 392 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS F 401 " --> pdb=" O GLY F 452 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLY F 452 " --> pdb=" O LYS F 401 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 288 through 290 removed outlier: 6.772A pdb=" N SER F 289 " --> pdb=" O LEU F 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 407 through 408 901 hydrogen bonds defined for protein. 2541 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: 3.53 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6492 1.34 - 1.46: 3765 1.46 - 1.58: 9201 1.58 - 1.69: 24 1.69 - 1.81: 144 Bond restraints: 19626 Sorted by residual: bond pdb=" C1' ANP C 602 " pdb=" C2' ANP C 602 " ideal model delta sigma weight residual 1.542 1.305 0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C1' ANP D 602 " pdb=" C2' ANP D 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP F 602 " pdb=" C2' ANP F 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP B 602 " pdb=" C2' ANP B 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP E 602 " pdb=" C2' ANP E 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 ... (remaining 19621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 26100 2.38 - 4.77: 344 4.77 - 7.15: 100 7.15 - 9.53: 42 9.53 - 11.92: 18 Bond angle restraints: 26604 Sorted by residual: angle pdb=" C TYR C 131 " pdb=" N ASP C 132 " pdb=" CA ASP C 132 " ideal model delta sigma weight residual 121.54 129.90 -8.36 1.91e+00 2.74e-01 1.92e+01 angle pdb=" C TYR A 131 " pdb=" N ASP A 132 " pdb=" CA ASP A 132 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C TYR F 131 " pdb=" N ASP F 132 " pdb=" CA ASP F 132 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C TYR D 131 " pdb=" N ASP D 132 " pdb=" CA ASP D 132 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C TYR B 131 " pdb=" N ASP B 132 " pdb=" CA ASP B 132 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 ... (remaining 26599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.37: 11712 32.37 - 64.73: 294 64.73 - 97.10: 36 97.10 - 129.46: 0 129.46 - 161.83: 6 Dihedral angle restraints: 12048 sinusoidal: 4848 harmonic: 7200 Sorted by residual: dihedral pdb=" O1A ANP E 602 " pdb=" O3A ANP E 602 " pdb=" PA ANP E 602 " pdb=" PB ANP E 602 " ideal model delta sinusoidal sigma weight residual 83.11 -78.72 161.83 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" O1A ANP B 602 " pdb=" O3A ANP B 602 " pdb=" PA ANP B 602 " pdb=" PB ANP B 602 " ideal model delta sinusoidal sigma weight residual 83.11 -78.70 161.81 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" O1A ANP C 602 " pdb=" O3A ANP C 602 " pdb=" PA ANP C 602 " pdb=" PB ANP C 602 " ideal model delta sinusoidal sigma weight residual 83.11 -78.67 161.78 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 12045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2681 0.067 - 0.134: 372 0.134 - 0.201: 1 0.201 - 0.268: 6 0.268 - 0.336: 6 Chirality restraints: 3066 Sorted by residual: chirality pdb=" C2' ANP C 602 " pdb=" C1' ANP C 602 " pdb=" C3' ANP C 602 " pdb=" O2' ANP C 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.39 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C2' ANP D 602 " pdb=" C1' ANP D 602 " pdb=" C3' ANP D 602 " pdb=" O2' ANP D 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.39 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C2' ANP B 602 " pdb=" C1' ANP B 602 " pdb=" C3' ANP B 602 " pdb=" O2' ANP B 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.39 -0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 3063 not shown) Planarity restraints: 3402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 132 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.41e+00 pdb=" C ASP D 132 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP D 132 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA D 133 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 132 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C ASP B 132 " 0.020 2.00e-02 2.50e+03 pdb=" O ASP B 132 " -0.008 2.00e-02 2.50e+03 pdb=" N ALA B 133 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 132 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.39e+00 pdb=" C ASP E 132 " -0.020 2.00e-02 2.50e+03 pdb=" O ASP E 132 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA E 133 " 0.007 2.00e-02 2.50e+03 ... (remaining 3399 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4897 2.81 - 3.33: 18370 3.33 - 3.85: 30912 3.85 - 4.38: 33376 4.38 - 4.90: 60209 Nonbonded interactions: 147764 Sorted by model distance: nonbonded pdb=" O THR B 350 " pdb=" OG1 THR B 354 " model vdw 2.285 3.040 nonbonded pdb=" O THR D 350 " pdb=" OG1 THR D 354 " model vdw 2.286 3.040 nonbonded pdb=" O THR E 350 " pdb=" OG1 THR E 354 " model vdw 2.286 3.040 nonbonded pdb=" O THR C 350 " pdb=" OG1 THR C 354 " model vdw 2.286 3.040 nonbonded pdb=" O THR A 350 " pdb=" OG1 THR A 354 " model vdw 2.286 3.040 ... (remaining 147759 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.050 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.620 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 : 0.007 0.237 19650 Z= 0.379 Angle : 0.813 11.916 26640 Z= 0.380 Chirality : 0.046 0.336 3066 Planarity : 0.003 0.024 3402 Dihedral : 13.483 161.831 7380 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.17 % Favored : 93.58 % Rotamer: Outliers : 2.98 % Allowed : 8.04 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.17), residues: 2430 helix: 0.67 (0.16), residues: 1002 sheet: 2.18 (0.27), residues: 408 loop : -1.99 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 320 TYR 0.006 0.001 TYR F 278 PHE 0.005 0.001 PHE D 204 TRP 0.003 0.001 TRP D 359 HIS 0.002 0.000 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00750 (19626) covalent geometry : angle 0.80930 (26604) hydrogen bonds : bond 0.20073 ( 901) hydrogen bonds : angle 5.66357 ( 2541) metal coordination : bond 0.00248 ( 24) metal coordination : angle 2.29781 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 386 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.9309 (tpp) cc_final: 0.8895 (tpp) REVERT: A 121 MET cc_start: 0.8906 (ttt) cc_final: 0.8684 (ttm) REVERT: A 132 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8830 (p0) REVERT: A 180 GLN cc_start: 0.7385 (mp10) cc_final: 0.6645 (mp10) REVERT: A 314 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8282 (tm-30) REVERT: A 479 GLN cc_start: 0.7889 (tt0) cc_final: 