Starting phenix.real_space_refine on Sun Aug 24 06:13:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x8o_38151/08_2025/8x8o_38151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x8o_38151/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8x8o_38151/08_2025/8x8o_38151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x8o_38151/08_2025/8x8o_38151.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x8o_38151/08_2025/8x8o_38151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x8o_38151/08_2025/8x8o_38151.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 11199 2.51 5 N 3012 2.21 5 O 3408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17682 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5894 Classifications: {'peptide': 775} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 741} Chain: "B" Number of atoms: 5894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5894 Classifications: {'peptide': 775} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 741} Chain: "C" Number of atoms: 5894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5894 Classifications: {'peptide': 775} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 741} Time building chain proxies: 4.58, per 1000 atoms: 0.26 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: 1.64 Conformation dependent library (CDL) restraints added in 905.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4152 Finding SS restraints... Secondary structure from input PDB file: 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: 0.67 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: 3.42 Time building geometry restraints manager: 2.19 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.500 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.700 ------------------------------------------------------------------------------- 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 : 2.35 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (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 ARG 0.010 0.000 ARG A 405 TYR 0.013 0.002 TYR A 814 PHE 0.018 0.002 PHE C 532 TRP 0.009 0.001 TRP C 411 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00498 (18090) covalent geometry : angle 0.55238 (24636) hydrogen bonds : bond 0.24692 ( 331) hydrogen bonds : angle 7.90183 ( 876) *********************** 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 : 0.762 Fit side-chains outliers start: 31 outliers final: 27 residues processed: 126 average time/residue: 0.6710 time to fit residues: 94.9104 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 : 0.698 ------------------------------------------------------------------------------- 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 216 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 overall best weight: 3.3390 ------------------------------------------------------------------------------- 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 = 0.2735 r_free = 0.2735 target = 0.066172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.055687 restraints weight = 29461.315| |-----------------------------------------------------------------------------| r_work (start): 0.2538 rms_B_bonded: 1.93 r_work: 0.2425 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2315 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.0468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 18090 Z= 0.197 Angle : 0.566 5.570 24636 Z= 0.320 Chirality : 0.048 0.177 2742 Planarity : 0.004 0.045 3225 Dihedral : 6.221 59.299 2567 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.64 % Allowed : 12.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.17), residues: 2319 helix: -0.02 (0.39), residues: 174 sheet: 0.07 (0.20), residues: 732 loop : -1.34 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 405 TYR 0.012 0.002 TYR A 814 PHE 0.018 0.002 PHE C 532 TRP 0.011 0.001 TRP C 411 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00472 (18090) covalent geometry : angle 0.56594 (24636) hydrogen bonds : bond 0.05843 ( 331) hydrogen bonds : angle 5.92545 ( 876) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 97 time to evaluate : 0.706 Fit side-chains REVERT: A 244 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6368 (mtmm) REVERT: A 287 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7328 (ttpt) REVERT: A 772 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8132 (tttp) REVERT: B 983 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8179 (mp0) REVERT: C 462 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8617 (p0) REVERT: C 799 ASN cc_start: 0.9314 (t0) cc_final: 0.9089 (t0) outliers start: 50 outliers final: 19 residues processed: 135 average time/residue: 0.6808 time to fit residues: 102.7848 Evaluate side-chains 116 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 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 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 41 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 201 optimal weight: 0.5980 chunk 80 optimal weight: 0.0670 chunk 16 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 187 optimal weight: 0.1980 overall best weight: 0.5120 ------------------------------------------------------------------------------- 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 = 0.2850 r_free = 0.2850 target = 0.072273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.061614 restraints weight = 29270.811| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 1.92 r_work: 0.2547 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2440 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.034 18090 Z= 0.074 Angle : 0.438 5.603 24636 Z= 0.244 Chirality : 0.044 0.167 2742 Planarity : 0.003 0.043 3225 Dihedral : 5.076 57.137 2542 