Starting phenix.real_space_refine on Mon Nov 18 21:41:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8m_38149/11_2024/8x8m_38149.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8m_38149/11_2024/8x8m_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8m_38149/11_2024/8x8m_38149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8m_38149/11_2024/8x8m_38149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8m_38149/11_2024/8x8m_38149.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8m_38149/11_2024/8x8m_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 10.24, per 1000 atoms: 0.58 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: 4.43 Conformation dependent library (CDL) restraints added in 2.6 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: 1.91 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: 6.98 Time building geometry restraints manager: 5.11 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: 0.00 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: 1.420 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: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 42.040 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 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:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.400 ------------------------------------------------------------------------------- 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= 0.130 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 *********************** 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 : 1.961 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: 1.3891 time to fit residues: 209.3727 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 : 1.944 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 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= 0.151 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 *********************** 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 : 2.038 Fit side-chains REVERT: B 463 ASN cc_start: 0.8347 (t0) cc_final: 0.8071 (t0) REVERT: B 770 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7194 (m-30) REVERT: C 772 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7751 (mtmt) outliers start: 35 outliers final: 16 residues processed: 136 average time/residue: 1.4491 time to fit residues: 220.8699 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 : 1.909 ------------------------------------------------------------------------------- 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 116 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 208 optimal weight: 0.0670 chunk 71 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 18090 Z= 0.350 Angle : 0.602 7.930 24636 Z= 0.339 Chirality : 0.050 0.153 2742 Planarity : 0.004 0.045 3225 Dihedral : 5.793 55.139 2540 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.64 % Allowed : 10.50 % Favored : 86.87 % 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: -1.01 (0.16), residues: 2319 helix: 0.65 (0.41), residues: 156 sheet: 0.20 (0.20), residues: 690 loop : -1.31 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 411 HIS 0.006 0.001 HIS C 806 PHE 0.019 0.002 PHE C 532 TYR 0.013 0.002 TYR B 814 ARG 0.003 0.000 ARG B 619 *********************** 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 150 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 100 time to evaluate : 1.874 Fit side-chains REVERT: A 380 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: A 556 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7798 (mm-40) REVERT: A 620 GLU cc_start: 0.7765 (tt0) cc_final: 0.7524 (tt0) REVERT: A 871 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.6851 (m-10) REVERT: B 770 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7283 (m-30) REVERT: C 244 LYS cc_start: 0.6475 (OUTLIER) cc_final: 0.5197 (mptt) REVERT: C 380 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7657 (mm-30) REVERT: C 556 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7118 (mm-40) outliers start: 50 outliers final: 29 residues processed: 134 average time/residue: 1.4798 time to fit residues: 221.5622 Evaluate side-chains 132 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 2.084 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 199 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 985 ASN C 477 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 18090 Z= 0.263 Angle : 0.553 7.121 24636 Z= 0.311 Chirality : 0.048 0.143 2742 Planarity : 0.004 0.046 3225 Dihedral : 5.635 58.933 2537 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.53 % Allowed : 10.50 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.00 (0.16), residues: 2319 helix: 0.81 (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 0.005 0.001 HIS B 574 PHE 0.015 0.001 PHE C 532 TYR 0.011 0.001 TYR A 720 ARG 0.002 0.000 ARG B 628 *********************** 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 154 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 106 time to evaluate : 1.947 Fit side-chains REVERT: A 380 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: A 556 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7830 (mm-40) REVERT: A 620 GLU cc_start: 0.7763 (tt0) cc_final: 0.7520 (tt0) REVERT: B 463 ASN cc_start: 0.8449 (t0) cc_final: 0.8154 (t0) REVERT: B 770 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7247 (m-30) REVERT: C 262 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8464 (ttmt) REVERT: C 556 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.7070 (mm-40) REVERT: C 785 THR cc_start: 0.8494 (m) cc_final: 0.8204 (p) outliers start: 48 outliers final: 27 residues processed: 140 average time/residue: 1.5436 time to fit residues: 240.2491 Evaluate side-chains 132 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 1.973 ------------------------------------------------------------------------------- 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 262 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 420 ARG Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 796 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 0.1980 chunk 126 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 154 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.6564 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 18090 Z= 0.170 Angle : 0.499 8.290 24636 Z= 0.280 Chirality : 0.046 0.143 2742 Planarity : 0.003 0.047 3225 Dihedral : 5.259 59.868 2537 