0.7537 (tt0) REVERT: A 483 LEU cc_start: 0.9266 (tp) cc_final: 0.9023 (mt) REVERT: B 113 MET cc_start: 0.9237 (tpp) cc_final: 0.8742 (tpp) REVERT: B 132 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8748 (p0) REVERT: B 203 GLN cc_start: 0.6351 (tm-30) cc_final: 0.5880 (tm-30) REVERT: B 314 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8330 (tm-30) REVERT: B 503 GLU cc_start: 0.8428 (tp30) cc_final: 0.8223 (tp30) REVERT: C 113 MET cc_start: 0.9318 (tpp) cc_final: 0.8818 (tpp) REVERT: C 132 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8723 (p0) REVERT: C 203 GLN cc_start: 0.6377 (tm-30) cc_final: 0.5479 (tm-30) REVERT: C 398 LEU cc_start: 0.9151 (mt) cc_final: 0.8915 (mt) REVERT: C 503 GLU cc_start: 0.8461 (tp30) cc_final: 0.8139 (tp30) REVERT: C 531 ASP cc_start: 0.7909 (t0) cc_final: 0.7595 (t0) REVERT: D 113 MET cc_start: 0.9316 (tpp) cc_final: 0.8896 (tpp) REVERT: D 121 MET cc_start: 0.8883 (ttt) cc_final: 0.8668 (ttm) REVERT: D 132 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8805 (p0) REVERT: D 180 GLN cc_start: 0.7455 (mp10) cc_final: 0.6741 (mp10) REVERT: D 314 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8287 (tm-30) REVERT: D 479 GLN cc_start: 0.7874 (tt0) cc_final: 0.7492 (tt0) REVERT: D 483 LEU cc_start: 0.9253 (tp) cc_final: 0.9012 (mt) REVERT: E 113 MET cc_start: 0.9282 (tpp) cc_final: 0.8772 (tpp) REVERT: E 116 PHE cc_start: 0.8956 (t80) cc_final: 0.8753 (t80) REVERT: E 132 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8792 (p0) REVERT: E 139 ILE cc_start: 0.8953 (pt) cc_final: 0.8710 (pt) REVERT: E 314 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8289 (tm-30) REVERT: E 479 GLN cc_start: 0.7896 (tt0) cc_final: 0.7596 (tt0) REVERT: E 503 GLU cc_start: 0.8423 (tp30) cc_final: 0.8214 (tp30) REVERT: F 113 MET cc_start: 0.9273 (tpp) cc_final: 0.8910 (tpp) REVERT: F 132 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8617 (p0) REVERT: F 203 GLN cc_start: 0.6361 (tm-30) cc_final: 0.5667 (tm-30) REVERT: F 248 MET cc_start: 0.9037 (ttm) cc_final: 0.8746 (ttm) REVERT: F 314 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8174 (tm-30) REVERT: F 388 GLU cc_start: 0.8560 (tp30) cc_final: 0.8162 (tp30) REVERT: F 398 LEU cc_start: 0.9136 (mt) cc_final: 0.8922 (mt) REVERT: F 503 GLU cc_start: 0.8446 (tp30) cc_final: 0.8128 (tp30) REVERT: F 531 ASP cc_start: 0.7883 (t0) cc_final: 0.7569 (t0) outliers start: 60 outliers final: 8 residues processed: 426 average time/residue: 0.1282 time to fit residues: 85.2915 Evaluate side-chains 263 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 249 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 385 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 357 GLN B 256 ASN B 272 ASN B 357 GLN C 272 ASN C 357 GLN D 272 ASN D 357 GLN E 256 ASN E 272 ASN E 357 GLN F 256 ASN F 272 ASN F 357 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.101071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.077638 restraints weight = 42295.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.081232 restraints weight = 21970.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.083718 restraints weight = 14090.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085355 restraints weight = 10269.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.086616 restraints weight = 8238.254| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19650 Z= 0.123 Angle : 0.600 7.071 26640 Z= 0.294 Chirality : 0.043 0.136 3066 Planarity : 0.003 0.034 3402 Dihedral : 13.161 150.452 2896 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.45 % Favored : 92.30 % Rotamer: Outliers : 2.08 % Allowed : 12.95 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.18), residues: 2430 helix: 1.46 (0.17), residues: 1008 sheet: 2.07 (0.26), residues: 408 loop : -1.97 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 212 TYR 0.008 0.001 TYR C 319 PHE 0.014 0.001 PHE C 204 TRP 0.004 0.001 TRP A 359 HIS 0.006 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00261 (19626) covalent geometry : angle 0.58727 (26604) hydrogen bonds : bond 0.04236 ( 901) hydrogen bonds : angle 4.48994 ( 2541) metal coordination : bond 0.00180 ( 24) metal coordination : angle 3.34999 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 0.733 Fit side-chains REVERT: A 113 MET cc_start: 0.9206 (tpp) cc_final: 0.8793 (tpp) REVERT: A 180 GLN cc_start: 0.7580 (mp10) cc_final: 0.6757 (mp10) REVERT: A 203 GLN cc_start: 0.6717 (tm-30) cc_final: 0.6505 (tm-30) REVERT: A 264 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.8195 (m) REVERT: A 291 GLU cc_start: 0.8615 (tp30) cc_final: 0.8388 (tp30) REVERT: A 314 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8409 (tm-30) REVERT: A 319 TYR cc_start: 0.8811 (t80) cc_final: 0.8594 (t80) REVERT: A 335 MET cc_start: 0.8113 (tpp) cc_final: 0.7813 (tpp) REVERT: A 338 GLU cc_start: 0.6837 (tp30) cc_final: 0.6587 (tm-30) REVERT: A 479 GLN cc_start: 0.7996 (tt0) cc_final: 0.7678 (tt0) REVERT: A 483 LEU cc_start: 0.9315 (tp) cc_final: 0.9039 (mt) REVERT: A 503 GLU cc_start: 0.8323 (tp30) cc_final: 0.8055 (tp30) REVERT: B 125 ASP cc_start: 0.7491 (m-30) cc_final: 0.7255 (m-30) REVERT: B 164 TYR cc_start: 0.7612 (t80) cc_final: 0.7375 (t80) REVERT: B 203 GLN cc_start: 0.6948 (tm-30) cc_final: 0.6478 (tm-30) REVERT: B 314 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 350 THR cc_start: 0.9180 (p) cc_final: 0.8970 (p) REVERT: B 503 GLU cc_start: 0.8364 (tp30) cc_final: 0.8160 (tp30) REVERT: C 113 MET cc_start: 0.9207 (tpp) cc_final: 0.8714 (tpp) REVERT: C 353 MET cc_start: 0.8663 (ptm) cc_final: 0.8463 (ptm) REVERT: C 503 GLU cc_start: 0.8451 (tp30) cc_final: 0.8158 (tp30) REVERT: D 113 MET cc_start: 0.9169 (tpp) cc_final: 0.8760 (tpp) REVERT: D 180 GLN cc_start: 0.7656 (mp10) cc_final: 0.6877 (mp10) REVERT: D 203 GLN cc_start: 0.6842 (tm-30) cc_final: 0.6614 (tm-30) REVERT: D 291 GLU cc_start: 0.8592 (tp30) cc_final: 0.8377 (tp30) REVERT: D 314 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8414 (tm-30) REVERT: D 338 GLU cc_start: 0.6905 (tp30) cc_final: 0.6664 (tm-30) REVERT: D 479 GLN cc_start: 0.7978 (tt0) cc_final: 0.7659 (tt0) REVERT: D 483 LEU cc_start: 0.9302 (tp) cc_final: 0.9002 (mt) REVERT: D 503 GLU cc_start: 0.8269 (tp30) cc_final: 0.8015 (tp30) REVERT: E 204 PHE cc_start: 0.8084 (m-80) cc_final: 0.7866 (m-80) REVERT: E 314 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8453 (tm-30) REVERT: E 338 GLU cc_start: 0.6965 (tp30) cc_final: 0.6657 (tm-30) REVERT: E 350 THR cc_start: 0.9154 (p) cc_final: 0.8944 (p) REVERT: E 503 GLU cc_start: 0.8380 (tp30) cc_final: 0.8169 (tp30) REVERT: F 204 PHE cc_start: 0.7926 (m-80) cc_final: 0.7670 (m-80) REVERT: F 314 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8247 (tm-30) REVERT: F 353 MET cc_start: 0.8746 (ptm) cc_final: 0.8533 (ptm) REVERT: F 388 GLU cc_start: 0.8486 (tp30) cc_final: 0.8149 (tp30) REVERT: F 503 GLU cc_start: 0.8453 (tp30) cc_final: 0.8151 (tp30) outliers start: 42 outliers final: 19 residues processed: 292 average time/residue: 0.1031 time to fit residues: 51.3070 Evaluate side-chains 230 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 385 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 195 optimal weight: 4.9990 chunk 197 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 200 optimal weight: 0.0770 chunk 223 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN C 256 ASN D 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.099186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.075379 restraints weight = 42629.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.078863 restraints weight = 22334.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.081385 restraints weight = 14480.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.083103 restraints weight = 10640.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084276 restraints weight = 8540.535| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19650 Z= 0.131 Angle : 0.593 8.476 26640 Z= 0.288 Chirality : 0.043 0.132 3066 Planarity : 0.003 0.024 3402 Dihedral : 12.332 146.562 2892 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.82 % Favored : 91.93 % Rotamer: Outliers : 3.32 % Allowed : 12.70 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.18), residues: 2430 helix: 1.66 (0.17), residues: 1008 sheet: 1.99 (0.26), residues: 408 loop : -1.95 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 140 TYR 0.015 0.001 TYR F 319 PHE 0.012 0.001 PHE A 204 TRP 0.005 0.001 TRP F 482 HIS 0.002 0.000 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00295 (19626) covalent geometry : angle 0.57837 (26604) hydrogen bonds : bond 0.03444 ( 901) hydrogen bonds : angle 4.27086 ( 2541) metal coordination : bond 0.00242 ( 24) metal coordination : angle 3.56915 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 0.780 Fit side-chains REVERT: A 113 MET cc_start: 0.9199 (tpp) cc_final: 0.8793 (tpp) REVERT: A 180 GLN cc_start: 0.7587 (mp10) cc_final: 0.6850 (mp10) REVERT: A 291 GLU cc_start: 0.8748 (tp30) cc_final: 0.8524 (tp30) REVERT: A 314 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8390 (tm-30) REVERT: A 335 MET cc_start: 0.8169 (tpp) cc_final: 0.7789 (tpp) REVERT: A 338 GLU cc_start: 0.6931 (tp30) cc_final: 0.6643 (tm-30) REVERT: A 479 GLN cc_start: 0.7944 (tt0) cc_final: 0.7659 (tt0) REVERT: A 483 LEU cc_start: 0.9370 (tp) cc_final: 0.9033 (mt) REVERT: A 503 GLU cc_start: 0.8349 (tp30) cc_final: 0.8025 (tp30) REVERT: B 125 ASP cc_start: 0.7590 (m-30) cc_final: 0.7328 (m-30) REVERT: B 164 TYR cc_start: 0.7665 (t80) cc_final: 0.7438 (t80) REVERT: B 203 GLN cc_start: 0.6988 (tm-30) cc_final: 0.6582 (tm-30) REVERT: B 314 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8415 (tm-30) REVERT: C 113 MET cc_start: 0.9229 (tpp) cc_final: 0.8735 (tpp) REVERT: C 203 GLN cc_start: 0.6954 (tm-30) cc_final: 0.6679 (tm-30) REVERT: C 338 GLU cc_start: 0.6694 (tp30) cc_final: 0.6265 (tp30) REVERT: C 482 TRP cc_start: 0.8613 (t60) cc_final: 0.8377 (t60) REVERT: C 503 GLU cc_start: 0.8435 (tp30) cc_final: 0.8201 (tp30) REVERT: D 113 MET cc_start: 0.9163 (tpp) cc_final: 0.8756 (tpp) REVERT: D 180 GLN cc_start: 0.7648 (mp10) cc_final: 0.6952 (mp10) REVERT: D 291 GLU cc_start: 0.8715 (tp30) cc_final: 0.8504 (tp30) REVERT: D 314 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8400 (tm-30) REVERT: D 479 GLN cc_start: 0.7971 (tt0) cc_final: 0.7690 (tt0) REVERT: D 483 LEU cc_start: 0.9366 (tp) cc_final: 0.9021 (mt) REVERT: D 503 GLU cc_start: 0.8367 (tp30) cc_final: 0.8041 (tp30) REVERT: E 314 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8441 (tm-30) REVERT: E 338 GLU cc_start: 0.7066 (tp30) cc_final: 0.6747 (tm-30) REVERT: F 113 MET cc_start: 0.8850 (mtt) cc_final: 0.8521 (mpp) REVERT: F 203 GLN cc_start: 0.7083 (tm-30) cc_final: 0.6815 (tm-30) REVERT: F 314 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8445 (tm-30) REVERT: F 388 GLU cc_start: 0.8557 (tp30) cc_final: 0.8155 (tp30) REVERT: F 455 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8688 (mp) REVERT: F 503 GLU cc_start: 0.8449 (tp30) cc_final: 0.8202 (tp30) outliers start: 67 outliers final: 31 residues processed: 275 average time/residue: 0.1086 time to fit residues: 51.0785 Evaluate side-chains 227 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 218 PHE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 455 ILE Chi-restraints excluded: chain F residue 470 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 77 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 236 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 205 optimal weight: 10.0000 chunk 240 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 193 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.100831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.076628 restraints weight = 41331.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.080296 restraints weight = 21240.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.082899 restraints weight = 13621.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.084623 restraints weight = 9931.