Starting phenix.real_space_refine on Mon Oct 14 10:58:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8o_38151/10_2024/8x8o_38151.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8o_38151/10_2024/8x8o_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8o_38151/10_2024/8x8o_38151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8o_38151/10_2024/8x8o_38151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8o_38151/10_2024/8x8o_38151.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8o_38151/10_2024/8x8o_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-5477/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: 11.61, per 1000 atoms: 0.66 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: 4.36 Conformation dependent library (CDL) restraints added in 2.4 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: 2.12 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: 6.81 Time building geometry restraints manager: 5.02 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 42.450 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.960 ------------------------------------------------------------------------------- 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= 0.329 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 *********************** 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 fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 2.250 Fit side-chains outliers start: 31 outliers final: 27 residues processed: 126 average time/residue: 1.4160 time to fit residues: 202.2226 Evaluate side-chains 119 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 2.133 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 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= 0.213 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 *********************** 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 fitting. rotamer outliers: 47 poor density : 97 time to evaluate : 2.258 Fit side-chains REVERT: A 244 LYS cc_start: 0.6873 (OUTLIER) cc_final: 0.6381 (mtmm) REVERT: A 287 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7354 (ttpt) REVERT: A 772 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7800 (tttp) REVERT: B 983 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: C 785 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8613 (p) outliers start: 47 outliers final: 22 residues processed: 132 average time/residue: 1.4216 time to fit residues: 210.5849 Evaluate side-chains 122 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 2.180 ------------------------------------------------------------------------------- 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 116 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 227 optimal weight: 20.0000 chunk 187 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN C 799 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.0547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 18090 Z= 0.490 Angle : 0.645 6.315 24636 Z= 0.364 Chirality : 0.052 0.183 2742 Planarity : 0.005 0.045 3225 Dihedral : 6.195 59.442 2542 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.22 % Allowed : 11.97 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.10 (0.16), residues: 2319 helix: 0.53 (0.42), residues: 156 sheet: 0.06 (0.19), residues: 732 loop : -1.35 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 411 HIS 0.004 0.001 HIS A 721 PHE 0.022 0.002 PHE C 532 TYR 0.015 0.002 TYR A 750 ARG 0.007 0.001 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 89 time to evaluate : 2.250 Fit side-chains REVERT: A 244 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6420 (mtmm) REVERT: A 287 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.7342 (ttpt) REVERT: A 420 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8902 (ptp90) REVERT: A 772 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7811 (tttp) REVERT: C 710 ILE cc_start: 0.9598 (OUTLIER) cc_final: 0.9158 (mm) outliers start: 61 outliers final: 23 residues processed: 136 average time/residue: 1.5483 time to fit residues: 234.4281 Evaluate side-chains 115 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 87 time to evaluate : 2.220 ------------------------------------------------------------------------------- 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 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 469 LEU 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 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 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 961 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18090 Z= 0.148 Angle : 0.479 5.966 24636 Z= 0.270 Chirality : 0.046 0.164 2742 Planarity : 0.003 0.045 3225 Dihedral : 5.476 58.481 2540 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.06 % Allowed : 13.19 % 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: -1.03 (0.17), residues: 2319 helix: 0.54 (0.40), residues: 174 sheet: -0.03 (0.19), residues: 771 loop : -1.26 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 411 HIS 0.002 0.000 HIS B 618 PHE 0.011 0.001 PHE C 532 TYR 0.009 0.001 TYR A 814 ARG 0.008 0.000 ARG A 405 *********************** 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 140 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 101 time to evaluate : 2.260 Fit side-chains REVERT: B 772 LYS cc_start: 0.8249 (tttm) cc_final: 0.7984 (ttpp) REVERT: C 701 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8864 (ttt180) outliers start: 39 outliers final: 21 residues processed: 127 average time/residue: 1.4299 time to fit residues: 203.6987 Evaluate side-chains 117 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 2.080 ------------------------------------------------------------------------------- 