Starting phenix.real_space_refine on Tue Jun 17 05:59:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dzf_27796/06_2025/8dzf_27796_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dzf_27796/06_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_27796/06_2025/8dzf_27796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dzf_27796/06_2025/8dzf_27796.map" model { file = "/net/cci-nas-00/data/ceres_data/8dzf_27796/06_2025/8dzf_27796_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dzf_27796/06_2025/8dzf_27796_neut.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2} 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: C, B, E, D, F Time building chain proxies: 7.41, per 1000 atoms: 0.38 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: 4.35 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.06 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: 5.45 Time building geometry restraints manager: 5.19 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.160 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: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.510 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.850 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (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 TRP 0.003 0.001 TRP D 359 HIS 0.002 0.000 HIS B 356 PHE 0.005 0.001 PHE D 204 TYR 0.006 0.001 TYR F 278 ARG 0.002 0.000 ARG D 320 Details of bonding type rmsd hydrogen bonds : bond 0.20073 ( 901) hydrogen bonds : angle 5.66357 ( 2541) metal coordination : bond 0.00248 ( 24) metal coordination : angle 2.29781 ( 36) covalent geometry : bond 0.00750 (19626) covalent geometry : angle 0.80930 (26604) *********************** 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 : 2.434 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: 0.2932 time to fit residues: 193.0073 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 : 2.430 ------------------------------------------------------------------------------- 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 207 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 223 optimal weight: 0.0570 overall best weight: 0.7702 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.101585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.078270 restraints weight = 42124.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.081860 restraints weight = 21842.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.084365 restraints weight = 13956.856| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19650 Z= 0.118 Angle : 0.601 7.478 26640 Z= 0.295 Chirality : 0.044 0.137 3066 Planarity : 0.003 0.034 3402 Dihedral : 13.107 149.636 2896 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.53 % Favored : 92.22 % Rotamer: Outliers : 1.98 % Allowed : 12.85 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2430 helix: 1.61 (0.17), residues: 972 sheet: 2.07 (0.26), residues: 408 loop : -1.85 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 359 HIS 0.004 0.001 HIS B 127 PHE 0.015 0.001 PHE C 204 TYR 0.008 0.001 TYR C 319 ARG 0.002 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 901) hydrogen bonds : angle 4.48053 ( 2541) metal coordination : bond 0.00140 ( 24) metal coordination : angle 3.29340 ( 36) covalent geometry : bond 0.00249 (19626) covalent geometry : angle 0.58925 (26604) *********************** 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 306 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 2.288 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.9214 (tpp) cc_final: 0.8798 (tpp) REVERT: A 179 TYR cc_start: 0.8651 (m-80) cc_final: 0.8417 (m-80) REVERT: A 180 GLN cc_start: 0.7583 (mp10) cc_final: 0.6760 (mp10) REVERT: A 203 GLN cc_start: 0.6712 (tm-30) cc_final: 0.6495 (tm-30) REVERT: A 291 GLU cc_start: 0.8712 (tp30) cc_final: 0.8455 (tp30) REVERT: A 314 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8379 (tm-30) REVERT: A 319 TYR cc_start: 0.8798 (t80) cc_final: 0.8594 (t80) REVERT: A 335 MET cc_start: 0.8063 (tpp) cc_final: 0.7691 (tpp) REVERT: A 338 GLU cc_start: 0.6815 (tp30) cc_final: 0.6561 (tm-30) REVERT: A 479 GLN cc_start: 0.7985 (tt0) cc_final: 0.7768 (tt0) REVERT: A 503 GLU cc_start: 0.8296 (tp30) cc_final: 0.8036 (tp30) REVERT: B 125 ASP cc_start: 0.7515 (m-30) cc_final: 0.7233 (m-30) REVERT: B 164 TYR cc_start: 0.7600 (t80) cc_final: 0.7354 (t80) REVERT: B 203 GLN cc_start: 0.6969 (tm-30) cc_final: 0.6497 (tm-30) REVERT: B 314 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8448 (tm-30) REVERT: B 350 THR cc_start: 0.9185 (p) cc_final: 0.8981 (p) REVERT: C 113 MET cc_start: 0.9219 (tpp) cc_final: 0.8721 (tpp) REVERT: C 503 GLU cc_start: 0.8440 (tp30) cc_final: 0.8164 (tp30) REVERT: D 113 MET cc_start: 0.9185 (tpp) cc_final: 0.8765 (tpp) REVERT: D 179 TYR cc_start: 0.8687 (m-80) cc_final: 0.8457 (m-80) REVERT: D 180 GLN cc_start: 0.7669 (mp10) cc_final: 0.6889 (mp10) REVERT: D 203 GLN cc_start: 0.6893 (tm-30) cc_final: 0.6668 (tm-30) REVERT: D 291 GLU cc_start: 0.8690 (tp30) cc_final: 0.8436 (tp30) REVERT: D 314 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8392 (tm-30) REVERT: D 338 GLU cc_start: 0.6888 (tp30) cc_final: 0.6644 (tm-30) REVERT: D 479 GLN cc_start: 0.7967 (tt0) cc_final: 0.7755 (tt0) REVERT: D 503 GLU cc_start: 0.8243 (tp30) cc_final: 0.7997 (tp30) REVERT: E 164 TYR cc_start: 0.7646 (t80) cc_final: 0.7444 (t80) REVERT: E 204 PHE cc_start: 0.8132 (m-80) cc_final: 0.7911 (m-80) REVERT: E 314 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8407 (tm-30) REVERT: E 338 GLU cc_start: 0.6954 (tp30) cc_final: 0.6642 (tm-30) REVERT: E 350 THR cc_start: 0.9149 (p) cc_final: 0.8935 (p) REVERT: F 204 PHE cc_start: 0.7923 (m-80) cc_final: 0.7666 (m-80) REVERT: F 314 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8210 (tm-30) REVERT: F 353 MET cc_start: 0.8731 (ptm) cc_final: 0.8521 (ptm) REVERT: F 388 GLU cc_start: 0.8489 (tp30) cc_final: 0.8153 (tp30) REVERT: F 503 GLU cc_start: 0.8444 (tp30) cc_final: 0.8159 (tp30) outliers start: 40 outliers final: 19 residues processed: 297 average time/residue: 0.2516 time to fit residues: 126.3265 Evaluate side-chains 234 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 2.257 ------------------------------------------------------------------------------- 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 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 170 optimal weight: 0.3980 chunk 63 optimal weight: 0.6980 chunk 208 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 112 optimal weight: 0.2980 chunk 225 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 218 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.100598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.076705 restraints weight = 41800.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.080324 restraints weight = 22011.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.082850 restraints weight = 14286.659| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1989 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= 0.102 Angle : 0.571 8.672 26640 Z= 0.275 Chirality : 0.042 0.132 3066 Planarity : 0.003 0.028 3402 Dihedral : 12.192 145.476 2892 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.08 % Favored : 92.67 % Rotamer: Outliers : 2.98 % Allowed : 12.95 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2430 helix: 1.64 (0.17), residues: 1008 sheet: 2.01 (0.26), residues: 408 loop : -1.95 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 482 HIS 0.002 0.000 HIS D 356 PHE 0.014 0.001 PHE C 204 TYR 0.014 0.001 TYR F 319 ARG 0.002 0.000 ARG A 475 Details of bonding type rmsd hydrogen bonds : bond 0.03257 ( 901) hydrogen bonds : angle 4.19771 ( 2541) metal coordination : bond 0.00163 ( 24) metal coordination : angle 3.11315 ( 36) covalent geometry : bond 0.00220 (19626) covalent geometry : angle 0.55933 (26604) *********************** 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 295 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 235 time to evaluate : 2.208 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.9198 (tpp) cc_final: 0.8791 (tpp) REVERT: A 180 GLN cc_start: 0.7605 (mp10) cc_final: 0.6857 (mp10) REVERT: A 291 GLU cc_start: 0.8824 (tp30) cc_final: 0.8565 (tp30) REVERT: A 314 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8386 (tm-30) REVERT: A 338 GLU cc_start: 0.6779 (tp30) cc_final: 0.6564 (tm-30) REVERT: A 482 TRP cc_start: 0.8879 (t60) cc_final: 0.8488 (t60) REVERT: A 503 GLU cc_start: 0.8297 (tp30) cc_final: 0.7986 (tp30) REVERT: B 113 MET cc_start: 0.8842 (mtt) cc_final: 0.8558 (mpp) REVERT: B 125 ASP cc_start: 0.7514 (m-30) cc_final: 0.7188 (m-30) REVERT: B 164 TYR cc_start: 0.7629 (t80) cc_final: 0.7378 (t80) REVERT: B 203 GLN cc_start: 0.7038 (tm-30) cc_final: 0.6578 (tm-30) REVERT: B 314 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8435 (tm-30) REVERT: B 332 ASP cc_start: 0.7367 (m-30) cc_final: 0.7139 (m-30) REVERT: C 203 GLN cc_start: 0.6942 (tm-30) cc_final: 0.6669 (tm-30) REVERT: D 113 MET cc_start: 0.9156 (tpp) cc_final: 0.8741 (tpp) REVERT: D 179 TYR cc_start: 0.8701 (m-80) cc_final: 0.8495 (m-80) REVERT: D 180 GLN cc_start: 0.7683 (mp10) cc_final: 0.6924 (mp10) REVERT: D 291 GLU cc_start: 0.8751 (tp30) cc_final: 0.8517 (tp30) REVERT: D 314 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8413 (tm-30) REVERT: D 482 TRP cc_start: 0.8828 (t60) cc_final: 0.8439 (t60) REVERT: D 503 GLU cc_start: 0.8301 (tp30) cc_final: 0.7998 (tp30) REVERT: E 113 MET cc_start: 0.8839 (mtt) cc_final: 0.8459 (mpp) REVERT: E 314 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8390 (tm-30) REVERT: F 203 GLN cc_start: 0.7038 (tm-30) cc_final: 0.6763 (tm-30) REVERT: F 314 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8235 (tm-30) REVERT: F 353 MET cc_start: 0.8531 (ptm) cc_final: 0.8274 (ptm) REVERT: F 388 GLU cc_start: 0.8518 (tp30) cc_final: 0.8173 (tp30) outliers start: 60 outliers final: 28 residues processed: 280 average time/residue: 0.2448 time to fit residues: 114.4990 Evaluate side-chains 235 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 2.276 ------------------------------------------------------------------------------- 