Starting phenix.real_space_refine on Mon Aug 25 07:09:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cc3_45433/08_2025/9cc3_45433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cc3_45433/08_2025/9cc3_45433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cc3_45433/08_2025/9cc3_45433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cc3_45433/08_2025/9cc3_45433.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cc3_45433/08_2025/9cc3_45433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cc3_45433/08_2025/9cc3_45433.map" } resolution = 3.23 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= 0.001 sd= 0.074 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 119 5.16 5 C 16312 2.51 5 N 4426 2.21 5 O 4910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s 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: 25779 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 151 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4303 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 25, 'TRANS': 537} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'GLU:plan': 5, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 4202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4202 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 25, 'TRANS': 518} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 4322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4322 Classifications: {'peptide': 566} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain breaks: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 3, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 4184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4184 Classifications: {'peptide': 543} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 25, 'TRANS': 517} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4319 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 25, 'TRANS': 539} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "F" Number of atoms: 4186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4186 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 25, 'TRANS': 516} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.82, per 1000 atoms: 0.26 Number of scatterers: 25779 At special positions: 0 Unit cell: (136.664, 134.061, 161.394, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 119 16.00 P 8 15.00 Mg 4 11.99 O 4910 8.00 N 4426 7.00 C 16312 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: 2.25 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6254 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 35 sheets defined 54.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'G' and resid -1 through 1 No H-bonds generated for 'chain 'G' and resid -1 through 1' Processing helix chain 'G' and resid 2 through 15 removed outlier: 3.928A pdb=" N UNK G 6 " --> pdb=" O UNK G 2 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N UNK G 13 " --> pdb=" O UNK G 9 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N UNK G 14 " --> pdb=" O UNK G 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 408 removed outlier: 3.819A pdb=" N ARG A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.896A pdb=" N ARG A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 4.559A pdb=" N VAL A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'A' and resid 528 through 541 removed outlier: 3.663A pdb=" N ILE A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.726A pdb=" N ILE A 595 " --> pdb=" O VAL A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 615 through 618 removed outlier: 3.596A pdb=" N ASN A 618 " --> pdb=" O GLN A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 615 through 618' Processing helix chain 'A' and resid 629 through 633 removed outlier: 4.254A pdb=" N LYS A 632 " --> pdb=" O ASP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 651 removed outlier: 4.039A pdb=" N ASP A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 692 through 704 removed outlier: 3.522A pdb=" N CYS A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 729 Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 807 through 829 Processing helix chain 'A' and resid 833 through 838 removed outlier: 3.583A pdb=" N THR A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 938 through 947 removed outlier: 3.993A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 removed outlier: 3.836A pdb=" N LYS B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 431 through 448 removed outlier: 3.802A pdb=" N LEU B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.693A pdb=" N ASP B 490 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 512 Processing helix chain 'B' and resid 531 through 541 removed outlier: 3.888A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.888A pdb=" N ILE B 595 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 611 removed outlier: 3.716A pdb=" N LEU B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 619 Processing helix chain 'B' and resid 641 through 645 removed outlier: 4.043A pdb=" N THR B 644 " --> pdb=" O VAL B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.520A pdb=" N ARG B 652 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 673 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 692 through 704 Processing helix chain 'B' and resid 709 through 729 Processing helix chain 'B' and resid 741 through 745 Processing helix chain 'B' and resid 807 through 829 removed outlier: 3.531A pdb=" N GLN B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 838 Processing helix chain 'B' and resid 853 through 855 No H-bonds generated for 'chain 'B' and resid 853 through 855' Processing helix chain 'B' and resid 856 through 870 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 916 through 922 Processing helix chain 'B' and resid 924 through 929 removed outlier: 3.568A pdb=" N THR B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 947 removed