Starting phenix.real_space_refine on Sun Jun 15 16:38:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x8m_38149/06_2025/8x8m_38149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x8m_38149/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x8m_38149/06_2025/8x8m_38149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x8m_38149/06_2025/8x8m_38149.map" model { file = "/net/cci-nas-00/data/ceres_data/8x8m_38149/06_2025/8x8m_38149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x8m_38149/06_2025/8x8m_38149.cif" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.51, per 1000 atoms: 0.65 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: 4.65 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.20 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: 6.19 Time building geometry restraints manager: 5.51 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: 0.06 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 1.590 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 44.110 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:28.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (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 TRP 0.014 0.001 TRP B 411 HIS 0.004 0.001 HIS B 574 PHE 0.008 0.001 PHE C 532 TYR 0.010 0.001 TYR B 871 ARG 0.003 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.24388 ( 331) hydrogen bonds : angle 7.96480 ( 870) covalent geometry : bond 0.00198 (18090) covalent geometry : angle 0.48914 (24636) *********************** 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 : 2.707 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: 1.5502 time to fit residues: 231.8479 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 : 2.288 ------------------------------------------------------------------------------- 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 195 optimal weight: 0.5980 chunk 175 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 C 477 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.077336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.066070 restraints weight = 27223.224| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 1.84 r_work: 0.2659 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18090 Z= 0.105 Angle : 0.489 7.235 24636 Z= 0.274 Chirality : 0.046 0.135 2742 Planarity : 0.003 0.047 3225 Dihedral : 5.843 54.473 2566 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.85 % Allowed : 10.07 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2319 helix: 0.17 (0.39), residues: 174 sheet: 0.18 (0.20), residues: 738 loop : -1.19 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 411 HIS 0.004 0.001 HIS C 806 PHE 0.010 0.001 PHE C 532 TYR 0.010 0.001 TYR A 720 ARG 0.003 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 331) hydrogen bonds : angle 5.69704 ( 870) covalent geometry : bond 0.00230 (18090) covalent geometry : angle 0.48862 (24636) *********************** 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 147 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 2.048 Fit side-chains REVERT: B 463 ASN cc_start: 0.8546 (t0) cc_final: 0.8317 (t0) REVERT: B 770 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: C 772 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8373 (mtmt) outliers start: 35 outliers final: 16 residues processed: 136 average time/residue: 1.4612 time to fit residues: 222.2767 Evaluate side-chains 125 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR 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 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 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 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 890 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 148 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 149 optimal weight: 0.1980 chunk 112 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- 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 = 0.2882 r_free = 0.2882 target = 0.073387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.062247 restraints weight = 27524.111| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 1.84 r_work: 0.2579 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9169 moved from start: 0.0941 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= 0.254 Angle : 0.632 7.869 24636 Z= 0.356 Chirality : 0.051 0.159 2742 Planarity : 0.005 0.045 3225 Dihedral : 5.922 57.576 2540 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.74 % Allowed : 10.44 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.16), residues: 2319 helix: 0.58 (0.41), residues: 156 sheet: 0.18 (0.20), residues: 690 loop : -1.34 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 411 HIS 0.006 0.001 HIS C 806 PHE 0.020 0.002 PHE C 532 TYR 0.014 0.002 TYR A 750 ARG 0.004 0.001 ARG B 619 Details of bonding type rmsd hydrogen bonds : bond 0.05766 ( 331) hydrogen bonds : angle 5.94681 ( 870) covalent geometry : bond 0.00616 (18090) covalent geometry : angle 0.63172 (24636) *********************** 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 152 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 100 time to evaluate : 1.915 Fit side-chains REVERT: A 380 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: A 556 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8304 (mm-40) REVERT: A 620 GLU cc_start: 0.8258 (tt0) cc_final: 0.8045 (tt0) REVERT: A 871 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7314 (m-10) REVERT: B 770 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: C 244 LYS cc_start: 0.6721 (OUTLIER) cc_final: 0.5353 (mptt) REVERT: C 262 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8788 (ttmt) REVERT: C 380 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8065 (mm-30) REVERT: C 556 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.7687 (mm-40) outliers start: 52 outliers final: 30 residues processed: 136 average time/residue: 1.4659 time to fit residues: 222.3158 Evaluate side-chains 133 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 1.929 ------------------------------------------------------------------------------- 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 395 MET Chi-restraints excluded: chain A residue 469 LEU 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 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 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 929 THR Chi-restraints excluded: chain B residue 955 SER Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain C residue 244 LYS 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 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 87 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 176 optimal weight: 0.0670 chunk 108 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN B 985 ASN C 477 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.075178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.064011 restraints weight = 27319.809| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 1.83 r_work: 0.2614 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18090 Z= 0.149 Angle : 0.536 7.266 24636 Z= 0.302 Chirality : 0.047 0.143 2742 Planarity : 0.004 0.046 3225 Dihedral : 5.559 58.843 2537 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.48 % Allowed : 10.