Starting phenix.real_space_refine on Sun Aug 24 06:15:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x8m_38149/08_2025/8x8m_38149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x8m_38149/08_2025/8x8m_38149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x8m_38149/08_2025/8x8m_38149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x8m_38149/08_2025/8x8m_38149.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x8m_38149/08_2025/8x8m_38149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x8m_38149/08_2025/8x8m_38149.map" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 11199 2.51 5 N 3012 2.21 5 O 3408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17682 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5894 Classifications: {'peptide': 775} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 741} Chain: "B" Number of atoms: 5894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5894 Classifications: {'peptide': 775} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 741} Chain: "C" Number of atoms: 5894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5894 Classifications: {'peptide': 775} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 741} Time building chain proxies: 3.63, per 1000 atoms: 0.21 Number of scatterers: 17682 At special positions: 0 Unit cell: (101.269, 133.607, 149.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 3408 8.00 N 3012 7.00 C 11199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 651.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4152 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 16 sheets defined 10.4% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 245 through 252 Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.613A pdb=" N ALA A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 289 through 304 Processing helix chain 'A' and resid 360 through 368 Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.698A pdb=" N VAL A 383 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 removed outlier: 3.811A pdb=" N GLY A 632 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 658 Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 892 through 902 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.501A pdb=" N GLY B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 259 removed outlier: 4.570A pdb=" N ALA B 256 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU B 257 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 259 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.580A pdb=" N ALA B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 289 through 304 Processing helix chain 'B' and resid 360 through 368 Processing helix chain 'B' and resid 379 through 383 removed outlier: 3.599A pdb=" N VAL B 383 " --> pdb=" O GLU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 658 removed outlier: 3.649A pdb=" N THR B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.785A pdb=" N PHE B 763 " --> pdb=" O THR B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 871 Processing helix chain 'B' and resid 892 through 901 Processing helix chain 'C' and resid 245 through 252 removed outlier: 3.520A pdb=" N ALA C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 252 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 289 through 304 Processing helix chain 'C' and resid 360 through 368 Processing helix chain 'C' and resid 379 through 383 removed outlier: 3.614A pdb=" N VAL C 383 " --> pdb=" O GLU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 658 removed outlier: 3.664A pdb=" N THR C 656 " --> pdb=" O ALA C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 871 Processing helix chain 'C' and resid 892 through 901 Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 275 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 273 through 275 current: chain 'A' and resid 494 through 511 removed outlier: 7.051A pdb=" N ILE A 495 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N PHE A 532 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N SER A 497 " --> pdb=" O PHE A 532 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N ASP A 534 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASN A 499 " --> pdb=" O ASP A 534 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N ALA A 536 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS A 501 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA A 538 " --> pdb=" O CYS A 501 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA A 503 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 10.651A pdb=" N PHE A 540 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N LYS A 505 " --> pdb=" O PHE A 540 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ASN A 542 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR A 507 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ASN A 544 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE A 509 " --> pdb=" O ASN A 544 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 553 through 556 current: chain 'A' and resid 592 through 609 removed outlier: 6.365A pdb=" N ILE A 593 " --> pdb=" O ASN A 626 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 623 through 626 current: chain 'A' and resid 767 through 772 removed outlier: 3.609A pdb=" N SER A 905 