outlier: 3.936A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 408 removed outlier: 3.838A pdb=" N GLU C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 removed outlier: 3.927A pdb=" N GLU C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 428 removed outlier: 3.847A pdb=" N GLU C 427 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 452 through 466 Processing helix chain 'C' and resid 479 through 489 Processing helix chain 'C' and resid 494 through 511 removed outlier: 3.787A pdb=" N ARG C 511 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 541 removed outlier: 3.968A pdb=" N ALA C 533 " --> pdb=" O LYS C 529 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 591 through 595 removed outlier: 3.637A pdb=" N ILE C 595 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 608 removed outlier: 3.662A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 618 Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.616A pdb=" N ARG C 652 " --> pdb=" O PRO C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 673 removed outlier: 3.507A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 692 through 703 Processing helix chain 'C' and resid 709 through 729 Processing helix chain 'C' and resid 742 through 747 Processing helix chain 'C' and resid 807 through 829 Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 853 through 855 No H-bonds generated for 'chain 'C' and resid 853 through 855' Processing helix chain 'C' and resid 856 through 870 Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 924 through 929 removed outlier: 3.553A pdb=" N THR C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 947 removed outlier: 3.910A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP C 944 " --> pdb=" O ARG C 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 408 removed outlier: 3.563A pdb=" N GLY D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 426 removed outlier: 4.441A pdb=" N GLU D 419 " --> pdb=" O ASP D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.631A pdb=" N ASP D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL D 437 " --> pdb=" O HIS D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 467 Processing helix chain 'D' and resid 479 through 491 Processing helix chain 'D' and resid 494 through 512 Processing helix chain 'D' and resid 528 through 541 removed outlier: 3.754A pdb=" N ALA D 533 " --> pdb=" O LYS D 529 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 560 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 592 through 595 removed outlier: 3.514A pdb=" N ILE D 595 " --> pdb=" O VAL D 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 592 through 595' Processing helix chain 'D' and resid 602 through 602 No H-bonds generated for 'chain 'D' and resid 602 through 602' Processing helix chain 'D' and resid 603 through 611 removed outlier: 4.266A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 662 through 673 Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 692 through 703 Processing helix chain 'D' and resid 709 through 729 Processing helix chain 'D' and resid 741 through 745 Processing helix chain 'D' and resid 807 through 829 Processing helix chain 'D' and resid 833 through 838 Processing helix chain 'D' and resid 853 through 855 No H-bonds generated for 'chain 'D' and resid 853 through 855' Processing helix chain 'D' and resid 856 through 870 Processing helix chain 'D' and resid 894 through 905 removed outlier: 3.670A pdb=" N LYS D 898 " --> pdb=" O GLY D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 924 through 929 removed outlier: 3.511A pdb=" N THR D 928 " --> pdb=" O ALA D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 947 removed outlier: 3.788A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP D 944 " --> pdb=" O ARG D 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 408 removed outlier: 3.674A pdb=" N ARG E 381 " --> pdb=" O GLN E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 411 No H-bonds generated for 'chain 'E' and resid 409 through 411' Processing helix chain 'E' and resid 413 through 424 removed outlier: 4.082A pdb=" N ILE E 417 " --> pdb=" O ASP E 413 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU E 418 " --> pdb=" O LYS E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 448 removed outlier: 4.257A pdb=" N VAL E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 467 Processing helix chain 'E' and resid 479 through 490 removed outlier: 3.676A pdb=" N ASP E 490 " --> pdb=" O VAL E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 512 Processing helix chain 'E' and resid 528 through 541 removed outlier: 3.591A pdb=" N ALA E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 572 through 581 Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.828A pdb=" N ILE E 595 " --> pdb=" O VAL E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 612 removed outlier: 4.004A pdb=" N LEU E 607 " --> pdb=" O PRO E 603 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 618 Processing helix chain 'E' and resid 646 through 651 removed outlier: 3.530A pdb=" N ASP E 651 " --> pdb=" O GLU E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 673 Processing helix chain 'E' and resid 673 through 683 Processing helix chain 'E' and resid 692 through 703 removed outlier: 3.605A pdb=" N LEU E 696 " --> pdb=" O SER E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 729 Processing helix chain 'E' and resid 738 through 745 removed outlier: 3.656A pdb=" N LEU E 742 " --> pdb=" O PRO E 739 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN E 743 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 829 removed outlier: 3.598A pdb=" N GLN E 827 " --> pdb=" O ALA E 823 " (cutoff:3.500A) Processing helix chain 'E' and resid 833 through 838 Processing helix chain 'E' and resid 853 through 855 No H-bonds generated for 'chain 'E' and resid 853 through 855' Processing helix chain 'E' and