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.22 % Allowed : 11.02 % 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: -0.88 (0.17), residues: 2319 helix: 1.00 (0.42), residues: 156 sheet: 0.15 (0.20), residues: 738 loop : -1.21 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 411 HIS 0.003 0.001 HIS C 806 PHE 0.013 0.001 PHE A 811 TYR 0.010 0.001 TYR A 720 ARG 0.002 0.000 ARG C 467 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 2.098 Fit side-chains revert: symmetry clash REVERT: A 380 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: A 556 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: A 620 GLU cc_start: 0.7698 (tt0) cc_final: 0.7458 (tt0) REVERT: B 463 ASN cc_start: 0.8344 (t0) cc_final: 0.8062 (t0) REVERT: B 770 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: C 380 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7693 (mm-30) REVERT: C 556 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7065 (mm-40) REVERT: C 785 THR cc_start: 0.8425 (m) cc_final: 0.8202 (p) REVERT: C 1005 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7429 (ttt180) outliers start: 42 outliers final: 24 residues processed: 138 average time/residue: 1.5590 time to fit residues: 240.3778 Evaluate side-chains 135 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 2.099 ------------------------------------------------------------------------------- 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 937 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 642 LYS 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 469 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 223 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 117 optimal weight: 0.0970 overall best weight: 1.5582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18090 Z= 0.161 Angle : 0.490 7.457 24636 Z= 0.275 Chirality : 0.046 0.144 2742 Planarity : 0.003 0.046 3225 Dihedral : 5.152 59.783 2537 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.16 % Allowed : 11.18 % Favored : 86.66 % 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: 1.13 (0.43), residues: 156 sheet: 0.17 (0.20), residues: 738 loop : -1.17 (0.15), residues: 1425 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 0.012 0.001 PHE A 811 TYR 0.010 0.001 TYR A 720 ARG 0.003 0.000 ARG B 450 *********************** 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 150 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 1.971 Fit side-chains REVERT: A 380 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: A 556 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7781 (mt0) REVERT: A 620 GLU cc_start: 0.7677 (tt0) cc_final: 0.7434 (tt0) REVERT: B 463 ASN cc_start: 0.8354 (t0) cc_final: 0.8069 (t0) REVERT: B 770 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7137 (m-30) REVERT: B 890 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7004 (mp0) REVERT: C 262 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8467 (ttmt) REVERT: C 380 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7688 (mm-30) REVERT: C 556 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7068 (mm-40) REVERT: C 701 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8308 (ttt180) REVERT: C 1005 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7446 (ttt180) outliers start: 41 outliers final: 25 residues processed: 136 average time/residue: 1.4696 time to fit residues: 223.3215 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 : 2.044 ------------------------------------------------------------------------------- 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 937 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 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 961 THR Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 469 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 18090 Z= 0.366 Angle : 0.607 8.818 24636 Z= 0.341 Chirality : 0.050 0.163 2742 Planarity : 0.004 0.045 3225 Dihedral : 5.712 56.525 2536 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.43 % Allowed : 10.81 % 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: -0.98 (0.17), residues: 2319 helix: 0.84 (0.42), residues: 156 sheet: 0.22 (0.20), residues: 690 loop : -1.31 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 411 HIS 0.005 0.001 HIS B 574 PHE 0.019 0.002 PHE C 532 TYR 0.014 0.002 TYR A 750 ARG 0.004 0.000 ARG B 450 *********************** 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 147 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 1.690 Fit side-chains revert: symmetry clash REVERT: A 380 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: A 556 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7843 (mm-40) REVERT: A 620 GLU cc_start: 0.7772 (tt0) cc_final: 0.7522 (tt0) REVERT: B 420 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8478 (ptp90) REVERT: B 770 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7282 (m-30) REVERT: B 890 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7058 (mp0) REVERT: C 244 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.5216 (mptt) REVERT: C 380 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7563 (mm-30) REVERT: C 556 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.7091 (mm-40) REVERT: C 1005 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7632 (ttt180) outliers start: 46 outliers final: 29 residues processed: 131 average time/residue: 1.5834 time to fit residues: 230.4593 Evaluate side-chains 134 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 961 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 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 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 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 137 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 67 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 575 ASN C 477 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 18090 Z= 0.167 Angle : 0.500 8.730 24636 Z= 0.280 Chirality : 0.046 0.146 2742 Planarity : 0.003 0.046 3225 Dihedral : 5.277 57.508 2536 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.95 % Allowed : 11.23 % 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: -0.87 (0.17), residues: 2319 helix: 1.03 (0.42), residues: 156 sheet: 0.15 (0.20), residues: 738 loop : -1.20 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 411 HIS 0.003 0.001 HIS C 806 PHE 0.011 0.001 PHE B 532 TYR 0.010 0.001 TYR A 720 ARG 0.003 0.000 