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 219 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 ILE 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 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 132 ASP 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 479 GLN Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 196 VAL 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 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 219 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 170 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 231 optimal weight: 0.5980 chunk 185 optimal weight: 0.4980 chunk 198 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.097723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.073292 restraints weight = 42630.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.076770 restraints weight = 22649.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.079244 restraints weight = 14863.158| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19650 Z= 0.166 Angle : 0.608 7.726 26640 Z= 0.296 Chirality : 0.044 0.142 3066 Planarity : 0.003 0.029 3402 Dihedral : 11.709 139.956 2892 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.94 % Favored : 91.81 % Rotamer: Outliers : 2.93 % Allowed : 13.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.18), residues: 2430 helix: 1.76 (0.17), residues: 1008 sheet: 1.91 (0.27), residues: 408 loop : -1.93 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 482 HIS 0.002 0.001 HIS D 238 PHE 0.010 0.001 PHE A 204 TYR 0.014 0.001 TYR E 164 ARG 0.003 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 901) hydrogen bonds : angle 4.28026 ( 2541) metal coordination : bond 0.00326 ( 24) metal coordination : angle 3.74930 ( 36) covalent geometry : bond 0.00385 (19626) covalent geometry : angle 0.59293 (26604) *********************** 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 267 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 208 time to evaluate : 2.314 Fit side-chains REVERT: A 113 MET cc_start: 0.9254 (tpp) cc_final: 0.8848 (tpp) REVERT: A 180 GLN cc_start: 0.7612 (mp10) cc_final: 0.6974 (mp10) REVERT: A 203 GLN cc_start: 0.6934 (tm-30) cc_final: 0.6694 (tm-30) REVERT: A 314 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8336 (tm-30) REVERT: A 335 MET cc_start: 0.8240 (tpp) cc_final: 0.7889 (tpp) REVERT: A 341 ASP cc_start: 0.8614 (t0) cc_final: 0.8363 (t70) REVERT: A 503 GLU cc_start: 0.8364 (tp30) cc_final: 0.8021 (tp30) REVERT: B 113 MET cc_start: 0.8879 (mtt) cc_final: 0.8631 (mpp) REVERT: B 125 ASP cc_start: 0.7621 (m-30) cc_final: 0.7323 (m-30) REVERT: B 179 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8735 (m-10) REVERT: B 203 GLN cc_start: 0.6957 (tm-30) cc_final: 0.6591 (tm-30) REVERT: B 314 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8367 (tm-30) REVERT: B 341 ASP cc_start: 0.8691 (t0) cc_final: 0.8269 (t70) REVERT: C 113 MET cc_start: 0.8901 (mtt) cc_final: 0.8565 (mpp) REVERT: C 314 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8431 (tm-30) REVERT: C 338 GLU cc_start: 0.6798 (tp30) cc_final: 0.6317 (tp30) REVERT: C 455 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8773 (mp) REVERT: D 113 MET cc_start: 0.9224 (tpp) cc_final: 0.8810 (tpp) REVERT: D 180 GLN cc_start: 0.7552 (mp10) cc_final: 0.6834 (mp10) REVERT: D 203 GLN cc_start: 0.7118 (tm-30) cc_final: 0.6882 (tm-30) REVERT: D 314 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8384 (tm-30) REVERT: D 503 GLU cc_start: 0.8390 (tp30) cc_final: 0.8041 (tp30) REVERT: E 113 MET cc_start: 0.8857 (mtt) cc_final: 0.8529 (mpp) REVERT: E 314 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8397 (tm-30) REVERT: E 341 ASP cc_start: 0.8693 (t0) cc_final: 0.8312 (t70) REVERT: E 493 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: F 314 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8251 (tm-30) REVERT: F 388 GLU cc_start: 0.8663 (tp30) cc_final: 0.8168 (tp30) outliers start: 59 outliers final: 41 residues processed: 248 average time/residue: 0.2462 time to fit residues: 102.9410 Evaluate side-chains 238 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 2.338 ------------------------------------------------------------------------------- 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 385 THR Chi-restraints excluded: chain A residue 455 ILE 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 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 288 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 455 ILE 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 290 ILE Chi-restraints excluded: chain D residue 347 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 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 347 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 470 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 11 optimal weight: 0.0970 chunk 129 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 109 optimal weight: 0.0770 chunk 50 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 192 optimal weight: 6.