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085954 restraints weight = 7975.925| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19650 Z= 0.108 Angle : 0.573 8.361 26640 Z= 0.276 Chirality : 0.043 0.140 3066 Planarity : 0.003 0.028 3402 Dihedral : 11.724 140.952 2892 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.41 % Favored : 92.35 % Rotamer: Outliers : 2.33 % Allowed : 13.69 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.18), residues: 2430 helix: 1.78 (0.17), residues: 1002 sheet: 1.99 (0.27), residues: 408 loop : -1.95 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 475 TYR 0.010 0.001 TYR E 164 PHE 0.012 0.001 PHE A 204 TRP 0.006 0.001 TRP B 482 HIS 0.002 0.000 HIS E 356 Details of bonding type rmsd covalent geometry : bond 0.00244 (19626) covalent geometry : angle 0.56135 (26604) hydrogen bonds : bond 0.02999 ( 901) hydrogen bonds : angle 4.18230 ( 2541) metal coordination : bond 0.00223 ( 24) metal coordination : angle 3.17433 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.635 Fit side-chains REVERT: A 113 MET cc_start: 0.9219 (tpp) cc_final: 0.8808 (tpp) REVERT: A 180 GLN cc_start: 0.7548 (mp10) cc_final: 0.6812 (mp10) REVERT: A 203 GLN cc_start: 0.6830 (tm-30) cc_final: 0.6616 (tm-30) REVERT: A 291 GLU cc_start: 0.8798 (tp30) cc_final: 0.8553 (tp30) REVERT: A 314 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8388 (tm-30) REVERT: A 479 GLN cc_start: 0.7873 (tt0) cc_final: 0.7572 (tt0) REVERT: A 483 LEU cc_start: 0.9389 (tp) cc_final: 0.9010 (mt) REVERT: A 503 GLU cc_start: 0.8393 (tp30) cc_final: 0.7997 (tp30) REVERT: B 113 MET cc_start: 0.8851 (mpp) cc_final: 0.8637 (mpp) REVERT: B 125 ASP cc_start: 0.7566 (m-30) cc_final: 0.7243 (m-30) REVERT: B 164 TYR cc_start: 0.7721 (t80) cc_final: 0.7502 (t80) REVERT: B 179 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8630 (m-10) REVERT: B 203 GLN cc_start: 0.6878 (tm-30) cc_final: 0.6512 (tm-30) REVERT: B 314 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8395 (tm-30) REVERT: B 341 ASP cc_start: 0.8651 (t0) cc_final: 0.8248 (t70) REVERT: C 113 MET cc_start: 0.9234 (tpp) cc_final: 0.8755 (tpp) REVERT: C 314 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8411 (tm-30) REVERT: C 493 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: C 503 GLU cc_start: 0.8453 (tp30) cc_final: 0.8171 (tp30) REVERT: D 113 MET cc_start: 0.9192 (tpp) cc_final: 0.8772 (tpp) REVERT: D 180 GLN cc_start: 0.7606 (mp10) cc_final: 0.6891 (mp10) REVERT: D 203 GLN cc_start: 0.6933 (tm-30) cc_final: 0.6704 (tm-30) REVERT: D 258 ILE cc_start: 0.7740 (mm) cc_final: 0.7519 (mm) REVERT: D 291 GLU cc_start: 0.8751 (tp30) cc_final: 0.8526 (tp30) REVERT: D 314 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8417 (tm-30) REVERT: D 479 GLN cc_start: 0.7887 (tt0) cc_final: 0.7600 (tt0) REVERT: D 483 LEU cc_start: 0.9375 (tp) cc_final: 0.9018 (mt) REVERT: D 503 GLU cc_start: 0.8407 (tp30) cc_final: 0.8020 (tp30) REVERT: E 113 MET cc_start: 0.8861 (mpp) cc_final: 0.8635 (mpp) REVERT: E 314 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8419 (tm-30) REVERT: E 338 GLU cc_start: 0.7080 (tp30) cc_final: 0.6748 (tm-30) REVERT: E 341 ASP cc_start: 0.8590 (t0) cc_final: 0.8264 (t70) REVERT: E 493 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: E 507 MET cc_start: 0.7935 (mmm) cc_final: 0.7672 (mtp) REVERT: F 314 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8258 (tm-30) REVERT: F 503 GLU cc_start: 0.8467 (tp30) cc_final: 0.8177 (tp30) outliers start: 47 outliers final: 28 residues processed: 249 average time/residue: 0.1000 time to fit residues: 42.1880 Evaluate side-chains 233 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 218 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 218 PHE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 385 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 223 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 48 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 177 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 0.0670 chunk 140 optimal weight: 5.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.099535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.075276 restraints weight = 41906.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.078803 restraints weight = 21856.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.081424 restraints weight = 14206.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.083156 restraints weight = 10431.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.084486 restraints weight = 8397.049| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19650 Z= 0.109 Angle : 0.554 6.944 26640 Z= 0.270 Chirality : 0.043 0.155 3066 Planarity : 0.003 0.034 3402 Dihedral : 11.241 134.838 2892 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.07 % Favored : 91.69 % Rotamer: Outliers : 2.98 % Allowed : 13.39 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.18), residues: 2430 helix: 1.87 (0.17), residues: 1008 sheet: 1.93 (0.27), residues: 408 loop : -1.95 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.017 0.001 TYR F 319 PHE 0.013 0.001 PHE A 204 TRP 0.006 0.001 TRP B 359 HIS 0.002 0.000 HIS E 356 Details of bonding type rmsd covalent geometry : bond 0.00251 (19626) covalent geometry : angle 0.54366 (26604) hydrogen bonds : bond 0.02804 ( 901) hydrogen bonds : angle 4.05761 ( 2541) metal coordination : bond 0.00218 ( 24) metal coordination : angle 3.00421 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 217 time to evaluate : 0.800 Fit side-chains REVERT: A 113 MET cc_start: 0.9217 (tpp) cc_final: 0.8812 (tpp) REVERT: A 180 GLN cc_start: 0.7557 (mp10) cc_final: 0.6815 (mp10) REVERT: A 314 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8377 (tm-30) REVERT: A 341 ASP cc_start: 0.8581 (t0) cc_final: 0.8367 (t70) REVERT: A 479 GLN cc_start: 0.7852 (tt0) cc_final: 0.7527 (tt0) REVERT: A 483 LEU cc_start: 0.9385 (tp) cc_final: 0.9025 (mt) REVERT: A 503 GLU cc_start: 0.8346 (tp30) cc_final: 0.7941 (tp30) REVERT: B 113 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8651 (mpp) REVERT: B 125 ASP cc_start: 0.7595 (m-30) cc_final: 0.7277 (m-30) REVERT: B 164 TYR cc_start: 0.7735 (t80) cc_final: 0.7513 (t80) REVERT: B 179 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.8640 (m-10) REVERT: B 203 GLN cc_start: 0.6952 (tm-30) cc_final: 0.6581 (tm-30) REVERT: B 204 PHE cc_start: 0.8099 (m-80) cc_final: 0.7894 (m-80) REVERT: B 314 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8413 (tm-30) REVERT: B 341 ASP cc_start: 0.8637 (t0) cc_final: 0.8240 (t70) REVERT: C 203 GLN cc_start: 0.7020 (tm-30) cc_final: 0.6774 (tm-30) REVERT: C 314 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8381 (tm-30) REVERT: C 493 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: C 503 GLU cc_start: 0.8438 (tp30) cc_final: 0.8118 (tp30) REVERT: D 113 MET cc_start: 0.9189 (tpp) cc_final: 0.8773 (tpp) REVERT: D 180 GLN cc_start: 0.7615 (mp10) cc_final: 0.6882 (mp10) REVERT: D 258 ILE cc_start: 0.7806 (mm) cc_final: 0.7565 (mm) REVERT: D 314 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8383 (tm-30) REVERT: D 341 ASP cc_start: 0.8570 (t0) cc_final: 