Starting phenix.real_space_refine on Sun Jun 15 16:38:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x8o_38151/06_2025/8x8o_38151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x8o_38151/06_2025/8x8o_38151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x8o_38151/06_2025/8x8o_38151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x8o_38151/06_2025/8x8o_38151.map" model { file = "/net/cci-nas-00/data/ceres_data/8x8o_38151/06_2025/8x8o_38151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x8o_38151/06_2025/8x8o_38151.cif" } resolution = 2.5 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 10 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: 11.17, per 1000 atoms: 0.63 Number of scatterers: 17682 At special positions: 0 Unit cell: (104.673, 131.054, 154.031, 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: 4.51 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: 32 helices and 17 sheets defined 10.5% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 245 through 252 Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.738A 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: 3.756A pdb=" N VAL A 383 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 removed outlier: 3.825A 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 Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.510A pdb=" N VAL B 259 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.738A pdb=" N ALA B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 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: 3.782A pdb=" N VAL B 383 " --> pdb=" O GLU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 658 removed outlier: 3.579A pdb=" N GLU B 654 " --> pdb=" O ALA B 650 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.894A 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 251 removed outlier: 3.553A pdb=" N ALA C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 266 through 271 removed outlier: 3.730A pdb=" N ALA C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 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: 3.638A pdb=" N VAL C 383 " --> pdb=" O GLU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 658 removed outlier: 3.696A pdb=" N THR C 656 " --> pdb=" O ALA C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 763 removed outlier: 3.878A pdb=" N PHE C 763 " --> pdb=" O THR C 760 " (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 507 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 494 through 507 current: chain 'A' and resid 567 through 584 removed outlier: 8.542A pdb=" N ASN A 567 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N THR A 590 " --> pdb=" O ASN A 567 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N ASN A 569 " --> pdb=" O THR A 590 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY A 592 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 596 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASN A 575 " --> pdb=" O SER A 596 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N MET A 598 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR A 577 " --> pdb=" O MET A 598 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP A 600 " --> pdb=" O TYR A 577 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY A 579 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N TYR A 602 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 581 " --> pdb=" O TYR A 602 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLU A 604 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 583 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL A 606 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ILE A 624 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP A 591 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN A 626 " --> pdb=" O TRP A 591 " (cutoff:3.500A) removed outlier: 6.296A 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: 3.514A 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: 6.613A pdb=" N GLU A 396 " --> pdb=" O THR A 435 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE A 437 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 394 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA A 439 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A 392 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TRP A 411 " --> pdb=" O GLY A 397 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP A 399 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS A 409 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU A 401 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 11.240A 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: 6.200A pdb=" N LEU A 779 " --> pdb=" O TYR A 814 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N PHE A 811 " --> pdb=" O GLN A 830 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL A 832 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU A 813 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 6.217A 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 926 removed outlier: 6.465A pdb=" N VAL A1013 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER A 923 " --> pdb=" O THR A1011 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR A1011 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ALA A 925 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N THR A1009 " --> pdb=" O ALA A 925 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE A1010 " --> pdb=" O SER A 948 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER A 948 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 3.851A 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: 7.587A pdb=" N ALA A 931 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ARG A1005 " --> pdb=" O ALA A 931 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA A 933 " --> pdb=" O LEU A1003 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU A1003 " --> pdb=" O ALA A 933 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 935 " --> pdb=" O VAL A1001 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY A 991 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL A1004 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLN A 989 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS A1006 " --> pdb=" O ASN A 987 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN A 987 " --> pdb=" O CYS A1006 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 984 " --> pdb=" O GLY A 979 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 274 through 275 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 274 through 275 current: chain 'B' and resid 494 through 506 removed outlier: 7.052A pdb=" N THR B 529 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 535 " --> pdb=" O TYR B 500 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 502 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASP B 537 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 504 " --> pdb=" O ASP B 537 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLY B 554 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 530 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLN B 556 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE B 532 " --> pdb=" O GLN B 556 " (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 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: 8.323A pdb=" N ILE B 434 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA B 398 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS B 436 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP B 411 " --> pdb=" O GLY B 397 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP B 399 " --> pdb=" O LYS B 409 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS B 409 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N LEU B 401 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 11.285A 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: 6.148A pdb=" N LEU B 779 " --> pdb=" O TYR B 814 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU B 813 " --> pdb=" O GLN B 829 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE B 831 " --> pdb=" O LEU B 813 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR B 815 " --> pdb=" O ILE B 831 " (cutoff:3.500A) removed outlier: 6.211A 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 926 removed outlier: 6.569A pdb=" N VAL B1013 " --> pdb=" O LEU B 921 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER B 923 " --> pdb=" O THR B1011 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N THR B1011 " --> pdb=" O SER B 923 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ALA B 925 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR B1009 " --> pdb=" O ALA B 925 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE B1010 " --> pdb=" O SER B 948 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N SER B 948 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 3.812A 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: 7.558A pdb=" N ALA B 931 " --> pdb=" O ARG B1005 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG B1005 " --> pdb=" O ALA B 931 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA B 933 " --> pdb=" O LEU B1003 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B1003 " --> pdb=" O ALA B 933 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG B 995 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N VAL B1001 " --> pdb=" O ASN B 993 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN B 993 " --> pdb=" O VAL B1001 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU B1003 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 3.823A 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 507 removed outlier: 7.048A pdb=" N VAL C 494 " --> pdb=" O THR C 529 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ASN C 531 " --> pdb=" O VAL C 494 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE C 496 " --> pdb=" O ASN C 531 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ASN C 533 " --> pdb=" O ILE C 496 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C 498 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 535 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N TYR C 500 " --> pdb=" O ILE C 535 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N ASP C 537 " --> pdb=" O TYR C 500 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA C 502 " --> pdb=" O ASP C 537 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N VAL C 539 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE C 504 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N GLU C 541 " --> pdb=" O PHE C 504 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA C 506 " --> pdb=" O GLU C 541 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 553 through 556 current: chain 'C' and resid 570 through 584 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 570 through 584 current: chain 'C' and resid 592 through 609 removed outlier: 6.378A 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: 6.701A pdb=" N ASN C 767 " --> pdb=" O ASP C 794 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASN C 796 " --> pdb=" O ASN C 767 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 769 " --> pdb=" O ASN C 796 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL C 798 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 771 " --> pdb=" O VAL C 798 " (cutoff:3.500A) removed outlier: 7.083A 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: 8.330A pdb=" N ILE C 434 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA C 398 " --> pdb=" O ILE C 434 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 436 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TRP C 411 " --> pdb=" O GLY C 397 