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.100043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075821 restraints weight = 41866.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.079434 restraints weight = 21753.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.082020 restraints weight = 14010.610| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19650 Z= 0.100 Angle : 0.563 7.458 26640 Z= 0.272 Chirality : 0.043 0.165 3066 Planarity : 0.003 0.034 3402 Dihedral : 11.304 135.654 2892 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.49 % Favored : 92.26 % Rotamer: Outliers : 2.23 % Allowed : 14.09 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2430 helix: 1.88 (0.17), residues: 1008 sheet: 1.92 (0.27), residues: 408 loop : -1.95 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.002 0.000 HIS C 356 PHE 0.014 0.001 PHE A 204 TYR 0.014 0.001 TYR F 319 ARG 0.002 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.02791 ( 901) hydrogen bonds : angle 4.08555 ( 2541) metal coordination : bond 0.00226 ( 24) metal coordination : angle 2.94360 ( 36) covalent geometry : bond 0.00225 (19626) covalent geometry : angle 0.55246 (26604) *********************** 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 265 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 2.457 Fit side-chains REVERT: A 113 MET cc_start: 0.9254 (tpp) cc_final: 0.8845 (tpp) REVERT: A 180 GLN cc_start: 0.7521 (mp10) cc_final: 0.6840 (mp10) REVERT: A 203 GLN cc_start: 0.6912 (tm-30) cc_final: 0.6656 (tm-30) REVERT: A 314 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8337 (tm-30) REVERT: A 341 ASP cc_start: 0.8601 (t0) cc_final: 0.8341 (t70) REVERT: A 503 GLU cc_start: 0.8366 (tp30) cc_final: 0.7951 (tp30) REVERT: B 113 MET cc_start: 0.8895 (mtt) cc_final: 0.8690 (mpp) REVERT: B 125 ASP cc_start: 0.7577 (m-30) cc_final: 0.7276 (m-30) REVERT: B 164 TYR cc_start: 0.7677 (t80) cc_final: 0.7446 (t80) REVERT: B 179 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8615 (m-10) REVERT: B 203 GLN cc_start: 0.6961 (tm-30) cc_final: 0.6584 (tm-30) REVERT: B 314 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8381 (tm-30) REVERT: B 341 ASP cc_start: 0.8671 (t0) cc_final: 0.8249 (t70) REVERT: B 507 MET cc_start: 0.7974 (mmm) cc_final: 0.7681 (mtp) REVERT: C 113 MET cc_start: 0.8874 (mtt) cc_final: 0.8588 (mpp) REVERT: C 203 GLN cc_start: 0.7013 (tm-30) cc_final: 0.6765 (tm-30) REVERT: C 314 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8343 (tm-30) REVERT: D 113 MET cc_start: 0.9224 (tpp) cc_final: 0.8810 (tpp) REVERT: D 180 GLN cc_start: 0.7503 (mp10) cc_final: 0.6789 (mp10) REVERT: D 314 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8370 (tm-30) REVERT: D 341 ASP cc_start: 0.8615 (t0) cc_final: 0.8342 (t70) REVERT: D 503 GLU cc_start: 0.8372 (tp30) cc_final: 0.7931 (tp30) REVERT: E 113 MET cc_start: 0.8880 (mtt) cc_final: 0.8655 (mpp) REVERT: E 314 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8365 (tm-30) REVERT: E 335 MET cc_start: 0.8173 (tpp) cc_final: 0.7958 (tpp) REVERT: E 341 ASP cc_start: 0.8672 (t0) cc_final: 0.8306 (t70) REVERT: E 507 MET cc_start: 0.7981 (mmm) cc_final: 0.7700 (mtp) REVERT: F 113 MET cc_start: 0.8912 (ptp) cc_final: 0.8450 (tmm) REVERT: F 203 GLN cc_start: 0.7056 (tm-30) cc_final: 0.6794 (tm-30) REVERT: F 314 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8194 (tm-30) outliers start: 45 outliers final: 29 residues processed: 249 average time/residue: 0.2456 time to fit residues: 103.0346 Evaluate side-chains 232 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 2.135 ------------------------------------------------------------------------------- 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 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 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 277 LEU 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 393 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 277 LEU 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 277 LEU Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 385 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 148 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 198 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 GLN D 165 ASN D 303 GLN E 165 ASN E 396 GLN F 165 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.094235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.070438 restraints weight = 42135.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.073726 restraints weight = 22042.