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 356 removed outlier: 6.718A pdb=" N GLU A 396 " --> pdb=" O THR A 435 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE A 437 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE A 394 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA A 439 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE A 392 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRP A 411 " --> pdb=" O GLY A 397 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP A 399 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS A 409 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N LEU A 401 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 11.147A pdb=" N THR A 407 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 738 through 741 removed outlier: 6.165A pdb=" N LEU A 779 " --> pdb=" O TYR A 814 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N PHE A 811 " --> pdb=" O GLN A 830 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N VAL A 832 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU A 813 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU A 828 " --> pdb=" O ASN A 856 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 854 through 856 current: chain 'A' and resid 908 through 910 Processing sheet with id=AA4, first strand: chain 'A' and resid 920 through 923 removed outlier: 6.459A pdb=" N VAL A1013 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER A 923 " --> pdb=" O THR A1011 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR A1011 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ILE A1010 " --> pdb=" O SER A 948 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER A 948 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A1012 " --> pdb=" O ASN A 946 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 931 through 938 removed outlier: 4.058A pdb=" N GLY A1002 " --> pdb=" O ALA A 933 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE A 935 " --> pdb=" O ASN A1000 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN A1000 " --> pdb=" O PHE A 935 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL A 937 " --> pdb=" O LYS A 998 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS A 998 " --> pdb=" O VAL A 937 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 991 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL A1004 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLN A 989 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N CYS A1006 " --> pdb=" O ASN A 987 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN A 987 " --> pdb=" O CYS A1006 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 984 " --> pdb=" O GLY A 979 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 284 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 284 through 288 current: chain 'B' and resid 494 through 506 removed outlier: 7.093A pdb=" N THR B 529 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE B 535 " --> pdb=" O TYR B 500 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA B 502 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP B 537 " --> pdb=" O ALA B 502 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 553 through 556 current: chain 'B' and resid 570 through 584 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 570 through 584 current: chain 'B' and resid 592 through 609 removed outlier: 6.352A pdb=" N ILE B 593 " --> pdb=" O ASN B 626 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 623 through 626 current: chain 'B' and resid 767 through 772 Processing sheet with id=AA7, first strand: chain 'B' and resid 353 through 356 removed outlier: 8.451A pdb=" N ILE B 434 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA B 398 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B 436 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TRP B 411 " --> pdb=" O GLY B 397 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B 399 " --> pdb=" O LYS B 409 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS B 409 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LEU B 401 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 11.176A pdb=" N THR B 407 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 510 through 511 Processing sheet with id=AA9, first strand: chain 'B' and resid 738 through 741 removed outlier: 5.985A pdb=" N LEU B 779 " --> pdb=" O TYR B 814 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU B 813 " --> pdb=" O GLN B 829 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE B 831 " --> pdb=" O LEU B 813 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR B 815 " --> pdb=" O ILE B 831 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU B 828 " --> pdb=" O ASN B 856 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 854 through 856 current: chain 'B' and resid 908 through 910 Processing sheet with id=AB1, first strand: chain 'B' and resid 920 through 923 removed outlier: 6.537A pdb=" N VAL B1013 " --> pdb=" O LEU B 921 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER B 923 " --> pdb=" O THR B1011 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR B1011 " --> pdb=" O SER B 923 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE B1010 " --> pdb=" O SER B 948 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER B 948 