0.8338 (t70) REVERT: D 479 GLN cc_start: 0.7866 (tt0) cc_final: 0.7546 (tt0) REVERT: D 483 LEU cc_start: 0.9377 (tp) cc_final: 0.9017 (mt) REVERT: D 503 GLU cc_start: 0.8407 (tp30) cc_final: 0.7967 (tp30) REVERT: E 113 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8669 (mpp) REVERT: E 314 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8410 (tm-30) REVERT: E 341 ASP cc_start: 0.8619 (t0) cc_final: 0.8258 (t70) REVERT: E 493 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: E 507 MET cc_start: 0.7975 (mmm) cc_final: 0.7672 (mtp) REVERT: F 203 GLN cc_start: 0.7086 (tm-30) cc_final: 0.6878 (tm-30) REVERT: F 314 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8238 (tm-30) REVERT: F 386 ASP cc_start: 0.7864 (m-30) cc_final: 0.7577 (m-30) REVERT: F 503 GLU cc_start: 0.8427 (tp30) cc_final: 0.8121 (tp30) outliers start: 60 outliers final: 41 residues processed: 256 average time/residue: 0.1103 time to fit residues: 48.4054 Evaluate side-chains 250 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 349 PHE Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 218 PHE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 470 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 181 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 191 optimal weight: 0.0970 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.099320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.075348 restraints weight = 40913.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.078868 restraints weight = 21066.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081469 restraints weight = 13566.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.083287 restraints weight = 9905.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.084559 restraints weight = 7889.313| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19650 Z= 0.118 Angle : 0.563 8.184 26640 Z= 0.274 Chirality : 0.043 0.149 3066 Planarity : 0.003 0.035 3402 Dihedral : 11.034 131.318 2892 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.02 % Favored : 91.73 % Rotamer: Outliers : 3.32 % Allowed : 13.49 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.18), residues: 2430 helix: 1.91 (0.17), residues: 1008 sheet: 1.92 (0.27), residues: 408 loop : -1.96 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.014 0.001 TYR F 319 PHE 0.013 0.001 PHE A 204 TRP 0.006 0.001 TRP D 359 HIS 0.002 0.000 HIS E 356 Details of bonding type rmsd covalent geometry : bond 0.00274 (19626) covalent geometry : angle 0.55205 (26604) hydrogen bonds : bond 0.02746 ( 901) hydrogen bonds : angle 4.05431 ( 2541) metal coordination : bond 0.00236 ( 24) metal coordination : angle 3.00720 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 217 time to evaluate : 0.874 Fit side-chains REVERT: A 113 MET cc_start: 0.9215 (tpp) cc_final: 0.8804 (tpp) REVERT: A 180 GLN cc_start: 0.7507 (mp10) cc_final: 0.6803 (mp10) REVERT: A 314 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8356 (tm-30) REVERT: A 341 ASP cc_start: 0.8592 (t0) cc_final: 0.8353 (t70) REVERT: A 479 GLN cc_start: 0.7885 (tt0) cc_final: 0.7586 (tt0) REVERT: A 483 LEU cc_start: 0.9369 (tp) cc_final: 0.9050 (mt) REVERT: A 503 GLU cc_start: 0.8353 (tp30) cc_final: 0.7915 (tp30) REVERT: B 113 MET cc_start: 0.8873 (mpp) cc_final: 0.8607 (mpp) REVERT: B 118 CYS cc_start: 0.9509 (t) cc_final: 0.9137 (t) REVERT: B 125 ASP cc_start: 0.7704 (m-30) cc_final: 0.7377 (m-30) REVERT: B 203 GLN cc_start: 0.6973 (tm-30) cc_final: 0.6620 (tm-30) REVERT: B 314 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8428 (tm-30) REVERT: B 341 ASP cc_start: 0.8633 (t0) cc_final: 0.8260 (t70) REVERT: B 507 MET cc_start: 0.7956 (mmm) cc_final: 0.7691 (mtp) REVERT: C 113 MET cc_start: 0.8824 (mtt) cc_final: 0.8564 (mpp) REVERT: C 203 GLN cc_start: 0.6957 (tm-30) cc_final: 0.6652 (tm-30) REVERT: C 314 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8406 (tm-30) REVERT: C 493 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: C 503 GLU cc_start: 0.8444 (tp30) cc_final: 0.8112 (tp30) REVERT: D 113 MET cc_start: 0.9189 (tpp) cc_final: 0.8771 (tpp) REVERT: D 258 ILE cc_start: 0.7880 (mm) cc_final: 0.7640 (mm) REVERT: D 341 ASP cc_start: 0.8577 (t0) cc_final: 0.8327 (t70) REVERT: D 479 GLN cc_start: 0.7859 (tt0) cc_final: 0.7566 (tt0) REVERT: D 483 LEU cc_start: 0.9365 (tp) cc_final: 0.9049 (mt) REVERT: D 503 GLU cc_start: 0.8381 (tp30) cc_final: 0.7921 (tp30) REVERT: E 113 MET cc_start: 0.8877 (mpp) cc_final: 0.8620 (mpp) REVERT: E 118 CYS cc_start: 0.9519 (t) cc_final: 0.9150 (t) REVERT: E 314 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8411 (tm-30) REVERT: E 341 ASP cc_start: 0.8589 (t0) cc_final: 0.8243 (t70) REVERT: E 493 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: E 507 MET cc_start: 0.7977 (mmm) cc_final: 0.7690 (mtp) REVERT: F 113 MET cc_start: 0.8842 (ptp) cc_final: 0.8515 (mpp) REVERT: F 203 GLN cc_start: 0.7116 (tm-30) cc_final: 0.6845 (tm-30) REVERT: F 314 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8188 (tm-30) REVERT: F 503 GLU cc_start: 0.8424 (tp30) cc_final: 0.8181 (tp30) outliers start: 67 outliers final: 44 residues processed: 264 average time/residue: 0.1146 time to fit residues: 51.5967 Evaluate side-chains 248 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 349 PHE Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 218 PHE Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 470 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.099404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.075500 restraints weight = 41055.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.079012 restraints weight = 21634.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.081493 restraints weight = 14089.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.083305 restraints weight = 10426.