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.076109 restraints weight = 14450.783| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19650 Z= 0.235 Angle : 0.685 7.983 26640 Z= 0.335 Chirality : 0.046 0.153 3066 Planarity : 0.004 0.039 3402 Dihedral : 11.500 132.281 2892 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.52 % Favored : 91.23 % Rotamer: Outliers : 3.67 % Allowed : 13.79 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2430 helix: 1.75 (0.17), residues: 1008 sheet: 1.67 (0.26), residues: 414 loop : -2.11 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 482 HIS 0.003 0.001 HIS C 238 PHE 0.013 0.002 PHE D 237 TYR 0.014 0.001 TYR E 164 ARG 0.004 0.001 ARG F 475 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 901) hydrogen bonds : angle 4.50051 ( 2541) metal coordination : bond 0.00502 ( 24) metal coordination : angle 4.49339 ( 36) covalent geometry : bond 0.00544 (19626) covalent geometry : angle 0.66554 (26604) *********************** 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 265 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 191 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.9260 (tpp) cc_final: 0.8851 (tpp) REVERT: A 203 GLN cc_start: 0.7078 (tm-30) cc_final: 0.6874 (tm-30) REVERT: A 314 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8369 (tm-30) REVERT: A 335 MET cc_start: 0.8350 (tpp) cc_final: 0.7945 (tpp) REVERT: A 341 ASP cc_start: 0.8609 (t0) cc_final: 0.8386 (t70) REVERT: A 503 GLU cc_start: 0.8372 (tp30) cc_final: 0.7978 (tp30) REVERT: B 113 MET cc_start: 0.8912 (mtt) cc_final: 0.8684 (mpp) REVERT: B 204 PHE cc_start: 0.8077 (m-80) cc_final: 0.7867 (m-80) REVERT: B 341 ASP cc_start: 0.8692 (t0) cc_final: 0.8272 (t70) REVERT: C 116 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8162 (m-80) REVERT: C 159 ILE cc_start: 0.9104 (pt) cc_final: 0.8875 (pt) REVERT: C 314 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8411 (tm-30) REVERT: C 455 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8736 (mp) REVERT: D 113 MET cc_start: 0.9250 (tpp) cc_final: 0.8828 (tpp) REVERT: D 203 GLN cc_start: 0.7265 (tm-30) cc_final: 0.7019 (tm-30) REVERT: D 204 PHE cc_start: 0.7515 (m-80) cc_final: 0.7197 (m-10) REVERT: D 314 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8385 (tm-30) REVERT: D 341 ASP cc_start: 0.8611 (t0) cc_final: 0.8343 (t70) REVERT: D 503 GLU cc_start: 0.8395 (tp30) cc_final: 0.7992 (tp30) REVERT: E 113 MET cc_start: 0.8964 (mtt) cc_final: 0.8735 (mpp) REVERT: E 341 ASP cc_start: 0.8666 (t0) cc_final: 0.8278 (t70) REVERT: E 493 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: F 116 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: F 314 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8227 (tm-30) REVERT: F 386 ASP cc_start: 0.8028 (m-30) cc_final: 0.7769 (m-30) REVERT: F 455 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8803 (mp) outliers start: 74 outliers final: 46 residues processed: 247 average time/residue: 0.2336 time to fit residues: 97.3820 Evaluate side-chains 228 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP 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 353 MET Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 THR 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 349 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 116 PHE 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 347 LEU 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 455 ILE Chi-restraints excluded: chain C residue 470 VAL 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 353 MET Chi-restraints excluded: chain D residue 385 THR 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 349 PHE Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 385 THR 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 347 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 455 ILE Chi-restraints excluded: chain F residue 470 VAL Chi-restraints excluded: chain F residue 477 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 108 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 226 optimal weight: 0.0570 chunk 91 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 213 optimal weight: 0.3980 chunk 159 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 242 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.097972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.074179 restraints weight = 41210.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077588 restraints weight = 21777.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.080066 restraints weight = 14250.732| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19650 Z= 0.105 Angle : 0.584 7.645 26640 Z= 0.281 Chirality : 0.043 0.153 3066 Planarity : 0.003 0.039 3402 Dihedral : 11.149 132.668 2892 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.16 % Favored : 92.59 % Rotamer: Outliers : 2.28 % Allowed : 15.67 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2430 helix: 1.86 (0.17), residues: 1008 sheet: 1.75 (0.27), residues: 408 loop : -2.00 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 359 HIS 0.001 0.000 HIS D 238 PHE 0.013 0.001 PHE C 204 TYR 0.009 0.001 TYR E 164 ARG 0.002 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.02750 ( 901) hydrogen bonds : angle 4.16742 ( 2541) metal coordination : bond 0.00244 ( 24) metal coordination : angle 3.17594 ( 36) covalent geometry : bond 0.00238 (19626) covalent geometry : angle 0.57282 (26604) *********************** 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 247 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 201 time to evaluate : 2.296 Fit side-chains REVERT: A 113 MET cc_start: 0.9255 (tpp) cc_final: 0.8834 (tpp) REVERT: A 203 GLN cc_start: 0.7042 (tm-30) cc_final: 0.6836 (tm-30) REVERT: A 314 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8341 (tm-30) REVERT: A 503 GLU cc_start: 0.8389 (tp30) cc_final: 0.7887 (tp30) REVERT: B 118 CYS cc_start: 0.9610 (t) cc_final: 0.9296 (t) REVERT: B 341 ASP cc_start: 0.8648 (t0) cc_final: 0.8231 (t70) REVERT: C 113 MET cc_start: 0.8893 (ptp) cc_final: 0.8656 (mpp) REVERT: C 314 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8333 (tm-30) REVERT: D 113 MET cc_start: 0.9235 (tpp) cc_final: 0.8804 (tpp) REVERT: D 203 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6931 (tm-30) REVERT: D 314 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8369 (tm-30) REVERT: D 335 MET cc_start: 0.8213 (tpp) cc_final: 0.7973 (tpp) REVERT: D 341 ASP cc_start: 0.8579 (t0) cc_final: 0.8300 (t70) REVERT: D 503 GLU cc_start: 0.8382 (tp30) cc_final: 0.7847 (tp30) REVERT: E 113 MET cc_start: 0.8970 (mtt) cc_final: 0.8703 (mpp) REVERT: E 341 ASP cc_start: 0.8629 (t0) cc_final: 0.8234 (t70) REVERT: F 116 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8083 (m-80) REVERT: F 314 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8113 (tm-30) outliers start: 46 outliers final: 36 residues processed: 231 average time/residue: 0.2459 time to fit residues: 96.4760 Evaluate side-chains 230 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP 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 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 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 277 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 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 132 ASP Chi-restraints excluded: chain E residue 277 LEU 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 F residue 116 PHE Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 219 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 35 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 170 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN B 303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.072810 restraints weight = 41503.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.076191 restraints weight = 21593.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.078679 restraints weight = 14055.808| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19650 Z= 0.144 Angle : 0.606 8.314 26640 Z= 0.293 Chirality : 0.044 0.152 3066 Planarity : 0.003 0.040 3402 Dihedral : 11.029 130.412 2892 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.27 % Favored : 91.48 % Rotamer: Outliers : 2.58 % Allowed : 15.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2430 helix: 1.85 (0.17), residues: 1008 sheet: 1.72 (0.27), residues: 408 loop : -2.03 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 482 HIS 0.002 0.000 HIS C 238 PHE 0.011 0.001 PHE A 204 TYR 0.011 0.001 TYR E 319 ARG 0.004 0.000 ARG D 523 Details of bonding type rmsd hydrogen bonds : bond 0.02924 ( 901) hydrogen bonds : angle 4.21914 ( 2541) metal coordination : bond 0.00304 ( 24) metal coordination : angle 3.48877 ( 36) covalent geometry : bond 0.00339 (19626) covalent geometry : angle 0.59315 (26604) *********************** 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 250 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 198 time to evaluate : 2.474 Fit side-chains REVERT: A 113 MET cc_start: 0.9237 (tpp) cc_final: 0.8822 (tpp) REVERT: A 203 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6876 (tm-30) REVERT: A 314 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8356 (tm-30) REVERT: A 341 ASP cc_start: 0.8642 (t0) cc_final: 0.8379 (t70) REVERT: A 503 GLU cc_start: 0.8389 (tp30) cc_final: 0.7927 (tp30) REVERT: B 118 CYS cc_start: 0.9623 (t) cc_final: 0.9280 (t) REVERT: B 203 GLN cc_start: 0.7089 (tm-30) cc_final: 0.6718 (tm-30) REVERT: B 314 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8356 (tm-30) REVERT: B 341 ASP cc_start: 0.8659 (t0) cc_final: 0.8264 (t70) REVERT: B 405 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8689 (mm-40) REVERT: C 116 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: C 193 LEU cc_start: 0.9204 (tp) cc_final: 0.9001 (tp) REVERT: C 503 GLU cc_start: 0.8380 (tp30) cc_final: 0.8041 (tp30) REVERT: D 113 MET cc_start: 0.9214 (tpp) cc_final: 0.8784 (tpp) REVERT: D 203 GLN cc_start: 0.7311 (tm-30) cc_final: 0.7087 (tm-30) REVERT: D 314 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8359 (tm-30) REVERT: D 341 ASP cc_start: 0.8586 (t0) cc_final: 0.8329 (t70) REVERT: D 503 GLU cc_start: 0.8380 (tp30) cc_final: 0.7893 (tp30) REVERT: E 113 MET cc_start: 0.8954 (mtt) cc_final: 0.8719 (mpp) REVERT: E 341 ASP cc_start: 0.8659 (t0) cc_final: 0.8279 (t70) REVERT: F 113 MET cc_start: 0.8932 (ptp) cc_final: 0.8570 (mpp) REVERT: F 116 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8128 (m-80) REVERT: F 386 ASP cc_start: 0.7949 (m-30) cc_final: 0.7658 (m-30) REVERT: F 503 GLU cc_start: 0.8395 (tp30) cc_final: 0.8040 (tp30) outliers start: 52 outliers final: 36 residues processed: 233 average time/residue: 0.2420 time to fit residues: 96.1689 Evaluate side-chains 232 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP 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 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 385 THR Chi-restraints excluded: chain C residue 116 PHE 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 D residue 121 MET 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 132 ASP 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 242 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.097219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.073398 restraints weight = 41303.