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B1012 " --> pdb=" O ASN B 946 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 931 through 938 removed outlier: 7.482A pdb=" N ALA B 931 " --> pdb=" O ARG B1005 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG B1005 " --> pdb=" O ALA B 931 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA B 933 " --> pdb=" O LEU B1003 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU B1003 " --> pdb=" O ALA B 933 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 935 " --> pdb=" O VAL B1001 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG B 995 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL B1001 " --> pdb=" O ASN B 993 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN B 993 " --> pdb=" O VAL B1001 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU B1003 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS B 984 " --> pdb=" O GLY B 979 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 273 through 274 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 274 current: chain 'C' and resid 494 through 511 removed outlier: 7.036A pdb=" N VAL C 494 " --> pdb=" O THR C 529 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ASN C 531 " --> pdb=" O VAL C 494 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE C 496 " --> pdb=" O ASN C 531 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ASN C 533 " --> pdb=" O ILE C 496 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU C 498 " --> pdb=" O ASN C 533 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 528 through 533 current: chain 'C' and resid 593 through 609 removed outlier: 6.338A pdb=" N ILE C 593 " --> pdb=" O ASN C 626 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 623 through 626 current: chain 'C' and resid 767 through 772 removed outlier: 3.584A pdb=" N THR C 847 " --> pdb=" O GLY C 819 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C 875 " --> pdb=" O GLN C 903 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 353 through 356 removed outlier: 8.470A pdb=" N ILE C 434 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA C 398 " --> pdb=" O ILE C 434 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS C 436 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP C 411 " --> pdb=" O GLY C 397 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP C 399 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS C 409 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LEU C 401 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 11.294A pdb=" N THR C 407 " --> pdb=" O LEU C 401 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 738 through 741 removed outlier: 6.144A pdb=" N LEU C 779 " --> pdb=" O TYR C 814 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU C 813 " --> pdb=" O GLN C 829 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE C 831 " --> pdb=" O LEU C 813 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR C 815 " --> pdb=" O ILE C 831 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU C 828 " --> pdb=" O ASN C 856 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 854 through 856 current: chain 'C' and resid 908 through 910 Processing sheet with id=AB6, first strand: chain 'C' and resid 920 through 923 removed outlier: 6.486A pdb=" N VAL C1013 " --> pdb=" O LEU C 921 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER C 923 " --> pdb=" O THR C1011 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR C1011 " --> pdb=" O SER C 923 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE C1010 " --> pdb=" O SER C 948 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER C 948 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY C1012 " --> pdb=" O ASN C 946 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 931 through 938 removed outlier: 7.710A pdb=" N ALA C 931 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ARG C1005 " --> pdb=" O ALA C 931 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA C 933 " --> pdb=" O LEU C1003 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU C1003 " --> pdb=" O ALA C 933 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY C 991 " --> pdb=" O GLY C1002 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL C1004 " --> pdb=" O GLN C 989 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN C 989 " --> pdb=" O VAL C1004 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS C1006 " --> pdb=" O ASN C 987 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN C 987 " --> pdb=" O CYS C1006 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5834 1.34 - 1.46: 3780 1.46 - 1.58: 8380 1.58 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 18090 Sorted by residual: bond pdb=" C SER C 809 " pdb=" N PRO C 810 " ideal model delta sigma weight residual 1.332 1.355 -0.024 1.30e-02 5.92e+03 3.27e+00 bond pdb=" CA GLY A 579 " pdb=" C GLY A 579 " ideal model delta sigma weight residual 1.514 1.530 -0.016 1.41e-02 5.03e+03 1.28e+00 bond pdb=" CA GLY C 579 " pdb=" C GLY C 579 " ideal model delta sigma weight residual 1.514 1.530 -0.016 1.41e-02 5.03e+03 1.22e+00 bond pdb=" CB ASP C 833 " pdb=" CG ASP C 833 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.21e+00 bond pdb=" N THR C 760 " pdb=" CA THR C 760 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.17e+00 ... (remaining 18085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 24413 1.96 - 3.93: 208 3.93 - 5.89: 14 5.89 - 7.86: 0 7.86 - 9.82: 1 Bond angle restraints: 24636 Sorted by residual: angle pdb=" C ASN C 759 " pdb=" N THR C 760 " pdb=" CA THR C 760 " ideal model delta sigma weight residual 121.54 131.36 -9.82 1.91e+00 2.74e-01 2.64e+01 angle pdb=" N VAL C 982 " pdb=" CA VAL C 982 " pdb=" C VAL C 982 " ideal model delta sigma weight residual 113.47 110.38 3.09 1.01e+00 9.80e-01 9.34e+00 angle pdb=" OG1 THR C 760 " pdb=" CB THR C 760 " pdb=" CG2 THR C 760 " ideal model delta sigma weight residual 109.30 103.50 5.80 2.00e+00 2.50e-01 8.40e+00 angle pdb=" CB GLU B 890 " pdb=" CG GLU B 890 " pdb=" CD GLU B 890 " ideal model delta sigma weight residual 112.60 117.44 -4.84 1.70e+00 3.46e-01 8.12e+00 angle pdb=" N THR C 760 " pdb=" CA THR C 760 " pdb=" CB THR C 760 " ideal model delta sigma weight residual 110.49 114.90 -4.41 1.69e+00 3.50e-01 6.80e+00 ... (remaining 24631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 9413 16.63 - 33.26: 798 33.26 - 49.89: 239 49.89 - 66.52: 40 66.52 - 83.15: 13 Dihedral angle restraints: 10503 sinusoidal: 3918 harmonic: 6585 Sorted by residual: dihedral pdb=" CA TYR B 507 " pdb=" C TYR B 507 " pdb=" N ASP B 508 " pdb=" CA ASP B 508 " ideal model delta harmonic sigma weight residual -180.00 -154.64 -25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA TYR C 507 " pdb=" C TYR C 507 " pdb=" N ASP C 508 " pdb=" CA ASP C 508 " ideal model delta harmonic sigma weight residual 180.00 155.92 24.08 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA TYR A 507 " pdb=" C TYR A 507 " pdb=" N ASP A 508 " pdb=" CA ASP A 508 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 10500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1617 0.028 - 0.057: 644 0.057 - 0.085: 213 0.085 - 0.113: 208 0.113 - 0.141: 60 Chirality restraints: 2742 Sorted by residual: chirality pdb=" CA ASP C 833 " pdb=" N ASP C 833 " pdb=" C ASP C 833 " pdb=" CB ASP C 833 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CB THR C 760 " pdb=" CA THR C 760 " pdb=" OG1 THR C 760 " pdb=" CG2 THR C 760 " both_signs ideal model delta sigma weight residual False 2.55 2.69 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE C 710 " pdb=" N ILE C 710 " pdb=" C ILE C 710 " pdb=" CB ILE C 710 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 2739 not shown) Planarity restraints: 3225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 721 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO B 722 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 722 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 722 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 721 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO C 722 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 722 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 722 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 721 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO A 722 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 722 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 722 " 0.024 5.00e-02 4.00e+02 ... (remaining 3222 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 573 2.72 - 3.27: 16421 3.27 - 3.81: 28927 3.81 - 4.36: 38047 4.36 - 4.90: 64583 Nonbonded interactions: 148551 Sorted by model distance: nonbonded pdb=" OD1 ASP C 872 " pdb=" OG SER C 996 " model vdw 2.178 3.040 nonbonded pdb=" OD1 ASP A 872 " pdb=" OG SER A 996 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR C 760 " pdb=" OD1 ASN C 792 " model vdw 2.270 3.040 nonbonded pdb=" OE1 GLN A 556 " pdb=" ND2 ASN A 575 " model vdw 2.277 3.120 nonbonded pdb=" OG1 THR A 760 " pdb=" OD1 ASN A 792 " model vdw 2.304 3.040 ... (remaining 148546 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.440 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 : 0.002 0.032 18090 Z= 0.103 Angle : 0.489 9.822 24636 Z= 0.283 Chirality : 0.045 0.141 2742 Planarity : 0.003 0.047 3225 Dihedral : 14.216 83.151 6351 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.48 % Allowed : 11.45 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.17), residues: 2319 helix: 0.10 (0.41), residues: 150 sheet: 0.32 (0.20), residues: 699 loop : -1.19 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 450 TYR 0.010 0.001 TYR B 871 PHE 0.008 0.001 PHE C 532 TRP 0.014 0.001 TRP B 411 HIS 0.004 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00198 (18090) covalent geometry : angle 0.48914 (24636) hydrogen bonds : bond 0.24388 ( 331) hydrogen bonds : angle 7.96480 ( 870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.646 Fit side-chains REVERT: A 302 ASP cc_start: 0.8185 (t0) cc_final: 0.7948 (t0) REVERT: A 954 THR cc_start: 0.8729 (m) cc_final: 0.8447 (p) REVERT: B 463 ASN cc_start: 0.8315 (t0) cc_final: 0.8099 (t0) REVERT: B 890 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7162 (mp0) REVERT: C 380 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7685 (mm-30) outliers start: 28 outliers final: 24 residues processed: 134 average time/residue: 0.5838 time to fit residues: 89.2239 Evaluate side-chains 131 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 615 HIS Chi-restraints excluded: chain C residue 