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.084495 restraints weight = 8351.268| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19650 Z= 0.116 Angle : 0.573 8.148 26640 Z= 0.278 Chirality : 0.043 0.147 3066 Planarity : 0.003 0.037 3402 Dihedral : 10.823 128.672 2892 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.07 % Favored : 91.69 % Rotamer: Outliers : 3.03 % Allowed : 14.24 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.18), residues: 2430 helix: 1.93 (0.17), residues: 1008 sheet: 1.87 (0.27), residues: 408 loop : -1.97 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.015 0.001 TYR E 164 PHE 0.013 0.001 PHE A 204 TRP 0.014 0.001 TRP C 482 HIS 0.002 0.000 HIS D 494 Details of bonding type rmsd covalent geometry : bond 0.00271 (19626) covalent geometry : angle 0.56313 (26604) hydrogen bonds : bond 0.02671 ( 901) hydrogen bonds : angle 4.02529 ( 2541) metal coordination : bond 0.00247 ( 24) metal coordination : angle 2.90320 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 0.804 Fit side-chains REVERT: A 113 MET cc_start: 0.9221 (tpp) cc_final: 0.8808 (tpp) REVERT: A 116 PHE cc_start: 0.8972 (t80) cc_final: 0.8682 (m-80) REVERT: A 180 GLN cc_start: 0.7524 (mp10) cc_final: 0.6831 (mp10) REVERT: A 314 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8362 (tm-30) REVERT: A 341 ASP cc_start: 0.8616 (t0) cc_final: 0.8369 (t70) REVERT: A 479 GLN cc_start: 0.7902 (tt0) cc_final: 0.7563 (tt0) REVERT: A 483 LEU cc_start: 0.9380 (tp) cc_final: 0.9053 (mt) REVERT: A 503 GLU cc_start: 0.8347 (tp30) cc_final: 0.7891 (tp30) REVERT: B 113 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8623 (mpp) REVERT: B 118 CYS cc_start: 0.9495 (t) cc_final: 0.9105 (t) REVERT: B 125 ASP cc_start: 0.7734 (m-30) cc_final: 0.7420 (m-30) REVERT: B 164 TYR cc_start: 0.7708 (t80) cc_final: 0.7487 (t80) REVERT: B 203 GLN cc_start: 0.6993 (tm-30) cc_final: 0.6631 (tm-30) REVERT: B 204 PHE cc_start: 0.8154 (m-80) cc_final: 0.7950 (m-80) REVERT: B 314 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8408 (tm-30) REVERT: B 341 ASP cc_start: 0.8628 (t0) cc_final: 0.8259 (t70) REVERT: B 507 MET cc_start: 0.7960 (mmm) cc_final: 0.7698 (mtp) REVERT: C 113 MET cc_start: 0.8804 (mtt) cc_final: 0.8563 (ptp) REVERT: C 193 LEU cc_start: 0.9326 (tp) cc_final: 0.9126 (tp) REVERT: C 203 GLN cc_start: 0.7021 (tm-30) cc_final: 0.6717 (tm-30) REVERT: C 314 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8387 (tm-30) REVERT: C 493 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: C 503 GLU cc_start: 0.8421 (tp30) cc_final: 0.8176 (tp30) REVERT: D 113 MET cc_start: 0.9200 (tpp) cc_final: 0.8777 (tpp) REVERT: D 116 PHE cc_start: 0.8952 (t80) cc_final: 0.8635 (m-80) REVERT: D 258 ILE cc_start: 0.7892 (mm) cc_final: 0.7685 (mm) REVERT: D 341 ASP cc_start: 0.8572 (t0) cc_final: 0.8351 (t70) REVERT: D 479 GLN cc_start: 0.7869 (tt0) cc_final: 0.7524 (tt0) REVERT: D 483 LEU cc_start: 0.9365 (tp) cc_final: 0.9034 (mt) REVERT: D 503 GLU cc_start: 0.8393 (tp30) cc_final: 0.7913 (tp30) REVERT: E 113 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8604 (mpp) REVERT: E 118 CYS cc_start: 0.9516 (t) cc_final: 0.9147 (t) REVERT: E 314 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8399 (tm-30) REVERT: E 341 ASP cc_start: 0.8590 (t0) cc_final: 0.8258 (t70) REVERT: E 493 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: E 507 MET cc_start: 0.7976 (mmm) cc_final: 0.7685 (mtp) REVERT: F 204 PHE cc_start: 0.7639 (m-80) cc_final: 0.7287 (m-80) REVERT: F 314 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8192 (tm-30) REVERT: F 503 GLU cc_start: 0.8394 (tp30) cc_final: 0.8143 (tp30) outliers start: 61 outliers final: 45 residues processed: 249 average time/residue: 0.1092 time to fit residues: 46.5273 Evaluate side-chains 252 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 349 PHE Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 218 PHE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 470 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 205 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 232 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 162 optimal weight: 0.0980 chunk 90 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.099457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.075372 restraints weight = 41134.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.078949 restraints weight = 21169.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081584 restraints weight = 13643.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.083396 restraints weight = 9958.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.084614 restraints weight = 7942.100| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19650 Z= 0.109 Angle : 0.574 9.166 26640 Z= 0.277 Chirality : 0.043 0.147 3066 Planarity : 0.003 0.038 3402 Dihedral : 10.616 126.442 2892 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.94 % Favored : 91.81 % Rotamer: Outliers : 2.83 % Allowed : 14.68 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.18), residues: 2430 helix: 1.94 (0.17), residues: 1008 sheet: 1.84 (0.27), residues: 408 loop : -1.99 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.017 0.001 TYR F 319 PHE 0.012 0.001 PHE A 204 TRP 0.013 0.001 TRP B 482 HIS 0.001 0.000 HIS E 356 Details of bonding type rmsd covalent geometry : bond 0.00255 (19626) covalent geometry : angle 0.56555 (26604) hydrogen bonds : bond 0.02571 ( 901) hydrogen bonds : angle 3.99739 ( 2541) metal coordination : bond 0.00233 ( 24) metal coordination : angle 2.80353 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 211 time to evaluate : 0.782 Fit side-chains REVERT: A 113 MET cc_start: 0.9228 (tpp) cc_final: 0.8802 (tpp) REVERT: A 116 PHE cc_start: 0.8971 (t80) cc_final: 0.8675 (m-80) REVERT: A 180 GLN cc_start: 0.7513 (mp10) cc_final: 0.6798 (mp10) REVERT: A 314 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8379 (tm-30) REVERT: A 341 ASP cc_start: 0.8590 (t0) cc_final: 0.8368 (t70) REVERT: A 479 GLN cc_start: 0.7876 (tt0) cc_final: 0.7587 (tt0) REVERT: A 483 LEU cc_start: 0.9385 (tp) cc_final: 0.9054 (mt) REVERT: A 503 GLU cc_start: 0.8336 (tp30) cc_final: 0.7864 (tp30) REVERT: B 113 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8612 (mpp) REVERT: B 118 CYS cc_start: 0.9481 (t) cc_final: 0.9091 (t) REVERT: B 125 ASP cc_start: 0.7737 (m-30) cc_final: 0.7435 (m-30) REVERT: B 164 TYR cc_start: 0.7705 (t80) cc_final: 0.7479 (t80) REVERT: B 203 GLN cc_start: 0.6951 (tm-30) cc_final: 0.6618 (tm-30) REVERT: B 204 PHE cc_start: 0.8112 (m-80) cc_final: 0.7901 (m-80) REVERT: B 314 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8399 (tm-30) REVERT: B 341 ASP cc_start: 0.8617 (t0) cc_final: 0.8251 (t70) REVERT: B 507 MET cc_start: 0.7960 (mmm) cc_final: 0.7685 (mtp) REVERT: C 113 MET cc_start: 0.8849 (mtt) cc_final: 0.8595 (ptp) REVERT: C 118 CYS cc_start: 0.9637 (t) cc_final: 0.9314 (t) REVERT: C 314 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8370 (tm-30) REVERT: C 335 