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.74 % Allowed : 13.24 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.17), residues: 2319 helix: 0.60 (0.41), residues: 174 sheet: 0.26 (0.20), residues: 726 loop : -1.16 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 405 TYR 0.007 0.001 TYR C 526 PHE 0.008 0.001 PHE A 474 TRP 0.011 0.001 TRP C 411 HIS 0.002 0.000 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00148 (18090) covalent geometry : angle 0.43759 (24636) hydrogen bonds : bond 0.03221 ( 331) hydrogen bonds : angle 5.08765 ( 876) *********************** 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 141 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.750 Fit side-chains REVERT: B 463 ASN cc_start: 0.8407 (t0) cc_final: 0.8151 (t0) REVERT: C 244 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6566 (pmmt) REVERT: C 799 ASN cc_start: 0.9295 (t0) cc_final: 0.9080 (t0) outliers start: 33 outliers final: 11 residues processed: 133 average time/residue: 0.6957 time to fit residues: 103.3797 Evaluate side-chains 111 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 522 ASN Chi-restraints excluded: chain C residue 615 HIS Chi-restraints excluded: chain C residue 700 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 93 optimal weight: 8.9990 chunk 108 optimal weight: 0.0870 chunk 68 optimal weight: 0.0970 chunk 11 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 overall best weight: 4.6362 ------------------------------------------------------------------------------- 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 = 0.2735 r_free = 0.2735 target = 0.066103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.055578 restraints weight = 29332.262| |-----------------------------------------------------------------------------| r_work (start): 0.2520 rms_B_bonded: 1.89 r_work: 0.2409 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2299 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9221 moved from start: 0.0606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 18090 Z= 0.262 Angle : 0.608 6.128 24636 Z= 0.342 Chirality : 0.050 0.186 2742 Planarity : 0.004 0.045 3225 Dihedral : 5.699 59.686 2536 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.43 % Allowed : 12.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.17), residues: 2319 helix: 0.47 (0.40), residues: 174 sheet: 0.13 (0.19), residues: 735 loop : -1.30 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 405 TYR 0.014 0.002 TYR A 814 PHE 0.023 0.002 PHE C 532 TRP 0.009 0.002 TRP C 411 HIS 0.004 0.001 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00642 (18090) covalent geometry : angle 0.60836 (24636) hydrogen bonds : bond 0.05774 ( 331) hydrogen bonds : angle 5.75129 ( 876) *********************** 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 136 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 90 time to evaluate : 0.703 Fit side-chains REVERT: A 244 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6392 (mtmm) REVERT: B 983 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: C 710 ILE cc_start: 0.9668 (OUTLIER) cc_final: 0.9222 (mm) outliers start: 46 outliers final: 20 residues processed: 125 average time/residue: 0.7427 time to fit residues: 103.0717 Evaluate side-chains 113 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 469 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 642 LYS Chi-restraints excluded: chain B residue 739 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 B residue 983 GLU 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 710 ILE Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 955 SER 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 66 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.2767 r_free = 0.2767 target = 0.067742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.057180 restraints weight = 29034.760| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 1.87 r_work: 0.2447 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2339 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9198 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18090 Z= 0.146 Angle : 0.518 5.305 24636 Z= 0.292 Chirality : 0.047 0.170 2742 Planarity : 0.004 0.044 3225 Dihedral : 5.436 59.663 2534 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.22 % Allowed : 13.45 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.17), residues: 2319 helix: 0.57 (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 ARG 0.008 0.000 ARG A 405 TYR 0.010 0.001 TYR A 814 PHE 0.015 0.001 PHE C 532 TRP 0.010 0.001 TRP B 411 HIS 0.003 0.001 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.00343 (18090) covalent geometry : angle 0.51778 (24636) hydrogen bonds : bond 0.04541 ( 331) hydrogen bonds : angle 5.45306 ( 876) *********************** 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 135 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.718 Fit side-chains REVERT: A 244 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6355 (mtmm) REVERT: C 701 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8966 (ttt180) outliers start: 42 outliers final: 20 residues processed: 125 average time/residue: 0.7259 time to fit residues: 100.8026 Evaluate side-chains 116 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 A residue 770 ASP Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 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 701 ARG Chi-restraints excluded: chain C residue 739 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 954 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 120 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 14 optimal weight: 0.0050 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- 