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP C 399 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS C 409 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LEU C 401 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 11.147A pdb=" N THR C 407 " --> pdb=" O LEU C 401 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 510 through 511 Processing sheet with id=AB6, first strand: chain 'C' and resid 738 through 741 removed outlier: 6.172A pdb=" N LEU C 779 " --> pdb=" O TYR C 814 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE C 811 " --> pdb=" O GLN C 829 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE C 831 " --> pdb=" O PHE C 811 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU C 813 " --> pdb=" O ILE C 831 " (cutoff:3.500A) removed outlier: 6.320A 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=AB7, first strand: chain 'C' and resid 920 through 923 removed outlier: 6.533A pdb=" N VAL C1013 " --> pdb=" O LEU C 921 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N SER C 923 " --> pdb=" O THR C1011 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR C1011 " --> pdb=" O SER C 923 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE C1010 " --> pdb=" O SER C 948 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER C 948 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY C1012 " --> pdb=" O ASN C 946 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 931 through 938 removed outlier: 7.709A pdb=" N ALA C 931 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ARG C1005 " --> pdb=" O ALA C 931 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA C 933 " --> pdb=" O LEU C1003 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU C1003 " --> pdb=" O ALA C 933 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY C 991 " --> pdb=" O GLY C1002 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL C1004 " --> pdb=" O GLN C 989 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLN C 989 " --> pdb=" O VAL C1004 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N CYS C1006 " --> pdb=" O ASN C 987 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C 987 " --> pdb=" O CYS C1006 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS C 984 " --> pdb=" O GLY C 979 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 876 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: 6.88 Time building geometry restraints manager: 5.31 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: 5781 1.34 - 1.45: 2990 1.45 - 1.57: 9223 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 18090 Sorted by residual: bond pdb=" C GLY B 579 " pdb=" O GLY B 579 " ideal model delta sigma weight residual 1.235 1.216 0.019 1.35e-02 5.49e+03 1.92e+00 bond pdb=" C LEU B 246 " pdb=" N GLY B 247 " ideal model delta sigma weight residual 1.331 1.314 0.017 1.46e-02 4.69e+03 1.33e+00 bond pdb=" C MET B 578 " pdb=" N GLY B 579 " ideal model delta sigma weight residual 1.331 1.314 0.016 1.46e-02 4.69e+03 1.22e+00 bond pdb=" CA GLY B 579 " pdb=" C GLY B 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 ASN B 816 " pdb=" CG ASN B 816 " ideal model delta sigma weight residual 1.516 1.492 0.024 2.50e-02 1.60e+03 8.95e-01 ... (remaining 18085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 23450 1.17 - 2.34: 983 2.34 - 3.51: 178 3.51 - 4.68: 16 4.68 - 5.85: 9 Bond angle restraints: 24636 Sorted by residual: angle pdb=" C ASN A 759 " pdb=" N THR A 760 " pdb=" CA THR A 760 " ideal model delta sigma weight residual 121.54 127.39 -5.85 1.91e+00 2.74e-01 9.38e+00 angle pdb=" CA LYS C 244 " pdb=" CB LYS C 244 " pdb=" CG LYS C 244 " ideal model delta sigma weight residual 114.10 119.71 -5.61 2.00e+00 2.50e-01 7.88e+00 angle pdb=" OG1 THR A 760 " pdb=" CB THR A 760 " pdb=" CG2 THR A 760 " ideal model delta sigma weight residual 109.30 104.17 5.13 2.00e+00 2.50e-01 6.58e+00 angle pdb=" N GLY C 617 " pdb=" CA GLY C 617 " pdb=" C GLY C 617 " ideal model delta sigma weight residual 113.18 107.46 5.72 2.37e+00 1.78e-01 5.82e+00 angle pdb=" N SER A 809 " pdb=" CA SER A 809 " pdb=" C SER A 809 " ideal model delta sigma weight residual 109.81 115.07 -5.26 2.21e+00 2.05e-01 5.66e+00 ... (remaining 24631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 9398 17.11 - 34.23: 821 34.23 - 51.34: 215 51.34 - 68.45: 51 68.45 - 85.57: 18 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 -151.46 -28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA GLY B 686 " pdb=" C GLY B 686 " pdb=" N PHE B 687 " pdb=" CA PHE B 687 " ideal model delta harmonic sigma weight residual 180.00 154.10 25.90 0 5.00e+00 4.00e-02 2.68e+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 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 10500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1575 0.033 - 0.066: 747 0.066 - 0.100: 227 0.100 - 0.133: 178 0.133 - 0.166: 15 Chirality restraints: 2742 Sorted by residual: chirality pdb=" CA ILE A 710 " pdb=" N ILE A 710 " pdb=" C ILE A 710 " pdb=" CB ILE A 710 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.88e-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 2.59 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ASP B 833 " pdb=" N ASP B 833 " pdb=" C ASP B 833 " pdb=" CB ASP B 833 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 2739 not shown) Planarity restraints: 3225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 721 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO C 722 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 722 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 722 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 759 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C ASN A 759 " 0.030 2.00e-02 2.50e+03 pdb=" O ASN A 759 " -0.011 2.00e-02 2.50e+03 pdb=" N THR A 760 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 721 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO B 722 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 722 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 722 " 0.023 5.00e-02 4.00e+02 ... (remaining 3222 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1175 2.74 - 3.28: 16154 3.28 - 3.82: 29192 3.82 - 4.36: 37293 4.36 - 4.90: 64159 Nonbonded interactions: 147973 Sorted by model distance: nonbonded pdb=" NH1 ARG A 704 " pdb=" O PHE A 737 " model vdw 2.200 3.120 nonbonded pdb=" NH1 ARG B 704 " pdb=" O PHE B 737 " model vdw 2.227 3.120 nonbonded pdb=" OD1 ASP A 872 " pdb=" OG SER A 996 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASP C 872 " pdb=" OG SER C 996 " model vdw 2.264 3.040 nonbonded pdb=" O ASN A 759 " pdb=" ND2 ASN A 759 " model vdw 2.294 3.120 ... (remaining 147968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 45.430 Find NCS groups from input model: 0.920 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:17.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 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 : 0.005 0.033 18090 Z= 0.207 Angle : 0.552 5.851 24636 Z= 0.310 Chirality : 0.048 0.166 2742 Planarity : 0.004 0.044 3225 Dihedral : 14.738 85.567 6351 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.64 % Allowed : 13.71 % Favored : 84.65 % 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: -1.15 (0.17), residues: 2319 helix: -0.33 (0.40), residues: 150 sheet: 0.01 (0.20), residues: 741 loop : -1.27 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 411 HIS 0.003 0.001 HIS A 721 PHE 0.018 0.002 PHE C 532 TYR 0.013 0.002 TYR A 814 ARG 0.010 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.24692 ( 331) hydrogen bonds : angle 7.90183 ( 876) covalent geometry : bond 0.00498 (18090) covalent geometry : angle 0.55238 (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 126 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 2.377 Fit side-chains outliers start: 31 outliers final: 27 residues processed: 126 average time/residue: 1.4964 time to fit residues: 213.6926 Evaluate side-chains 119 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 522 ASN Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 714 SER Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1007 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 0.0570 chunk 70 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 209 optimal weight: 9.9990 overall best weight: 2.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN B 453 ASN B 956 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.067457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.056871 restraints weight = 29486.907| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 1.94 r_work: 0.2448 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2337 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9182 moved from start: 0.0542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18090 Z= 0.139 Angle : 0.519 5.492 24636 Z= 0.293 Chirality : 0.047 0.175 2742 Planarity : 0.004 0.045 3225 Dihedral : 6.045 59.376 2567 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.48 % Allowed : 12.55 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.17), residues: 2319 helix: 0.02 (0.39), residues: 174 sheet: 0.01 (0.19), residues: 756 loop : -1.26 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 411 HIS 0.002 0.001 HIS B 806 PHE 0.014 0.001 PHE C 532 TYR 0.011 0.001 TYR A 814 ARG 0.007 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.05366 ( 331) hydrogen bonds : angle 5.85102 ( 876) covalent geometry : bond 0.00322 (18090) covalent geometry : angle 0.51885 (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 144 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 97 time to evaluate : 2.873 Fit side-chains REVERT: A 244 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6330 (mtmm) REVERT: A 287 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7282 (ttpt) REVERT: A 772 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8138 (tttp) REVERT: B 983 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: C 785 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8540 (p) REVERT: C 799 ASN cc_start: 0.9289 (t0) cc_final: 0.9063 (t0) outliers start: 47 outliers final: 22 residues processed: 132 average time/residue: 1.6821 time to fit residues: 251.4481 Evaluate side-chains 122 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 642 LYS Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 983 GLU 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 615 HIS Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 714 SER Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 785 THR Chi-restraints excluded: chain C residue 961 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 148 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 52 optimal weight: 0.0270 chunk 39 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.066028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.055600 restraints weight = 29132.973| |-----------------------------------------------------------------------------| r_work (start): 0.2519 rms_B_bonded: 1.87 r_work: 0.2408 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2298 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9209 moved from start: 0.0510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 18090 Z= 0.251 Angle : 0.603 5.884 24636 Z= 0.340 Chirality : 0.050 0.179 2742 Planarity : 0.004 0.044 3225 Dihedral : 6.055 59.859 2542 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.01 % Allowed : 12.24 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.11 (0.16), residues: 2319 helix: 0.26 (0.40), residues: 174 sheet: 0.09 (0.19), residues: 732 loop : -1.36 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 411 HIS 0.004 0.001 HIS A 721 PHE 0.021 0.002 PHE C 532 TYR 0.013 0.002 TYR A 814 ARG 0.008 0.001 