ARG B 450 *********************** 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 142 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 2.106 Fit side-chains revert: symmetry clash REVERT: A 380 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: A 620 GLU cc_start: 0.7709 (tt0) cc_final: 0.7464 (tt0) REVERT: A 770 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7266 (m-30) REVERT: B 463 ASN cc_start: 0.8315 (t0) cc_final: 0.8052 (t0) REVERT: B 770 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7235 (m-30) REVERT: C 380 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7613 (mm-30) REVERT: C 556 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.7055 (mm-40) REVERT: C 840 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7956 (mt-10) REVERT: C 1005 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7420 (ttt180) outliers start: 37 outliers final: 26 residues processed: 130 average time/residue: 1.5353 time to fit residues: 222.7474 Evaluate side-chains 134 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 2.070 ------------------------------------------------------------------------------- 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 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 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 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 213 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 206 optimal weight: 0.2980 chunk 136 optimal weight: 10.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 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 0.028 18090 Z= 0.285 Angle : 0.564 8.145 24636 Z= 0.317 Chirality : 0.048 0.184 2742 Planarity : 0.004 0.046 3225 Dihedral : 5.547 56.910 2536 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.00 % Allowed : 11.60 % Favored : 86.39 % 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: -0.94 (0.17), residues: 2319 helix: 0.93 (0.42), residues: 156 sheet: 0.17 (0.20), residues: 720 loop : -1.27 (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 B 580 ARG 0.004 0.000 ARG B 450 *********************** 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 139 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 2.115 Fit side-chains REVERT: A 380 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: A 620 GLU cc_start: 0.7766 (tt0) cc_final: 0.7517 (tt0) REVERT: A 770 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7234 (m-30) REVERT: B 770 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: B 890 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7106 (mp0) REVERT: C 380 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7528 (mm-30) REVERT: C 556 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.7076 (mm-40) REVERT: C 840 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8016 (mt-10) REVERT: C 1005 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7635 (ttt180) outliers start: 38 outliers final: 29 residues processed: 127 average time/residue: 1.5547 time to fit residues: 219.3666 Evaluate side-chains 133 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 2.179 ------------------------------------------------------------------------------- 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 689 GLU Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain 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 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 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 219 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 230 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 141 optimal weight: 0.3980 chunk 112 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 18090 Z= 0.320 Angle : 0.589 8.071 24636 Z= 0.331 Chirality : 0.049 0.192 2742 Planarity : 0.004 0.046 3225 Dihedral : 5.680 55.673 2536 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % 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: -1.00 (0.17), residues: 2319 helix: 0.85 (0.42), residues: 156 sheet: 0.12 (0.20), residues: 720 loop : -1.31 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 411 HIS 0.004 0.001 HIS C 806 PHE 0.018 0.002 PHE C 532 TYR 0.012 0.002 TYR B 580 ARG 0.004 0.000 ARG B 450 ********************** 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 137 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 2.123 Fit side-chains REVERT: A 380 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: A 620 GLU cc_start: 0.7781 (tt0) cc_final: 0.7532 (tt0) REVERT: A 770 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7284 (m-30) REVERT: B 770 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7258 (m-30) REVERT: B 890 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7135 (mp0) REVERT: C 380 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7492 (mm-30) REVERT: C 556 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.7059 (mm-40) REVERT: C 840 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7981 (mt-10) REVERT: C 1005 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7610 (ttt180) outliers start: 36 outliers final: 30 residues processed: 126 average time/residue: 1.7004 time to fit residues: 239.2641 Evaluate side-chains 133 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 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 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 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 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 195 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 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 = 0.076062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.064917 restraints weight = 27358.743| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 1.83 r_work: 0.2632 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18090 Z= 0.179 Angle : 0.506 8.191 24636 Z= 0.284 Chirality : 0.046 0.166 2742 Planarity : 0.003 0.046 3225 Dihedral : 5.303 57.041 2536 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.79 % Allowed : 11.66 % 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: -0.88 (0.17), residues: 2319 helix: 1.02 (0.42), residues: 156 sheet: 0.13 (0.20), residues: 738 loop : -1.20 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 411 HIS 0.006 0.001 HIS B 574 PHE 0.012 0.001 PHE B 532 TYR 0.011 0.001 TYR A 720 ARG 0.004 0.000 ARG B 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5194.61 seconds wall clock time: 95 minutes 47.74 seconds (5747.74 seconds total)