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 342 THR 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 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 615 HIS Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 701 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 190 optimal weight: 0.5980 chunk 154 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 200 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.0759 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= 0.200 Angle : 0.499 5.085 24636 Z= 0.281 Chirality : 0.046 0.166 2742 Planarity : 0.003 0.044 3225 Dihedral : 5.425 58.688 2538 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.16 % Allowed : 13.40 % 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 (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: -0.95 (0.17), residues: 2319 helix: 0.63 (0.41), residues: 174 sheet: 0.13 (0.19), residues: 750 loop : -1.27 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 411 HIS 0.004 0.001 HIS B 618 PHE 0.015 0.001 PHE C 532 TYR 0.010 0.001 TYR B 580 ARG 0.009 0.000 ARG A 405 *********************** 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 fitting. rotamer outliers: 41 poor density : 94 time to evaluate : 2.213 Fit side-chains REVERT: A 244 LYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6395 (mtmm) REVERT: B 739 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8186 (pttp) REVERT: B 772 LYS cc_start: 0.8257 (tttm) cc_final: 0.7980 (ttpp) REVERT: C 701 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8827 (ttt180) outliers start: 41 outliers final: 22 residues processed: 125 average time/residue: 1.4720 time to fit residues: 207.6526 Evaluate side-chains 119 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 2.108 ------------------------------------------------------------------------------- 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 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 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 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 961 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 0.4980 chunk 55 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.0607 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= 0.340 Angle : 0.574 5.867 24636 Z= 0.323 Chirality : 0.049 0.173 2742 Planarity : 0.004 0.044 3225 Dihedral : 5.709 59.534 2537 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.22 % Allowed : 13.13 % 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: -1.04 (0.16), residues: 2319 helix: 0.51 (0.40), residues: 174 sheet: 0.14 (0.20), residues: 732 loop : -1.35 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 411 HIS 0.003 0.001 HIS B 618 PHE 0.020 0.002 PHE C 532 TYR 0.012 0.002 TYR A 814 ARG 0.009 0.000 ARG A 405 *********************** 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 fitting. rotamer outliers: 42 poor density : 93 time to evaluate : 2.053 Fit side-chains REVERT: A 244 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6405 (mtmm) REVERT: B 739 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8341 (pttp) REVERT: B 772 LYS cc_start: 0.8268 (tttm) cc_final: 0.7981 (ttpp) REVERT: C 701 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8855 (ttt180) outliers start: 42 outliers final: 22 residues processed: 124 average time/residue: 1.5316 time to fit residues: 211.4610 Evaluate side-chains 118 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 1.977 ------------------------------------------------------------------------------- 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 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 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 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 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 215 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 139 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.0755 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= 0.207 Angle : 0.505 5.820 24636 Z= 0.284 Chirality : 0.046 0.160 2742 Planarity : 0.004 0.044 3225 Dihedral : 5.431 59.274 2537 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.00 % Allowed : 13.40 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.66 (0.41), 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 0.003 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 *********************** 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 135 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 97 time to evaluate : 2.020 Fit side-chains REVERT: A 244 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6461 (mtmm) REVERT: B 739 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8179 (pttp) REVERT: B 772 LYS cc_start: 0.8260 (tttm) cc_final: 0.8014 (ttpp) REVERT: C 701 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8865 (ttt180) REVERT: C 710 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9139 (mm) outliers start: 38 outliers final: 24 residues processed: 127 average time/residue: 1.4410 time to fit residues: 204.8723 Evaluate side-chains 121 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 1.979 ------------------------------------------------------------------------------- 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 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 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 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 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 137 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 175 optimal weight: 0.1980 chunk 202 optimal weight: 7.