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.05941 ( 331) hydrogen bonds : angle 5.87506 ( 876) covalent geometry : bond 0.00610 (18090) covalent geometry : angle 0.60251 (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 147 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 90 time to evaluate : 2.373 Fit side-chains REVERT: A 244 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6383 (mtmm) REVERT: A 287 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7309 (ttpt) outliers start: 57 outliers final: 22 residues processed: 136 average time/residue: 1.7812 time to fit residues: 272.8103 Evaluate side-chains 114 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 642 LYS Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 522 ASN Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 714 SER Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 961 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 87 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.066316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.055853 restraints weight = 29103.842| |-----------------------------------------------------------------------------| r_work (start): 0.2529 rms_B_bonded: 1.87 r_work: 0.2420 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9217 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 18090 Z= 0.217 Angle : 0.579 5.803 24636 Z= 0.327 Chirality : 0.049 0.174 2742 Planarity : 0.004 0.045 3225 Dihedral : 5.948 59.948 2540 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.69 % Allowed : 12.55 % Favored : 84.76 % 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: -1.12 (0.16), residues: 2319 helix: 0.38 (0.40), residues: 174 sheet: 0.03 (0.19), residues: 738 loop : -1.37 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 411 HIS 0.003 0.001 HIS A 721 PHE 0.018 0.002 PHE C 532 TYR 0.013 0.002 TYR A 814 ARG 0.008 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.05435 ( 331) hydrogen bonds : angle 5.71176 ( 876) covalent geometry : bond 0.00525 (18090) covalent geometry : angle 0.57902 (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 143 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 92 time to evaluate : 2.005 Fit side-chains REVERT: A 244 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6376 (mtmm) REVERT: A 420 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8896 (ptp90) REVERT: A 772 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8124 (tttp) REVERT: B 772 LYS cc_start: 0.8633 (tttm) cc_final: 0.8325 (ttpp) REVERT: C 701 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8923 (ttt180) REVERT: C 710 ILE cc_start: 0.9682 (OUTLIER) cc_final: 0.9206 (mm) REVERT: C 785 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8534 (p) outliers start: 51 outliers final: 24 residues processed: 130 average time/residue: 1.8784 time to fit residues: 273.2944 Evaluate side-chains 120 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 642 LYS Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 522 ASN Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 714 SER Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 785 THR Chi-restraints excluded: chain C residue 961 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 93 optimal weight: 0.0870 chunk 101 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 227 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.068581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.058008 restraints weight = 29160.261| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 1.89 r_work: 0.2465 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2358 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9185 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 18090 Z= 0.117 Angle : 0.490 5.328 24636 Z= 0.276 Chirality : 0.046 0.164 2742 Planarity : 0.003 0.045 3225 Dihedral : 5.526 58.991 2540 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.16 % Allowed : 13.13 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.17), residues: 2319 helix: 0.64 (0.40), residues: 174 sheet: 0.11 (0.19), residues: 750 loop : -1.28 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 411 HIS 0.002 0.000 HIS B 806 PHE 0.012 0.001 PHE C 532 TYR 0.010 0.001 TYR A 814 ARG 0.009 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 331) hydrogen bonds : angle 5.34139 ( 876) covalent geometry : bond 0.00266 (18090) covalent geometry : angle 0.48994 (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 141 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 2.071 Fit side-chains REVERT: A 244 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6554 (mtmm) REVERT: B 257 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: B 772 LYS cc_start: 0.8611 (tttm) cc_final: 0.8304 (ttpp) REVERT: C 785 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8590 (p) REVERT: C 799 ASN cc_start: 0.9349 (t0) cc_final: 0.9112 (t0) outliers start: 41 outliers final: 20 residues processed: 129 average time/residue: 1.3621 time to fit residues: 197.2331 Evaluate side-chains 117 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 642 LYS Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 522 ASN Chi-restraints excluded: chain C residue 615 HIS Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 714 SER Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 785 THR Chi-restraints excluded: chain C residue 961 THR 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: 10.0000 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 222 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.069851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.059219 restraints weight = 29104.148| |-----------------------------------------------------------------------------| r_work (start): 0.2597 rms_B_bonded: 1.89 r_work: 0.2490 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2383 