714 SER Chi-restraints excluded: chain C residue 796 ASN Chi-restraints excluded: chain C residue 945 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 477 GLN B 574 HIS B 956 GLN B 985 ASN C 477 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.073212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.062093 restraints weight = 27607.404| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 1.83 r_work: 0.2575 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 18090 Z= 0.264 Angle : 0.642 6.922 24636 Z= 0.362 Chirality : 0.051 0.162 2742 Planarity : 0.005 0.046 3225 Dihedral : 6.435 59.233 2566 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.21 % Favored : 93.70 % Rotamer: Outliers : 2.58 % Allowed : 10.13 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.16), residues: 2319 helix: 0.31 (0.40), residues: 156 sheet: 0.19 (0.20), residues: 690 loop : -1.36 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 619 TYR 0.014 0.002 TYR C 821 PHE 0.020 0.002 PHE C 532 TRP 0.013 0.002 TRP C 411 HIS 0.007 0.001 HIS C 806 Details of bonding type rmsd covalent geometry : bond 0.00638 (18090) covalent geometry : angle 0.64222 (24636) hydrogen bonds : bond 0.06105 ( 331) hydrogen bonds : angle 6.09634 ( 870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 100 time to evaluate : 0.561 Fit side-chains REVERT: A 556 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8490 (mm-40) REVERT: A 620 GLU cc_start: 0.8272 (tt0) cc_final: 0.8058 (tt0) REVERT: A 871 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7323 (m-10) REVERT: B 770 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: C 262 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8775 (ttmt) REVERT: C 380 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8106 (mm-30) outliers start: 49 outliers final: 26 residues processed: 134 average time/residue: 0.6026 time to fit residues: 89.5332 Evaluate side-chains 126 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 714 SER Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 796 ASN Chi-restraints excluded: chain C residue 890 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 41 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 201 optimal weight: 0.3980 chunk 80 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN C 477 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.075203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.063973 restraints weight = 27739.681| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 1.84 r_work: 0.2613 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18090 Z= 0.143 Angle : 0.532 6.912 24636 Z= 0.300 Chirality : 0.047 0.138 2742 Planarity : 0.004 0.047 3225 Dihedral : 5.733 58.611 2542 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.74 % Favored : 95.21 % Rotamer: Outliers : 2.22 % Allowed : 10.60 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.17), residues: 2319 helix: 0.67 (0.41), residues: 156 sheet: 0.08 (0.19), residues: 738 loop : -1.28 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 628 TYR 0.011 0.001 TYR A 720 PHE 0.012 0.001 PHE C 532 TRP 0.013 0.001 TRP C 411 HIS 0.004 0.001 HIS C 806 Details of bonding type rmsd covalent geometry : bond 0.00332 (18090) covalent geometry : angle 0.53156 (24636) hydrogen bonds : bond 0.04641 ( 331) hydrogen bonds : angle 5.66433 ( 870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 0.686 Fit side-chains REVERT: A 556 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8423 (mt0) REVERT: A 620 GLU cc_start: 0.8234 (tt0) cc_final: 0.8023 (tt0) REVERT: B 770 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8069 (m-30) REVERT: B 955 SER cc_start: 0.9410 (p) cc_final: 0.9173 (t) REVERT: C 556 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.7697 (mm-40) outliers start: 42 outliers final: 23 residues processed: 137 average time/residue: 0.6001 time to fit residues: 91.3102 Evaluate side-chains 129 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 420 ARG Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 796 ASN Chi-restraints excluded: chain C residue 890 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 93 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 759 ASN B 574 HIS C 477 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.074305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.063139 restraints weight = 27630.078| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 1.84 r_work: 0.2595 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 18090 Z= 0.179 Angle : 0.564 7.890 24636 Z= 0.318 Chirality : 0.048 0.150 2742 Planarity : 0.004 0.046 3225 Dihedral : 5.769 59.073 2541 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.78 % Favored : 94.18 % Rotamer: Outliers : 2.53 % Allowed : 10.50 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.16), residues: 2319 helix: 0.74 (0.42), residues: 156 sheet: 0.19 (0.20), residues: 690 loop : -1.32 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 450 TYR 0.012 0.002 TYR A 720 PHE 0.016 0.002 PHE C 532 TRP 0.012 0.001 TRP B 411 HIS 0.004 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00424 (18090) covalent geometry : angle 0.56393 (24636) hydrogen bonds : bond 0.04870 ( 331) hydrogen bonds : angle 5.69038 ( 870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 