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2319 helix: 0.84 (0.42), residues: 156 sheet: 0.07 (0.19), residues: 738 loop : -1.28 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 411 HIS 0.004 0.001 HIS C 806 PHE 0.013 0.001 PHE B 532 TYR 0.011 0.001 TYR A 720 ARG 0.002 0.000 ARG B 628 Details of bonding type rmsd hydrogen bonds : bond 0.04473 ( 331) hydrogen bonds : angle 5.58983 ( 870) covalent geometry : bond 0.00349 (18090) covalent geometry : angle 0.53624 (24636) *********************** 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 155 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 1.851 Fit side-chains REVERT: A 380 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8355 (mp0) REVERT: A 556 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: A 620 GLU cc_start: 0.8228 (tt0) cc_final: 0.8016 (tt0) REVERT: B 463 ASN cc_start: 0.8579 (t0) cc_final: 0.8345 (t0) REVERT: B 770 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: C 380 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8070 (mm-30) REVERT: C 556 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.7661 (mm-40) outliers start: 47 outliers final: 26 residues processed: 141 average time/residue: 1.4573 time to fit residues: 228.8094 Evaluate side-chains 135 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 1.955 ------------------------------------------------------------------------------- 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 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 469 LEU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 573 MET 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 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 380 GLU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 93 optimal weight: 0.0670 chunk 101 optimal weight: 0.0470 chunk 221 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 227 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 overall best weight: 2.6020 ------------------------------------------------------------------------------- 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 = 0.2906 r_free = 0.2906 target = 0.074823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.063669 restraints weight = 27583.509| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 1.83 r_work: 0.2606 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9148 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 18090 Z= 0.159 Angle : 0.547 8.305 24636 Z= 0.307 Chirality : 0.048 0.156 2742 Planarity : 0.004 0.046 3225 Dihedral : 5.524 59.471 2537 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.43 % Allowed : 10.86 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 2319 helix: 0.92 (0.42), residues: 156 sheet: 0.14 (0.20), residues: 720 loop : -1.30 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 411 HIS 0.004 0.001 HIS B 574 PHE 0.014 0.001 PHE C 532 TYR 0.011 0.001 TYR A 720 ARG 0.002 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 331) hydrogen bonds : angle 5.58231 ( 870) covalent geometry : bond 0.00374 (18090) covalent geometry : angle 0.54686 (24636) *********************** 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 155 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 1.962 Fit side-chains REVERT: A 380 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8355 (mp0) REVERT: A 556 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8298 (mm-40) REVERT: A 620 GLU cc_start: 0.8233 (tt0) cc_final: 0.8017 (tt0) REVERT: B 770 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: C 380 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8066 (mm-30) REVERT: C 556 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.7653 (mm-40) REVERT: C 1005 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8107 (ttt180) outliers start: 46 outliers final: 29 residues processed: 141 average time/residue: 1.4649 time to fit residues: 229.8248 Evaluate side-chains 134 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 1.931 ------------------------------------------------------------------------------- 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 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 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 929 THR Chi-restraints excluded: chain B residue 955 SER 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 380 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 165 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 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 = 0.072787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.061558 restraints weight = 27842.147| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 1.87 r_work: 0.2555 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 18090 Z= 0.251 Angle : 0.628 7.528 24636 Z= 0.353 Chirality : 0.051 0.174 2742 Planarity : 0.004 0.046 3225 Dihedral : 5.864 56.586 2537 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.95 % Favored : 93.96 % Rotamer: Outliers : 2.53 % Allowed : 10.76 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2319 helix: 0.73 (0.42), residues: 156 sheet: 0.16 (0.20), residues: 690 loop : -1.38 (0.14), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 411 HIS 0.005 0.001 HIS C 806 PHE 0.020 0.002 PHE C 532 TYR 0.014 0.002 TYR A 750 ARG 0.003 0.001 ARG B 619 Details of bonding type rmsd hydrogen bonds : bond 0.05437 ( 331) hydrogen bonds : angle 5.83360 ( 870) covalent geometry : bond 0.00605 (18090) covalent geometry : angle 0.62800 (24636) *********************** 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: 48 poor density : 101 time to evaluate : 1.912 Fit side-chains REVERT: A 380 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: A 556 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8292 (mm-40) REVERT: A 620 GLU cc_start: 0.8275 (tt0) cc_final: 0.8052 (tt0) REVERT: A 871 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7244 (m-10) REVERT: B 420 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8728 (ptp90) REVERT: B 770 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8129 (m-30) REVERT: B 890 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7874 (mp0) REVERT: C 244 LYS cc_start: 0.6748 (OUTLIER) cc_final: 0.5460 (mptt) REVERT: C 556 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.7607 (mm-40) REVERT: C 1005 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8045 (ttt180) outliers start: 48 outliers final: 32 residues processed: 135 average time/residue: 1.5723 time to fit residues: 236.0642 Evaluate side-chains 136 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 1.905 ------------------------------------------------------------------------------- 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 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 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 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 955 SER Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 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 469 LEU Chi-restraints excluded: chain C residue 476 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 97 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.2887 r_free = 0.2887 target = 0.074025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.062542 restraints weight = 27596.746| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 1.95 r_work: 0.2575 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.0934 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= 0.140 Angle : 0.529 7.441 24636 Z= 0.297 Chirality : 0.047 0.148 2742 Planarity : 0.004 0.047 3225 Dihedral : 5.487 56.964 2537 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.64 % Allowed : 10.65 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.17), residues: 2319 helix: 0.94 (0.42), residues: 156 sheet: 0.10 (0.20), residues: 738 loop : -1.27 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 411 HIS 0.005 0.001 HIS B 574 PHE 0.013 0.001 PHE B 532 TYR 0.011 0.001 TYR A 720 ARG 0.004 0.000 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 331) hydrogen bonds : angle 5.50019 ( 870) covalent geometry : bond 0.00325 (18090) covalent geometry : angle 0.52867 (24636) *********************** 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 153 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 103 time to evaluate : 1.915 Fit side-chains REVERT: A 380 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: A 620 GLU cc_start: 0.8240 (tt0) cc_final: 0.8020 (tt0) REVERT: A 770 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: B 420 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8729 (ptp90) REVERT: B 463 ASN cc_start: 0.8551 (t0) cc_final: 0.8304 (t0) REVERT: B 770 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: B 890 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7802 (mp0) REVERT: C 380 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8219 (mm-30) REVERT: C 556 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.7587 (mm-40) REVERT: C 840 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8510 (mt-10) REVERT: C 1005 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8137 (ttt180) outliers start: 50 outliers final: 29 residues processed: 138 average time/residue: 1.5139 time to fit residues: 232.5519 Evaluate side-chains 135 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 469 LEU Chi-restraints excluded: chain A residue 520 SER 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 954 THR 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 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 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 469 LEU Chi-restraints excluded: chain C residue 476 MET 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 890 GLU 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 64 optimal weight: 0.0770 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 230 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.3744 ------------------------------------------------------------------------------- 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 = 0.2929 r_free = 0.2929 target = 0.076398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.065106 restraints weight = 27333.035| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 1.85 r_work: 0.2630 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.0885 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= 0.101 Angle : 0.485 9.233 24636 Z= 0.272 Chirality : 0.046 0.160 2742 Planarity : 0.003 0.047 3225 Dihedral : 5.156 58.613 2537 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.90 % Allowed : 11.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.17), residues: 2319 helix: 1.09 (0.43), residues: 156 sheet: 0.16 (0.20), residues: 738 loop : -1.18 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 411 HIS 0.004 0.001 HIS B 615 PHE 0.010 0.001 PHE A 811 TYR 0.010 0.001 TYR A 720 ARG 0.003 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 331) hydrogen bonds : angle 5.25849 ( 870) covalent geometry : bond 0.00225 (18090) covalent geometry : angle 0.48512 (24636) *********************** 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 141 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 2.290 Fit side-chains REVERT: A 380 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8339 (mp0) REVERT: A 620 GLU cc_start: 0.8190 (tt0) cc_final: 0.7966 (tt0) REVERT: A 770 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: B 420 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8599 (mtt90) REVERT: B 463 ASN cc_start: 0.8492 (t0) cc_final: 0.8262 (t0) REVERT: B 770 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8005 (m-30) REVERT: C 313 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8524 (m) REVERT: C 380 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8218 (mm-30) REVERT: C 556 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.7565 (mm-40) REVERT: C 772 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8276 (mtmt) REVERT: C 840 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8461 (mt-10) REVERT: C 1005 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7679 (ttt180) outliers start: 36 outliers final: 22 residues processed: 130 average time/residue: 1.5069 time to fit residues: 217.7658 Evaluate side-chains 130 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 1.941 ------------------------------------------------------------------------------- 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 770 ASP 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 420 ARG 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 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 469 LEU Chi-restraints excluded: chain C residue 476 MET 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 890 GLU 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 137 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 179 optimal weight: 0.6980 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 = 0.2873 r_free = 0.2873 target = 0.073205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.061966 restraints weight = 27954.439| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 1.88 r_work: 0.2569 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18090 Z= 0.176 Angle : 0.560 8.781 24636 Z= 0.314 Chirality : 0.048 0.180 2742 Planarity : 0.004 0.046 3225 Dihedral : 5.511 57.712 2536 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.90 % Allowed : 11.