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.076869 restraints weight = 21365.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.079341 restraints weight = 13801.938| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2965 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= 0.118 Angle : 0.602 9.034 26640 Z= 0.289 Chirality : 0.043 0.159 3066 Planarity : 0.003 0.040 3402 Dihedral : 10.881 129.953 2892 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.57 % Favored : 92.18 % Rotamer: Outliers : 2.38 % Allowed : 15.92 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2430 helix: 1.83 (0.17), residues: 1014 sheet: 1.71 (0.27), residues: 408 loop : -2.00 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 482 HIS 0.002 0.000 HIS F 238 PHE 0.011 0.001 PHE A 204 TYR 0.012 0.001 TYR E 319 ARG 0.002 0.000 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.02692 ( 901) hydrogen bonds : angle 4.16885 ( 2541) metal coordination : bond 0.00238 ( 24) metal coordination : angle 3.15107 ( 36) covalent geometry : bond 0.00277 (19626) covalent geometry : angle 0.59080 (26604) *********************** 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 248 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 2.405 Fit side-chains REVERT: A 113 MET cc_start: 0.9226 (tpp) cc_final: 0.8807 (tpp) REVERT: A 116 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: A 203 GLN cc_start: 0.7106 (tm-30) cc_final: 0.6887 (tm-30) REVERT: A 314 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8328 (tm-30) REVERT: A 341 ASP cc_start: 0.8635 (t0) cc_final: 0.8373 (t70) REVERT: A 503 GLU cc_start: 0.8368 (tp30) cc_final: 0.7861 (tp30) REVERT: B 118 CYS cc_start: 0.9559 (t) cc_final: 0.9161 (t) REVERT: B 203 GLN cc_start: 0.7081 (tm-30) cc_final: 0.6705 (tm-30) REVERT: B 314 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8341 (tm-30) REVERT: B 341 ASP cc_start: 0.8654 (t0) cc_final: 0.8258 (t70) REVERT: B 405 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8670 (mm-40) REVERT: C 113 MET cc_start: 0.8891 (ptp) cc_final: 0.8574 (mpp) REVERT: C 116 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: C 118 CYS cc_start: 0.9678 (t) cc_final: 0.9369 (t) REVERT: C 193 LEU cc_start: 0.9214 (tp) cc_final: 0.9001 (tp) REVERT: C 335 MET cc_start: 0.8290 (tpp) cc_final: 0.8028 (tpp) REVERT: C 503 GLU cc_start: 0.8407 (tp30) cc_final: 0.8057 (tp30) REVERT: D 113 MET cc_start: 0.9211 (tpp) cc_final: 0.8780 (tpp) REVERT: D 116 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: D 203 GLN cc_start: 0.7309 (tm-30) cc_final: 0.7077 (tm-30) REVERT: D 314 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8342 (tm-30) REVERT: D 341 ASP cc_start: 0.8575 (t0) cc_final: 0.8320 (t70) REVERT: D 503 GLU cc_start: 0.8367 (tp30) cc_final: 0.7857 (tp30) REVERT: E 113 MET cc_start: 0.8971 (mtt) cc_final: 0.8732 (mpp) REVERT: E 341 ASP cc_start: 0.8644 (t0) cc_final: 0.8259 (t70) REVERT: F 116 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8161 (m-80) REVERT: F 335 MET cc_start: 0.8248 (tpp) cc_final: 0.7959 (tpp) REVERT: F 386 ASP cc_start: 0.7929 (m-30) cc_final: 0.7633 (m-30) REVERT: F 503 GLU cc_start: 0.8396 (tp30) cc_final: 0.8033 (tp30) outliers start: 48 outliers final: 39 residues processed: 230 average time/residue: 0.2536 time to fit residues: 98.9452 Evaluate side-chains 236 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 132 ASP 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 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 116 PHE 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 347 LEU 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 D residue 116 PHE 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 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 132 ASP 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 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 277 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 160 optimal weight: 2.9990 chunk 213 optimal weight: 0.0770 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 139 optimal weight: 0.0000 chunk 154 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.098727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.074880 restraints weight = 40948.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.078398 restraints weight = 21088.