MET cc_start: 0.8284 (tpp) cc_final: 0.8046 (tpp) REVERT: C 493 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: C 503 GLU cc_start: 0.8394 (tp30) cc_final: 0.8132 (tp30) REVERT: D 113 MET cc_start: 0.9214 (tpp) cc_final: 0.8788 (tpp) REVERT: D 116 PHE cc_start: 0.8974 (t80) cc_final: 0.8658 (m-80) REVERT: D 258 ILE cc_start: 0.7942 (mm) cc_final: 0.7729 (mm) REVERT: D 341 ASP cc_start: 0.8573 (t0) cc_final: 0.8346 (t70) REVERT: D 479 GLN cc_start: 0.7843 (tt0) cc_final: 0.7530 (tt0) REVERT: D 483 LEU cc_start: 0.9376 (tp) cc_final: 0.9049 (mt) REVERT: D 503 GLU cc_start: 0.8393 (tp30) cc_final: 0.7890 (tp30) REVERT: E 113 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8605 (mpp) REVERT: E 118 CYS cc_start: 0.9510 (t) cc_final: 0.9121 (t) REVERT: E 218 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7038 (m-80) REVERT: E 314 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8374 (tm-30) REVERT: E 341 ASP cc_start: 0.8588 (t0) cc_final: 0.8253 (t70) REVERT: E 493 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: E 507 MET cc_start: 0.7971 (mmm) cc_final: 0.7664 (mtp) REVERT: F 113 MET cc_start: 0.8920 (ptp) cc_final: 0.8595 (mpp) REVERT: F 116 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8020 (m-80) REVERT: F 204 PHE cc_start: 0.7728 (m-80) cc_final: 0.7414 (m-80) REVERT: F 314 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8175 (tm-30) REVERT: F 335 MET cc_start: 0.8192 (tpp) cc_final: 0.7953 (tpp) REVERT: F 503 GLU cc_start: 0.8387 (tp30) cc_final: 0.8132 (tp30) outliers start: 57 outliers final: 46 residues processed: 251 average time/residue: 0.1081 time to fit residues: 46.2263 Evaluate side-chains 257 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 218 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 349 PHE Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 116 PHE Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 218 PHE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 470 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 65 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 131 optimal weight: 0.2980 chunk 27 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 206 optimal weight: 0.6980 chunk 109 optimal weight: 0.0070 chunk 162 optimal weight: 6.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.076359 restraints weight = 41748.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.080001 restraints weight = 21853.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.082599 restraints weight = 14135.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084417 restraints weight = 10357.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.085609 restraints weight = 8265.191| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19650 Z= 0.099 Angle : 0.575 8.305 26640 Z= 0.278 Chirality : 0.042 0.146 3066 Planarity : 0.003 0.038 3402 Dihedral : 10.300 124.179 2892 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.65 % Favored : 92.10 % Rotamer: Outliers : 2.63 % Allowed : 15.13 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.18), residues: 2430 helix: 1.95 (0.17), residues: 1008 sheet: 1.86 (0.27), residues: 408 loop : -1.99 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 320 TYR 0.013 0.001 TYR C 164 PHE 0.014 0.001 PHE C 204 TRP 0.016 0.002 TRP F 482 HIS 0.001 0.000 HIS F 127 Details of bonding type rmsd covalent geometry : bond 0.00228 (19626) covalent geometry : angle 0.56844 (26604) hydrogen bonds : bond 0.02391 ( 901) hydrogen bonds : angle 3.92860 ( 2541) metal coordination : bond 0.00213 ( 24) metal coordination : angle 2.47708 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.782 Fit side-chains REVERT: A 113 MET cc_start: 0.9227 (tpp) cc_final: 0.8818 (tpp) REVERT: A 116 PHE cc_start: 0.8966 (t80) cc_final: 0.8678 (m-80) REVERT: A 180 GLN cc_start: 0.7535 (mp10) cc_final: 0.6845 (mp10) REVERT: A 314 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8346 (tm-30) REVERT: A 341 ASP cc_start: 0.8594 (t0) cc_final: 0.8374 (t70) REVERT: A 479 GLN cc_start: 0.7766 (tt0) cc_final: 0.7469 (tt0) REVERT: A 483 LEU cc_start: 0.9367 (tp) cc_final: 0.9044 (mt) REVERT: A 503 GLU cc_start: 0.8333 (tp30) cc_final: 0.7860 (tp30) REVERT: B 113 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8615 (mpp) REVERT: B 118 CYS cc_start: 0.9419 (t) cc_final: 0.9027 (t) REVERT: B 125 ASP cc_start: 0.7669 (m-30) cc_final: 0.7403 (m-30) REVERT: B 164 TYR cc_start: 0.7684 (t80) cc_final: 0.7475 (t80) REVERT: B 203 GLN cc_start: 0.6914 (tm-30) cc_final: 0.6599 (tm-30) REVERT: B 314 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 341 ASP cc_start: 0.8611 (t0) cc_final: 0.8243 (t70) REVERT: B 507 MET cc_start: 0.7932 (mmm) cc_final: 0.7624 (mtp) REVERT: C 113 MET cc_start: 0.8838 (mtt) cc_final: 0.8573 (ptp) REVERT: C 118 CYS cc_start: 0.9630 (t) cc_final: 0.9297 (t) REVERT: C 314 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8366 (tm-30) REVERT: C 493 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: C 503 GLU cc_start: 0.8368 (tp30) cc_final: 0.8086 (tp30) REVERT: D 113 MET cc_start: 0.9220 (tpp) cc_final: 0.8783 (tpp) REVERT: D 116 PHE cc_start: 0.8965 (t80) cc_final: 0.8659 (m-80) REVERT: D 180 GLN cc_start: 0.7613 (mp10) cc_final: 0.6835 (mp10) REVERT: D 258 ILE cc_start: 0.7846 (mm) cc_final: 0.7633 (mm) REVERT: D 314 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8353 (tm-30) REVERT: D 341 ASP cc_start: 0.8597 (t0) cc_final: 0.8383 (t70) REVERT: D 479 GLN cc_start: 0.7793 (tt0) cc_final: 0.7519 (tt0) REVERT: D 483 LEU cc_start: 0.9362 (tp) cc_final: 0.9042 (mt) REVERT: D 503 GLU cc_start: 0.8390 (tp30) cc_final: 0.7879 (tp30) REVERT: E 113 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8637 (mpp) REVERT: E 118 CYS cc_start: 0.9488 (t) cc_final: 0.9109 (t) REVERT: E 314 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8347 (tm-30) REVERT: E 341 ASP cc_start: 0.8592 (t0) cc_final: 0.8256 (t70) REVERT: E 493 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8416 (mt-10) REVERT: E 507 MET cc_start: 0.7941 (mmm) cc_final: 0.7636 (mtp) REVERT: F 113 MET cc_start: 0.8911 (ptp) cc_final: 0.8587 (mpp) REVERT: F 116 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: F 118 CYS cc_start: 0.9618 (t) cc_final: 0.9299 (t) REVERT: F 314 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8178 (tm-30) REVERT: F 335 MET cc_start: 0.8174 (tpp) cc_final: 0.7950 (tpp) REVERT: F 503 GLU cc_start: 0.8377 (tp30) cc_final: 0.8087 (tp30) outliers start: 53 outliers final: 40 residues processed: 260 average time/residue: 0.1011 time to fit residues: 45.1477 Evaluate side-chains 260 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 116 PHE Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 218 PHE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 79 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 21 optimal weight: 0.0970 chunk 178 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.099650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.075622 restraints weight = 41984.