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2319 helix: 0.99 (0.42), residues: 156 sheet: 0.17 (0.20), residues: 720 loop : -1.25 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 411 HIS 0.005 0.001 HIS B 574 PHE 0.016 0.002 PHE C 532 TYR 0.011 0.002 TYR A 720 ARG 0.004 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.04576 ( 331) hydrogen bonds : angle 5.53566 ( 870) covalent geometry : bond 0.00417 (18090) covalent geometry : angle 0.55963 (24636) *********************** 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 135 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 2.525 Fit side-chains REVERT: A 380 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: A 620 GLU cc_start: 0.8242 (tt0) cc_final: 0.8017 (tt0) REVERT: A 770 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8150 (m-30) REVERT: B 420 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8695 (ptp90) REVERT: B 770 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: B 890 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7811 (mp0) REVERT: C 380 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8180 (mm-30) REVERT: C 556 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.7573 (mm-40) REVERT: C 840 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8531 (mt-10) REVERT: C 1005 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8033 (ttt180) outliers start: 36 outliers final: 26 residues processed: 122 average time/residue: 2.0521 time to fit residues: 281.8176 Evaluate side-chains 128 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 1.903 ------------------------------------------------------------------------------- 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 770 ASP 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 420 ARG Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 573 MET 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 469 LEU Chi-restraints excluded: chain C residue 476 MET 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 890 GLU 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 202 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 175 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.2930 r_free = 0.2930 target = 0.076417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.065088 restraints weight = 27307.188| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 1.86 r_work: 0.2628 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18090 Z= 0.102 Angle : 0.490 9.018 24636 Z= 0.274 Chirality : 0.046 0.166 2742 Planarity : 0.003 0.047 3225 Dihedral : 5.165 59.195 2536 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.69 % Allowed : 11.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.17), residues: 2319 helix: 1.12 (0.43), residues: 156 sheet: 0.15 (0.20), residues: 738 loop : -1.16 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 411 HIS 0.003 0.001 HIS B 615 PHE 0.010 0.001 PHE B 532 TYR 0.010 0.001 TYR A 720 ARG 0.004 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 331) hydrogen bonds : angle 5.25683 ( 870) covalent geometry : bond 0.00227 (18090) covalent geometry : angle 0.48989 (24636) ********************** 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 135 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 2.545 Fit side-chains REVERT: A 380 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: A 620 GLU cc_start: 0.8148 (tt0) cc_final: 0.7924 (tt0) REVERT: A 770 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: A 881 MET cc_start: 0.9234 (mmp) cc_final: 0.8820 (mmt) REVERT: B 420 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8609 (mtt90) REVERT: B 770 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: B 890 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7778 (mp0) REVERT: C 313 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8569 (m) REVERT: C 380 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8196 (mm-30) REVERT: C 556 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.7590 (mm-40) REVERT: C 772 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8311 (mtmt) REVERT: C 840 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8503 (mt-10) REVERT: C 1005 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7874 (ttt180) outliers start: 32 outliers final: 22 residues processed: 124 average time/residue: 1.9893 time to fit residues: 274.3857 Evaluate side-chains 130 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 3.703 ------------------------------------------------------------------------------- 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 770 ASP 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 420 ARG Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 ASP 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 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 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 890 GLU 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 184 optimal weight: 10.0000 chunk 214 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN B 463 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 = 0.2891 r_free = 0.2891 target = 0.074224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.062933 restraints weight = 27504.625| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 1.87 r_work: 0.2585 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18090 Z= 0.171 Angle : 0.556 8.578 24636 Z= 0.313 Chirality : 0.048 0.163 2742 Planarity : 0.004 0.046 3225 Dihedral : 5.507 58.191 2536 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.79 % Allowed : 11.76 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2319 helix: 0.99 (0.42), residues: 156 sheet: 0.17 (0.20), residues: 720 loop : -1.24 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 411 HIS 0.005 0.001 HIS B 574 PHE 0.015 0.002 PHE C 532 TYR 0.011 0.001 TYR A 720 ARG 0.004 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.04540 ( 331) hydrogen bonds : angle 5.51944 ( 870) covalent geometry : bond 0.00404 (18090) covalent geometry : angle 0.55629 (24636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14756.85 seconds wall clock time: 262 minutes 30.31 seconds (15750.31 seconds total)