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.0801 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= 0.192 Angle : 0.496 5.531 24636 Z= 0.279 Chirality : 0.046 0.157 2742 Planarity : 0.003 0.044 3225 Dihedral : 5.317 58.943 2537 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.79 % Allowed : 13.71 % Favored : 84.49 % 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: 0.13 (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 0.003 0.001 HIS B 618 PHE 0.014 0.001 PHE C 532 TYR 0.009 0.001 TYR A 814 ARG 0.010 0.000 ARG A 405 *********************** 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 129 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 95 time to evaluate : 2.179 Fit side-chains REVERT: A 244 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6456 (mtmm) REVERT: B 739 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8156 (pttp) REVERT: B 772 LYS cc_start: 0.8247 (tttm) cc_final: 0.8003 (ttpp) REVERT: C 701 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8866 (ttt180) REVERT: C 710 ILE cc_start: 0.9576 (OUTLIER) cc_final: 0.9137 (mm) outliers start: 34 outliers final: 23 residues processed: 122 average time/residue: 1.5220 time to fit residues: 207.3686 Evaluate side-chains 120 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 1.958 ------------------------------------------------------------------------------- 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 847 THR Chi-restraints excluded: chain B residue 342 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 90 optimal weight: 0.0060 chunk 162 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.0649 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= 0.333 Angle : 0.571 6.352 24636 Z= 0.322 Chirality : 0.049 0.176 2742 Planarity : 0.004 0.044 3225 Dihedral : 5.628 59.510 2535 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.95 % Allowed : 13.55 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.17), residues: 2319 helix: 0.57 (0.40), residues: 174 sheet: 0.08 (0.19), residues: 738 loop : -1.34 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 411 HIS 0.003 0.001 HIS C 615 PHE 0.020 0.002 PHE C 532 TYR 0.012 0.002 TYR C 750 ARG 0.009 0.000 ARG A 405 *********************** 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 128 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 91 time to evaluate : 1.973 Fit side-chains REVERT: A 244 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6459 (mtmm) REVERT: B 739 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8332 (pttp) REVERT: B 772 LYS cc_start: 0.8251 (tttm) cc_final: 0.8008 (ttpp) REVERT: C 701 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8856 (ttt180) REVERT: C 710 ILE cc_start: 0.9597 (OUTLIER) cc_final: 0.9169 (mm) outliers start: 37 outliers final: 24 residues processed: 120 average time/residue: 1.5209 time to fit residues: 203.2006 Evaluate side-chains 119 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 2.106 ------------------------------------------------------------------------------- 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 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 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 982 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 230 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.0787 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= 0.196 Angle : 0.503 6.697 24636 Z= 0.283 Chirality : 0.046 0.162 2742 Planarity : 0.004 0.044 3225 Dihedral : 5.347 58.995 2535 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.53 % Allowed : 13.87 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.95 (0.17), residues: 2319 helix: 0.69 (0.41), residues: 174 sheet: 0.12 (0.19), residues: 750 loop : -1.27 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 411 HIS 0.003 0.001 HIS B 618 PHE 0.014 0.001 PHE C 532 TYR 0.009 0.001 TYR B 580 ARG 0.010 0.000 ARG A 405 ********************** 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 121 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 1.903 Fit side-chains REVERT: A 244 LYS cc_start: 0.6833 (OUTLIER) cc_final: 0.6435 (mtmm) REVERT: B 739 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8153 (pttp) REVERT: B 772 LYS cc_start: 0.8237 (tttm) cc_final: 0.8003 (ttpp) REVERT: C 701 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8862 (ttt180) outliers start: 29 outliers final: 22 residues processed: 115 average time/residue: 1.5337 time to fit residues: 197.9748 Evaluate side-chains 116 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 2.219 ------------------------------------------------------------------------------- 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 847 THR Chi-restraints excluded: chain B residue 342 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.2762 r_free = 0.2762 target = 0.067455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.056911 restraints weight = 29015.806| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 1.87 r_work: 0.2442 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2334 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9202 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18090 Z= 0.258 Angle : 0.534 6.343 24636 Z= 0.300 Chirality : 0.047 0.162 2742 Planarity : 0.004 0.044 3225 Dihedral : 5.471 59.606 2535 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.48 % Allowed : 13.82 % 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: -0.99 (0.17), residues: 2319 helix: 0.64 (0.40), residues: 174 sheet: 0.10 (0.19), residues: 750 loop : -1.30 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 411 HIS 0.003 0.001 HIS B 618 PHE 0.017 0.001 PHE C 532 TYR 0.011 0.001 TYR B 580 ARG 0.010 0.000 ARG A 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4953.66 seconds wall clock time: 90 minutes 33.85 seconds (5433.85 seconds total)