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9167 moved from start: 0.0928 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= 0.097 Angle : 0.465 6.308 24636 Z= 0.261 Chirality : 0.045 0.159 2742 Planarity : 0.003 0.044 3225 Dihedral : 5.205 57.674 2539 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.74 % Allowed : 13.87 % Favored : 84.39 % 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: -0.87 (0.17), residues: 2319 helix: 0.82 (0.41), residues: 174 sheet: 0.12 (0.19), residues: 756 loop : -1.20 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 411 HIS 0.005 0.001 HIS B 618 PHE 0.012 0.001 PHE C 532 TYR 0.009 0.001 TYR A 814 ARG 0.009 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 331) hydrogen bonds : angle 5.14986 ( 876) covalent geometry : bond 0.00214 (18090) covalent geometry : angle 0.46499 (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 135 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.913 Fit side-chains REVERT: B 257 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8176 (mp0) REVERT: B 772 LYS cc_start: 0.8585 (tttm) cc_final: 0.8311 (ttpp) REVERT: C 701 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8960 (ttt180) REVERT: C 799 ASN cc_start: 0.9322 (t0) cc_final: 0.9087 (t0) outliers start: 33 outliers final: 19 residues processed: 125 average time/residue: 1.3880 time to fit residues: 195.4691 Evaluate side-chains 117 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 642 LYS 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 954 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 522 ASN Chi-restraints excluded: chain C residue 615 HIS Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 961 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 97 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.066249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.055775 restraints weight = 29082.788| |-----------------------------------------------------------------------------| r_work (start): 0.2528 rms_B_bonded: 1.87 r_work: 0.2418 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2309 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9219 moved from start: 0.0628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 18090 Z= 0.239 Angle : 0.590 5.621 24636 Z= 0.332 Chirality : 0.050 0.174 2742 Planarity : 0.004 0.043 3225 Dihedral : 5.671 59.807 2535 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.43 % Allowed : 13.03 % Favored : 84.55 % 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: -1.03 (0.16), residues: 2319 helix: 0.56 (0.40), residues: 174 sheet: 0.14 (0.19), residues: 732 loop : -1.35 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 411 HIS 0.004 0.001 HIS B 618 PHE 0.021 0.002 PHE C 532 TYR 0.012 0.002 TYR A 814 ARG 0.009 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.05397 ( 331) hydrogen bonds : angle 5.64700 ( 876) covalent geometry : bond 0.00582 (18090) covalent geometry : angle 0.59018 (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 136 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 90 time to evaluate : 1.949 Fit side-chains REVERT: A 244 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6377 (mtmm) REVERT: B 772 LYS cc_start: 0.8594 (tttm) cc_final: 0.8320 (ttpp) REVERT: C 362 ILE cc_start: 0.8941 (tp) cc_final: 0.8733 (tp) REVERT: C 701 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8970 (ttt180) REVERT: C 710 ILE cc_start: 0.9684 (OUTLIER) cc_final: 0.9232 (mm) outliers start: 46 outliers final: 24 residues processed: 126 average time/residue: 1.4193 time to fit residues: 200.2619 Evaluate side-chains 118 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 642 LYS 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 954 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 522 ASN Chi-restraints excluded: chain C residue 615 HIS Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 961 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 64 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 184 optimal weight: 0.5980 chunk 230 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.068130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.057610 restraints weight = 28921.495| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 1.87 r_work: 0.2455 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2346 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9192 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 18090 Z= 0.139 Angle : 0.511 5.564 24636 Z= 0.288 Chirality : 0.047 0.159 2742 Planarity : 0.004 0.044 3225 Dihedral : 5.412 59.588 2535 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.74 % Allowed : 13.61 % Favored : 84.65 % 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: -0.97 (0.17), residues: 2319 helix: 0.67 (0.41), residues: 174 sheet: 0.11 (0.19), residues: 750 loop : -1.29 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 411 HIS 0.004 0.001 HIS B 618 PHE 0.014 0.001 PHE C 532 TYR 0.010 0.001 TYR A 814 ARG 0.009 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 331) hydrogen bonds : angle 5.37675 ( 876) covalent geometry : bond 0.00328 (18090) covalent geometry : angle 0.51092 (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 126 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 1.906 Fit side-chains REVERT: A 244 LYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6505 (mtmm) REVERT: B 772 LYS cc_start: 0.8591 (tttm) cc_final: 0.8334 (ttpp) REVERT: C 362 ILE cc_start: 0.8852 (tp) cc_final: 0.8638 (tp) REVERT: C 701 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8972 (ttt180) REVERT: C 710 ILE cc_start: 0.9665 (OUTLIER) cc_final: 0.9202 (mm) outliers start: 33 outliers final: 24 residues processed: 117 average time/residue: 1.4298 time to fit residues: 186.7277 Evaluate side-chains 120 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 