102 time to evaluate : 0.701 Fit side-chains REVERT: A 380 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: A 556 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8487 (mm-40) REVERT: A 620 GLU cc_start: 0.8253 (tt0) cc_final: 0.8008 (tt0) REVERT: B 420 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8749 (ptp90) REVERT: B 770 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8075 (m-30) REVERT: C 556 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.7667 (mm-40) REVERT: C 1005 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8110 (ttt180) outliers start: 48 outliers final: 30 residues processed: 136 average time/residue: 0.8220 time to fit residues: 122.8023 Evaluate side-chains 136 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 420 ARG Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 796 ASN Chi-restraints excluded: chain C residue 890 GLU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1005 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 66 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 212 optimal weight: 10.0000 chunk 205 optimal weight: 0.0470 chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 0.3980 chunk 35 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN C 477 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.077530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.066205 restraints weight = 27342.371| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 1.86 r_work: 0.2653 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18090 Z= 0.082 Angle : 0.462 7.282 24636 Z= 0.259 Chirality : 0.045 0.133 2742 Planarity : 0.003 0.048 3225 Dihedral : 5.154 59.838 2541 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.11 % Allowed : 11.13 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.17), residues: 2319 helix: 0.60 (0.40), residues: 174 sheet: 0.18 (0.20), residues: 738 loop : -1.20 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 467 TYR 0.009 0.001 TYR A 720 PHE 0.011 0.001 PHE A 811 TRP 0.013 0.001 TRP C 411 HIS 0.003 0.000 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00169 (18090) covalent geometry : angle 0.46228 (24636) hydrogen bonds : bond 0.03246 ( 331) hydrogen bonds : angle 5.20733 ( 870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 0.865 Fit side-chains REVERT: A 620 GLU cc_start: 0.8138 (tt0) cc_final: 0.7919 (tt0) REVERT: B 770 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: C 313 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8513 (m) REVERT: C 556 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.7570 (mm-40) REVERT: C 772 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8299 (mtmt) REVERT: C 840 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8461 (mt-10) outliers start: 40 outliers final: 19 residues processed: 139 average time/residue: 0.7409 time to fit residues: 114.4163 Evaluate side-chains 127 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 642 LYS Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 890 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 120 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN B 574 HIS B 575 ASN C 477 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.072911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.061884 restraints weight = 27582.356| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 1.81 r_work: 0.2568 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 18090 Z= 0.270 Angle : 0.638 8.147 24636 Z= 0.359 Chirality : 0.051 0.182 2742 Planarity : 0.004 0.045 3225 Dihedral : 5.827 56.767 2536 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.95 % Favored : 94.01 % Rotamer: Outliers : 2.64 % Allowed : 10.76 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.16), residues: 2319 helix: 0.68 (0.42), residues: 156 sheet: 0.19 (0.20), residues: 690 loop : -1.35 (0.14), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 619 TYR 0.015 0.002 TYR A 750 PHE 0.021 0.002 PHE C 532 TRP 0.009 0.002 TRP C 411 HIS 0.005 0.001 HIS C 806 Details of bonding type rmsd covalent geometry : bond 0.00652 (18090) covalent geometry : angle 0.63774 (24636) hydrogen bonds : bond 0.05562 ( 331) hydrogen bonds : angle 5.84696 ( 870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 99 time to evaluate : 0.723 Fit side-chains REVERT: A 380 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: A 620 GLU cc_start: 0.8275 (tt0) cc_final: 0.8029 (tt0) REVERT: A 770 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8189 (m-30) REVERT: B 420 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8767 (ptp90) REVERT: B 770 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8118 (m-30) REVERT: B 890 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7905 (mp0) REVERT: C 244 LYS cc_start: 0.6840 (OUTLIER) cc_final: 0.5446 (mptt) REVERT: C 556 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.7684 (mm-40) REVERT: C 997 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9027 (mt) REVERT: C 1005 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8133 (ttt180) outliers start: 50 outliers final: 29 residues processed: 132 average time/residue: 0.7989 time to fit residues: 116.2524 Evaluate side-chains 131 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 796 