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.080967 restraints weight = 13587.250| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19650 Z= 0.106 Angle : 0.598 10.093 26640 Z= 0.288 Chirality : 0.043 0.161 3066 Planarity : 0.003 0.040 3402 Dihedral : 10.629 128.472 2892 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.78 % Favored : 91.98 % Rotamer: Outliers : 2.23 % Allowed : 16.37 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2430 helix: 1.90 (0.17), residues: 1008 sheet: 1.52 (0.27), residues: 420 loop : -2.02 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 482 HIS 0.002 0.000 HIS D 127 PHE 0.011 0.001 PHE A 204 TYR 0.012 0.001 TYR B 164 ARG 0.003 0.000 ARG F 453 Details of bonding type rmsd hydrogen bonds : bond 0.02496 ( 901) hydrogen bonds : angle 4.09894 ( 2541) metal coordination : bond 0.00228 ( 24) metal coordination : angle 2.83529 ( 36) covalent geometry : bond 0.00246 (19626) covalent geometry : angle 0.58961 (26604) ********************** 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 250 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 2.149 Fit side-chains REVERT: A 113 MET cc_start: 0.9215 (tpp) cc_final: 0.8793 (tpp) REVERT: A 116 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: A 203 GLN cc_start: 0.7120 (tm-30) cc_final: 0.6913 (tm-30) REVERT: A 314 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8307 (tm-30) REVERT: A 341 ASP cc_start: 0.8622 (t0) cc_final: 0.8368 (t70) REVERT: A 503 GLU cc_start: 0.8360 (tp30) cc_final: 0.7860 (tp30) REVERT: B 118 CYS cc_start: 0.9476 (t) cc_final: 0.9001 (t) REVERT: B 203 GLN cc_start: 0.7060 (tm-30) cc_final: 0.6677 (tm-30) REVERT: B 204 PHE cc_start: 0.8086 (m-80) cc_final: 0.7876 (m-80) REVERT: B 314 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8344 (tm-30) REVERT: B 341 ASP cc_start: 0.8640 (t0) cc_final: 0.8248 (t70) REVERT: C 113 MET cc_start: 0.8914 (ptp) cc_final: 0.8588 (mpp) REVERT: C 116 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: C 118 CYS cc_start: 0.9663 (t) cc_final: 0.9346 (t) REVERT: C 335 MET cc_start: 0.8228 (tpp) cc_final: 0.7969 (tpp) REVERT: C 503 GLU cc_start: 0.8398 (tp30) cc_final: 0.8036 (tp30) REVERT: D 113 MET cc_start: 0.9195 (tpp) cc_final: 0.8752 (tpp) REVERT: D 116 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: D 180 GLN cc_start: 0.7453 (mp10) cc_final: 0.6713 (mp10) REVERT: D 203 GLN cc_start: 0.7293 (tm-30) cc_final: 0.7070 (tm-30) REVERT: D 314 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8348 (tm-30) REVERT: D 341 ASP cc_start: 0.8583 (t0) cc_final: 0.8338 (t70) REVERT: D 503 GLU cc_start: 0.8354 (tp30) cc_final: 0.7847 (tp30) REVERT: E 341 ASP cc_start: 0.8640 (t0) cc_final: 0.8267 (t70) REVERT: F 113 MET cc_start: 0.8958 (ptp) cc_final: 0.8611 (mpp) REVERT: F 116 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8146 (m-80) REVERT: F 314 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8138 (tm-30) REVERT: F 335 MET cc_start: 0.8222 (tpp) cc_final: 0.7969 (tpp) REVERT: F 386 ASP cc_start: 0.7928 (m-30) cc_final: 0.7625 (m-30) REVERT: F 503 GLU cc_start: 0.8388 (tp30) cc_final: 0.8017 (tp30) outliers start: 45 outliers final: 35 residues processed: 236 average time/residue: 0.2301 time to fit residues: 91.8774 Evaluate side-chains 235 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE 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 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 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 385 THR Chi-restraints excluded: chain C residue 116 PHE 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 347 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 218 PHE 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 132 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 385 THR 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 288 ILE Chi-restraints excluded: chain F residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 64 optimal weight: 0.6980 chunk 244 optimal weight: 0.0050 chunk 210 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.099279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.075445 restraints weight = 41062.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.079003 restraints weight = 21031.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.081611 restraints weight = 13510.912| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19650 Z= 0.105 Angle : 0.600 10.208 26640 Z= 0.289 Chirality : 0.043 0.158 3066 Planarity : 0.003 0.040 3402 Dihedral : 10.453 126.784 2892 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.41 % Favored : 92.30 % Rotamer: Outliers : 2.03 % Allowed : 16.62 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.18), residues: 2430 helix: 1.85 (0.17), residues: 1014 sheet: 1.48 (0.27), residues: 420 loop : -2.01 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 482 HIS 0.001 0.000 HIS D 356 PHE 0.013 0.001 PHE E 204 TYR 0.010 0.001 TYR E 319 ARG 0.001 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.02434 ( 901) hydrogen bonds : angle 4.06882 ( 2541) metal coordination : bond 0.00220 ( 24) metal coordination : angle 2.68276 ( 36) covalent geometry : bond 0.00241 (19626) covalent geometry : angle 0.59242 (26604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5482.46 seconds wall clock time: 96 minutes 12.02 seconds (5772.02 seconds total)