642 LYS Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 796 ASN Chi-restraints excluded: chain B residue 805 GLU Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 522 ASN Chi-restraints excluded: chain C residue 615 HIS Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 961 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 228 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.068421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.057839 restraints weight = 29082.961| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 1.88 r_work: 0.2461 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2352 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9188 moved from start: 0.0790 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= 0.128 Angle : 0.500 6.635 24636 Z= 0.281 Chirality : 0.046 0.157 2742 Planarity : 0.003 0.044 3225 Dihedral : 5.305 59.561 2535 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.64 % Allowed : 13.66 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2319 helix: 0.73 (0.41), residues: 174 sheet: 0.14 (0.19), residues: 750 loop : -1.26 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 411 HIS 0.004 0.001 HIS B 618 PHE 0.014 0.001 PHE C 532 TYR 0.010 0.001 TYR B 580 ARG 0.010 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 331) hydrogen bonds : angle 5.32323 ( 876) covalent geometry : bond 0.00297 (18090) covalent geometry : angle 0.49994 (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 124 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 2.100 Fit side-chains REVERT: A 244 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6507 (mtmm) REVERT: B 772 LYS cc_start: 0.8586 (tttm) cc_final: 0.8332 (ttpp) REVERT: C 362 ILE cc_start: 0.8822 (tp) cc_final: 0.8601 (tp) REVERT: C 701 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8969 (ttt180) REVERT: C 710 ILE cc_start: 0.9662 (OUTLIER) cc_final: 0.9201 (mm) outliers start: 31 outliers final: 24 residues processed: 116 average time/residue: 1.5079 time to fit residues: 195.7656 Evaluate side-chains 119 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 642 LYS Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 796 ASN Chi-restraints excluded: chain B residue 805 GLU Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 522 ASN Chi-restraints excluded: chain C residue 615 HIS Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 961 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 202 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.066115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.055654 restraints weight = 29154.835| |-----------------------------------------------------------------------------| r_work (start): 0.2526 rms_B_bonded: 1.87 r_work: 0.2417 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2308 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9221 moved from start: 0.0621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 18090 Z= 0.239 Angle : 0.595 6.276 24636 Z= 0.335 Chirality : 0.050 0.169 2742 Planarity : 0.004 0.043 3225 Dihedral : 5.717 59.554 2535 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.74 % Allowed : 13.66 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.07 (0.16), residues: 2319 helix: 0.53 (0.40), residues: 174 sheet: 0.12 (0.19), residues: 732 loop : -1.38 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 411 HIS 0.004 0.001 HIS B 618 PHE 0.021 0.002 PHE C 532 TYR 0.013 0.002 TYR A 750 ARG 0.010 0.001 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.05398 ( 331) hydrogen bonds : angle 5.66239 ( 876) covalent geometry : bond 0.00582 (18090) covalent geometry : angle 0.59513 (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 122 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 1.966 Fit side-chains REVERT: A 244 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6364 (mtmm) REVERT: B 772 LYS cc_start: 0.8600 (tttm) cc_final: 0.8344 (ttpp) REVERT: C 362 ILE cc_start: 0.8870 (tp) cc_final: 0.8651 (tp) REVERT: C 701 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8971 (ttt180) REVERT: C 710 ILE cc_start: 0.9685 (OUTLIER) cc_final: 0.9228 (mm) outliers start: 33 outliers final: 21 residues processed: 114 average time/residue: 1.5194 time to fit residues: 192.9700 Evaluate side-chains 112 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 642 LYS Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 522 ASN Chi-restraints excluded: chain C residue 615 HIS Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 961 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 184 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.068083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.057545 restraints weight = 29005.011| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 1.87 r_work: 0.2455 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2347 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9192 moved from start: 0.0746 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= 0.136 Angle : 0.512 6.689 24636 Z= 0.288 Chirality : 0.047 0.157 2742 Planarity : 0.004 0.044 3225 Dihedral : 5.412 59.443 2535 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.48 % Allowed : 13.98 % Favored : 84.55 % 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: -0.97 (0.17), residues: 2319 helix: 0.67 (0.41), residues: 174 sheet: 0.12 (0.19), residues: 750 loop : -1.29 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 411 HIS 0.004 0.001 HIS B 618 PHE 0.014 0.001 PHE C 532 TYR 0.010 0.001 TYR A 814 ARG 0.010 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 331) hydrogen bonds : angle 5.38188 ( 876) covalent geometry : bond 0.00317 (18090) covalent geometry : angle 0.51151 (24636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11146.25 seconds wall clock time: 196 minutes 36.77 seconds (11796.77 seconds total)