ASN Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 997 LEU Chi-restraints excluded: chain C residue 1005 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 121 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN C 477 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.074431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.063110 restraints weight = 27612.783| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 1.88 r_work: 0.2587 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18090 Z= 0.149 Angle : 0.536 8.062 24636 Z= 0.302 Chirality : 0.047 0.152 2742 Planarity : 0.004 0.046 3225 Dihedral : 5.517 56.378 2536 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.66 % Favored : 95.30 % Rotamer: Outliers : 2.16 % Allowed : 11.34 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.16), residues: 2319 helix: 0.81 (0.42), residues: 156 sheet: 0.14 (0.20), residues: 720 loop : -1.29 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 467 TYR 0.011 0.001 TYR A 720 PHE 0.013 0.001 PHE B 532 TRP 0.012 0.001 TRP B 411 HIS 0.004 0.001 HIS C 806 Details of bonding type rmsd covalent geometry : bond 0.00348 (18090) covalent geometry : angle 0.53603 (24636) hydrogen bonds : bond 0.04380 ( 331) hydrogen bonds : angle 5.52677 ( 870) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.697 Fit side-chains REVERT: A 380 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8372 (mp0) REVERT: A 556 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8197 (mm-40) REVERT: A 620 GLU cc_start: 0.8239 (tt0) cc_final: 0.8017 (tt0) REVERT: B 770 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: B 890 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7821 (mp0) REVERT: C 556 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.7573 (mm-40) REVERT: C 840 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8497 (mt-10) REVERT: C 1005 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7995 (ttt180) outliers start: 41 outliers final: 27 residues processed: 130 average time/residue: 0.7346 time to fit residues: 105.9379 Evaluate side-chains 134 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 796 ASN Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1005 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 122 optimal weight: 1.9990 chunk 118 optimal weight: 0.0970 chunk 115 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 120 optimal weight: 0.0370 chunk 215 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 201 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN B 574 HIS C 477 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.078070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.066727 restraints weight = 27331.247| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 1.87 r_work: 0.2662 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18090 Z= 0.078 Angle : 0.452 7.859 24636 Z= 0.252 Chirality : 0.045 0.142 2742 Planarity : 0.003 0.047 3225 Dihedral : 4.894 59.418 2536 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.53 % Allowed : 11.92 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.17), residues: 2319 helix: 0.67 (0.41), residues: 174 sheet: 0.18 (0.20), residues: 738 loop : -1.17 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 450 TYR 0.009 0.001 TYR A 720 PHE 0.009 0.001 PHE A 811 TRP 0.014 0.001 TRP C 411 HIS 0.004 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00161 (18090) covalent geometry : angle 0.45218 (24636) hydrogen bonds : bond 0.03001 ( 331) hydrogen bonds : angle 5.07975 ( 870) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.734 Fit side-chains REVERT: A 620 GLU cc_start: 0.8145 (tt0) cc_final: 0.7917 (tt0) REVERT: A 770 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: B 770 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8047 (m-30) REVERT: B 811 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8050 (p90) REVERT: C 556 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.7598 (mm-40) REVERT: C 701 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8556 (ttt180) REVERT: C 772 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8333 (mtmt) REVERT: C 840 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8463 (mt-10) REVERT: C 1005 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7680 (ttt180) outliers start: 29 outliers final: 18 residues processed: 132 average time/residue: 0.7612 time to fit residues: 111.1948 Evaluate side-chains 130 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 811 PHE Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1005 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 200 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN C 477 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.072855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.061617 restraints weight = 27712.759| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 1.86 r_work: 0.2557 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 18090 Z= 0.251 Angle : 0.622 7.099 24636 Z= 0.350 Chirality : 0.051 0.185 2742 Planarity : 0.004 0.045 3225 Dihedral : 5.751 56.952 2535 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 2.11 % Allowed : 11.66 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.16), residues: 2319 helix: 0.71 (0.42), residues: 156 sheet: 0.22 (0.20), residues: 690 loop : -1.30 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 450 TYR 0.015 0.002 TYR A 750 PHE 0.020 0.002 PHE C 532 TRP 0.008 0.002 TRP B 411 HIS 0.005 0.001 HIS C 806 Details of bonding type rmsd covalent geometry : bond 0.00607 (18090) covalent geometry : angle 0.62212 (24636) hydrogen bonds : bond 0.05361 ( 331) hydrogen bonds : angle 5.75893 ( 870) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.714 Fit side-chains REVERT: A 380 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: A 556 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8212 (mm-40) REVERT: A 620 GLU cc_start: 0.8264 (tt0) cc_final: 0.8038 (tt0) REVERT: A 770 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8167 (m-30) REVERT: B 770 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: B 811 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8237 (p90) REVERT: B 890 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7882 (mp0) REVERT: C 556 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.7611 (mm-40) REVERT: C 840 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8498 (mt-10) REVERT: C 997 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8983 (mt) REVERT: C 1005 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8052 (ttt180) outliers start: 40 outliers final: 25 residues processed: 126 average time/residue: 0.7792 time to fit residues: 108.5439 Evaluate side-chains 130 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 811 PHE Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 796 ASN Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 997 LEU Chi-restraints excluded: chain C residue 1005 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 89 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 226 optimal weight: 0.0070 chunk 2 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.073657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.062420 restraints weight = 27451.220| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 1.85 r_work: 0.2574 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 18090 Z= 0.189 Angle : 0.575 9.469 24636 Z= 0.324 Chirality : 0.049 0.177 2742 Planarity : 0.004 0.046 3225 Dihedral : 5.658 55.692 2535 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.95 % Rotamer: Outliers : 2.11 % Allowed : 11.66 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.16), residues: 2319 helix: 0.73 (0.42), residues: 156 sheet: 0.12 (0.20), residues: 720 loop : -1.32 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 450 TYR 0.012 0.002 TYR A 720 PHE 0.016 0.002 PHE C 532 TRP 0.010 0.001 TRP B 411 HIS 0.004 0.001 HIS C 574 Details of bonding type rmsd covalent geometry : bond 0.00450 (18090) covalent geometry : angle 0.57548 (24636) hydrogen bonds : bond 0.04794 ( 331) hydrogen bonds : angle 5.61902 ( 870) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.744 Fit side-chains REVERT: A 380 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: A 556 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8194 (mm-40) REVERT: A 620 GLU cc_start: 0.8262 (tt0) cc_final: 0.8039 (tt0) REVERT: A 770 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: B 770 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: B 811 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8290 (p90) REVERT: B 890 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7853 (mp0) REVERT: C 556 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.7558 (mm-40) REVERT: C 840 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8497 (mt-10) REVERT: C 1005 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8015 (ttt180) outliers start: 40 outliers final: 25 residues processed: 130 average time/residue: 0.7912 time to fit residues: 113.5751 Evaluate side-chains 129 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 811 PHE Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 796 ASN Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1005 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 168 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 167 optimal weight: 0.4980 chunk 102 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN C 477 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.075287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.063994 restraints weight = 27338.774| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 1.86 r_work: 0.2606 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18090 Z= 0.123 Angle : 0.513 9.471 24636 Z= 0.288 Chirality : 0.047 0.163 2742 Planarity : 0.004 0.046 3225 Dihedral : 5.335 57.462 2535 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.74 % Rotamer: Outliers : 1.58 % Allowed : 12.08 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.17), residues: 2319 helix: 0.87 (0.42), residues: 156 sheet: 0.11 (0.20), residues: 738 loop : -1.21 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 450 TYR 0.011 0.001 TYR A 720 PHE 0.012 0.001 PHE B 532 TRP 0.012 0.001 TRP B 411 HIS 0.003 0.001 HIS C 574 Details of bonding type rmsd covalent geometry : bond 0.00282 (18090) covalent geometry : angle 0.51260 (24636) hydrogen bonds : bond 0.03966 ( 331) hydrogen bonds : angle 5.36664 ( 870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5967.73 seconds wall clock time: 102 minutes 42.11 seconds (6162.11 seconds total)