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.079186 restraints weight = 21941.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081780 restraints weight = 14234.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.083509 restraints weight = 10430.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.084819 restraints weight = 8384.562| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19650 Z= 0.110 Angle : 0.586 8.369 26640 Z= 0.283 Chirality : 0.043 0.147 3066 Planarity : 0.003 0.038 3402 Dihedral : 10.146 120.892 2892 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.90 % Favored : 91.81 % Rotamer: Outliers : 2.28 % Allowed : 15.43 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.18), residues: 2430 helix: 1.99 (0.17), residues: 1008 sheet: 1.60 (0.27), residues: 420 loop : -1.98 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.012 0.001 TYR F 164 PHE 0.013 0.001 PHE A 204 TRP 0.012 0.001 TRP F 482 HIS 0.001 0.000 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00260 (19626) covalent geometry : angle 0.57815 (26604) hydrogen bonds : bond 0.02460 ( 901) hydrogen bonds : angle 3.94681 ( 2541) metal coordination : bond 0.00230 ( 24) metal coordination : angle 2.65480 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 0.720 Fit side-chains REVERT: A 113 MET cc_start: 0.9232 (tpp) cc_final: 0.8814 (tpp) REVERT: A 116 PHE cc_start: 0.8958 (t80) cc_final: 0.8690 (m-80) REVERT: A 180 GLN cc_start: 0.7547 (mp10) cc_final: 0.6858 (mp10) REVERT: A 314 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8351 (tm-30) REVERT: A 479 GLN cc_start: 0.7799 (tt0) cc_final: 0.7501 (tt0) REVERT: A 483 LEU cc_start: 0.9371 (tp) cc_final: 0.9057 (mt) REVERT: A 503 GLU cc_start: 0.8336 (tp30) cc_final: 0.7864 (tp30) REVERT: B 113 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8610 (mpp) REVERT: B 118 CYS cc_start: 0.9428 (t) cc_final: 0.9039 (t) REVERT: B 125 ASP cc_start: 0.7747 (m-30) cc_final: 0.7446 (m-30) REVERT: B 164 TYR cc_start: 0.7664 (t80) cc_final: 0.7442 (t80) REVERT: B 203 GLN cc_start: 0.6887 (tm-30) cc_final: 0.6613 (tm-30) REVERT: B 204 PHE cc_start: 0.7999 (m-80) cc_final: 0.7658 (m-80) REVERT: B 314 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8403 (tm-30) REVERT: B 341 ASP cc_start: 0.8625 (t0) cc_final: 0.8259 (t70) REVERT: B 507 MET cc_start: 0.7946 (mmm) cc_final: 0.7643 (mtp) REVERT: C 113 MET cc_start: 0.8866 (mtt) cc_final: 0.8598 (ptp) REVERT: C 116 PHE cc_start: 0.9101 (t80) cc_final: 0.8742 (m-80) REVERT: C 118 CYS cc_start: 0.9639 (t) cc_final: 0.9304 (t) REVERT: C 314 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8416 (tm-30) REVERT: C 493 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: C 503 GLU cc_start: 0.8366 (tp30) cc_final: 0.8078 (tp30) REVERT: D 113 MET cc_start: 0.9224 (tpp) cc_final: 0.8806 (tpp) REVERT: D 116 PHE cc_start: 0.8994 (t80) cc_final: 0.8670 (m-80) REVERT: D 180 GLN cc_start: 0.7609 (mp10) cc_final: 0.6886 (mp10) REVERT: D 314 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8360 (tm-30) REVERT: D 341 ASP cc_start: 0.8603 (t0) cc_final: 0.8403 (t70) REVERT: D 479 GLN cc_start: 0.7803 (tt0) cc_final: 0.7521 (tt0) REVERT: D 483 LEU cc_start: 0.9371 (tp) cc_final: 0.9057 (mt) REVERT: D 503 GLU cc_start: 0.8357 (tp30) cc_final: 0.7872 (tp30) REVERT: E 113 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8587 (mpp) REVERT: E 118 CYS cc_start: 0.9514 (t) cc_final: 0.9158 (t) REVERT: E 314 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8357 (tm-30) REVERT: E 341 ASP cc_start: 0.8571 (t0) cc_final: 0.8245 (t70) REVERT: E 493 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: E 507 MET cc_start: 0.7968 (mmm) cc_final: 0.7666 (mtp) REVERT: F 113 MET cc_start: 0.8909 (ptp) cc_final: 0.8589 (mpp) REVERT: F 116 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: F 118 CYS cc_start: 0.9626 (t) cc_final: 0.9313 (t) REVERT: F 314 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8194 (tm-30) REVERT: F 503 GLU cc_start: 0.8370 (tp30) cc_final: 0.8079 (tp30) outliers start: 46 outliers final: 41 residues processed: 247 average time/residue: 0.1039 time to fit residues: 43.8975 Evaluate side-chains 255 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 349 PHE Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 116 PHE Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 218 PHE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.074952 restraints weight = 41199.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.078521 restraints weight = 21324.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.081068 restraints weight = 13763.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.082781 restraints weight = 10094.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084115 restraints weight = 8103.342| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19650 Z= 0.127 Angle : 0.601 8.082 26640 Z= 0.291 Chirality : 0.043 0.199 3066 Planarity : 0.003 0.039 3402 Dihedral : 10.036 117.159 2892 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.19 % Favored : 91.52 % Rotamer: Outliers : 2.43 % Allowed : 15.62 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.18), residues: 2430 helix: 2.07 (0.17), residues: 1002 sheet: 1.59 (0.27), residues: 420 loop : -1.88 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 400 TYR 0.010 0.001 TYR E 319 PHE 0.012 0.001 PHE A 204 TRP 0.012 0.001 TRP F 482 HIS 0.002 0.000 HIS E 356 Details of bonding type rmsd covalent geometry : bond 0.00300 (19626) covalent geometry : angle 0.59139 (26604) hydrogen bonds : bond 0.02596 ( 901) hydrogen bonds : angle 4.00144 ( 2541) metal coordination : bond 0.00281 ( 24) metal coordination : angle 2.93821 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2672.06 seconds wall clock time: 47 minutes 7.26 seconds (2827.26 seconds total)