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 = 0.066291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.055816 restraints weight = 29059.132| |-----------------------------------------------------------------------------| r_work (start): 0.2527 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: 0.9218 moved from start: 0.0641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 18090 Z= 0.219 Angle : 0.576 5.797 24636 Z= 0.324 Chirality : 0.049 0.182 2742 Planarity : 0.004 0.044 3225 Dihedral : 5.649 59.939 2534 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.53 % Allowed : 13.24 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.16), residues: 2319 helix: 0.50 (0.40), residues: 174 sheet: 0.14 (0.19), residues: 732 loop : -1.36 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 405 TYR 0.013 0.002 TYR A 814 PHE 0.020 0.002 PHE C 532 TRP 0.010 0.001 TRP C 411 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00530 (18090) covalent geometry : angle 0.57558 (24636) hydrogen bonds : bond 0.05304 ( 331) hydrogen bonds : angle 5.65000 ( 876) *********************** 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 140 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 92 time to evaluate : 0.696 Fit side-chains REVERT: A 244 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6352 (mtmm) REVERT: A 420 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8822 (ptp90) REVERT: C 701 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8966 (ttt180) REVERT: C 710 ILE cc_start: 0.9683 (OUTLIER) cc_final: 0.9213 (mm) outliers start: 48 outliers final: 20 residues processed: 128 average time/residue: 0.7164 time to fit residues: 101.9166 Evaluate side-chains 113 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 348 THR 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 739 LYS Chi-restraints excluded: chain C residue 777 VAL 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 121 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.2744 r_free = 0.2744 target = 0.066480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.055960 restraints weight = 29246.966| |-----------------------------------------------------------------------------| r_work (start): 0.2531 rms_B_bonded: 1.88 r_work: 0.2421 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2313 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9216 moved from start: 0.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18090 Z= 0.208 Angle : 0.570 5.846 24636 Z= 0.321 Chirality : 0.049 0.179 2742 Planarity : 0.004 0.044 3225 Dihedral : 5.647 59.858 2534 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.16 % Allowed : 13.50 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.16), residues: 2319 helix: 0.51 (0.40), residues: 174 sheet: 0.07 (0.19), residues: 738 loop : -1.35 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 405 TYR 0.012 0.002 TYR A 814 PHE 0.019 0.002 PHE C 532 TRP 0.011 0.001 TRP C 411 HIS 0.003 0.001 HIS C 615 Details of bonding type rmsd covalent geometry : bond 0.00504 (18090) covalent geometry : angle 0.57023 (24636) hydrogen bonds : bond 0.05163 ( 331) hydrogen bonds : angle 5.61582 ( 876) *********************** 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 130 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 0.740 Fit side-chains REVERT: A 244 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6340 (mtmm) REVERT: A 420 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8779 (ptp90) REVERT: C 701 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8965 (ttt180) REVERT: C 710 ILE cc_start: 0.9683 (OUTLIER) cc_final: 0.9207 (mm) outliers start: 41 outliers final: 23 residues processed: 120 average time/residue: 0.7250 time to fit residues: 96.5501 Evaluate side-chains 116 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 348 THR Chi-restraints excluded: chain B residue 413 THR 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 739 LYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 954 THR 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 122 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 120 optimal weight: 0.0060 chunk 215 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 111 optimal weight: 0.0870 chunk 2 optimal weight: 0.0370 chunk 138 optimal weight: 0.0770 overall best weight: 0.8412 ------------------------------------------------------------------------------- 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 = 0.2823 r_free = 0.2823 target = 0.070851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.060211 restraints weight = 28873.606| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 1.89 r_work: 0.2513 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2406 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9140 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18090 Z= 0.081 Angle : 0.449 6.010 24636 Z= 0.250 Chirality : 0.045 0.155 2742 Planarity : 0.003 0.045 3225 Dihedral : 4.936 57.654 2534 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.69 % Allowed : 13.87 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.17), residues: 2319 helix: 0.80 (0.41), residues: 174 sheet: 0.07 (0.19), residues: 771 loop : -1.16 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 405 TYR 0.008 0.001 TYR A 814 PHE 0.009 0.001 PHE C 532 TRP 0.013 0.001 TRP C 411 HIS 0.003 0.000 HIS C 615 Details of bonding type rmsd covalent geometry : bond 0.00171 (18090) covalent geometry : angle 0.44882 (24636) hydrogen bonds : bond 0.03148 ( 331) hydrogen bonds : angle 5.05047 ( 876) *********************** 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 136 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.746 Fit side-chains REVERT: A 244 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6409 (mtmm) REVERT: B 257 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: B 463 ASN cc_start: 0.8438 (t0) cc_final: 0.8157 (t0) REVERT: C 799 ASN cc_start: 0.9298 (t0) cc_final: 0.9073 (t0) outliers start: 32 outliers final: 14 residues processed: 127 average time/residue: 0.6439 time to fit residues: 91.3017 Evaluate side-chains 112 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 469 LEU Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 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 700 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 200 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 2 optimal weight: 0.3980 chunk 138 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.2776 r_free = 0.2776 target = 0.068227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.057611 restraints weight = 29045.815| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 1.88 r_work: 0.2456 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2348 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9191 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18090 Z= 0.141 Angle : 0.509 6.461 24636 Z= 0.286 Chirality : 0.047 0.168 2742 Planarity : 0.003 0.045 3225 Dihedral : 5.217 58.497 2534 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.00 % Allowed : 14.77 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.17), residues: 2319 helix: 0.78 (0.41), residues: 174 sheet: 0.17 (0.19), residues: 750 loop : -1.21 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 405 TYR 0.010 0.001 TYR B 580 PHE 0.015 0.001 PHE C 532 TRP 0.010 0.001 TRP B 411 HIS 0.004 0.001 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.00333 (18090) covalent geometry : angle 0.50937 (24636) hydrogen bonds : bond 0.04283 ( 331) hydrogen bonds : angle 5.35372 ( 876) *********************** 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 112 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.806 Fit side-chains REVERT: A 244 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6440 (mtmm) REVERT: B 257 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: B 739 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8295 (pttp) outliers start: 19 outliers final: 14 residues processed: 105 average time/residue: 0.7245 time to fit residues: 84.8786 Evaluate side-chains 109 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 777 VAL 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 700 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 89 optimal weight: 0.9990 chunk 227 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 212 optimal weight: 6.9990 chunk 186 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 226 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.2790 r_free = 0.2790 target = 0.068980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.058356 restraints weight = 28859.398| |-----------------------------------------------------------------------------| r_work (start): 0.2580 rms_B_bonded: 1.89 r_work: 0.2472 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2364 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18090 Z= 0.115 Angle : 0.486 6.666 24636 Z= 0.273 Chirality : 0.046 0.162 2742 Planarity : 0.003 0.045 3225 Dihedral : 5.115 57.759 2534 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.11 % Allowed : 14.56 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.17), residues: 2319 helix: 0.80 (0.41), residues: 174 sheet: 0.19 (0.19), residues: 750 loop : -1.20 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 405 TYR 0.010 0.001 TYR A 814 PHE 0.013 0.001 PHE C 532 TRP 0.011 0.001 TRP B 411 HIS 0.004 0.001 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.00264 (18090) covalent geometry : angle 0.48621 (24636) hydrogen bonds : bond 0.03894 ( 331) hydrogen bonds : angle 5.25135 ( 876) ********************** 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 115 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.731 Fit side-chains REVERT: A 244 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6437 (mtmm) REVERT: B 257 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8176 (mp0) REVERT: B 739 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8222 (pttp) outliers start: 21 outliers final: 14 residues processed: 109 average time/residue: 0.7412 time to fit residues: 89.7425 Evaluate side-chains 110 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 469 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 739 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 168 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 142 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.069472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.058861 restraints weight = 28837.870| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 1.88 r_work: 0.2484 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2376 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18090 Z= 0.104 Angle : 0.474 6.590 24636 Z= 0.265 Chirality : 0.045 0.158 2742 Planarity : 0.003 0.045 3225 Dihedral : 4.992 56.770 2534 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.16 % Allowed : 14.50 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.17), residues: 2319 helix: 0.84 (0.41), residues: 174 sheet: 0.16 (0.19), residues: 756 loop : -1.16 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 405 TYR 0.009 0.001 TYR A 814 PHE 0.012 0.001 PHE C 532 TRP 0.011 0.001 TRP B 411 HIS 0.004 0.001 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.00237 (18090) covalent geometry : angle 0.47359 (24636) hydrogen bonds : bond 0.03690 ( 331) hydrogen bonds : angle 5.18535 ( 876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4909.38 seconds wall clock time: 84 minutes 56.61 seconds (5096.61 seconds total)