resid 856 through 870 Processing helix chain 'E' and resid 894 through 906 Processing helix chain 'E' and resid 916 through 921 removed outlier: 3.620A pdb=" N TYR E 921 " --> pdb=" O LYS E 917 " (cutoff:3.500A) Processing helix chain 'E' and resid 924 through 929 removed outlier: 3.603A pdb=" N THR E 928 " --> pdb=" O ALA E 924 " (cutoff:3.500A) Processing helix chain 'E' and resid 938 through 947 removed outlier: 3.947A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 409 removed outlier: 3.973A pdb=" N LYS F 401 " --> pdb=" O GLN F 397 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS F 404 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS F 405 " --> pdb=" O LYS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 425 removed outlier: 4.031A pdb=" N LEU F 425 " --> pdb=" O PHE F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 445 removed outlier: 4.952A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU F 440 " --> pdb=" O ASP F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 448 No H-bonds generated for 'chain 'F' and resid 446 through 448' Processing helix chain 'F' and resid 452 through 466 Processing helix chain 'F' and resid 479 through 491 Processing helix chain 'F' and resid 494 through 512 Processing helix chain 'F' and resid 528 through 540 removed outlier: 4.166A pdb=" N ILE F 532 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 571 through 581 Processing helix chain 'F' and resid 591 through 595 Processing helix chain 'F' and resid 603 through 612 removed outlier: 3.559A pdb=" N LEU F 607 " --> pdb=" O PRO F 603 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU F 609 " --> pdb=" O SER F 605 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 617 removed outlier: 4.066A pdb=" N ALA F 617 " --> pdb=" O PRO F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 652 removed outlier: 3.992A pdb=" N ARG F 650 " --> pdb=" O PRO F 646 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG F 652 " --> pdb=" O PRO F 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 646 through 652' Processing helix chain 'F' and resid 662 through 683 removed outlier: 3.534A pdb=" N LEU F 667 " --> pdb=" O ALA F 663 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA F 668 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL F 675 " --> pdb=" O GLU F 671 " (cutoff:3.500A) Proline residue: F 676 - end of helix Processing helix chain 'F' and resid 692 through 703 Processing helix chain 'F' and resid 709 through 729 Processing helix chain 'F' and resid 741 through 746 removed outlier: 4.124A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 829 Processing helix chain 'F' and resid 833 through 838 Processing helix chain 'F' and resid 853 through 855 No H-bonds generated for 'chain 'F' and resid 853 through 855' Processing helix chain 'F' and resid 856 through 870 Processing helix chain 'F' and resid 894 through 905 Processing helix chain 'F' and resid 916 through 922 Processing helix chain 'F' and resid 924 through 929 removed outlier: 3.772A pdb=" N THR F 928 " --> pdb=" O ALA F 924 " (cutoff:3.500A) Processing helix chain 'F' and resid 938 through 947 removed outlier: 3.886A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP F 944 " --> pdb=" O ARG F 940 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 548 removed outlier: 3.627A pdb=" N ASP A 590 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 519 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ALA A 639 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE A 521 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 654 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS A 520 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 619 through 620 Processing sheet with id=AA3, first strand: chain 'A' and resid 689 through 690 Processing sheet with id=AA4, first strand: chain 'A' and resid 764 through 769 removed outlier: 6.190A pdb=" N SER A 799 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU A 842 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 877 through 879 removed outlier: 6.735A pdb=" N ALA A 878 " --> pdb=" O VAL A 911 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 910 " --> pdb=" O HIS A 934 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL A 936 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 912 " --> pdb=" O VAL A 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 882 through 883 removed outlier: 3.565A pdb=" N GLU A 882 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 544 through 548 removed outlier: 3.649A pdb=" N ASP B 590 " --> pdb=" O PHE B 547 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR B 638 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 589 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 654 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 689 through 690 removed outlier: 3.594A pdb=" N LYS B 690 " --> pdb=" O VAL B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 764 through 770 removed outlier: 6.146A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 877 through 879 removed outlier: 6.931A pdb=" N ALA B 878 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AB3, first strand: chain 'C' and resid 544 through 548 removed outlier: 6.905A pdb=" N ILE C 518 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE C 656 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N CYS C 520 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 619 through 620 Processing sheet with id=AB5, first strand: chain 'C' and resid 689 through 690 removed outlier: 4.016A pdb=" N LYS C 690 " --> pdb=" O VAL C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 765 through 769 removed outlier: 6.102A pdb=" N SER C 799 " --> pdb=" O ILE C 840 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU C 842 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 877 through 879 removed outlier: 7.063A pdb=" N ALA C 878 " --> pdb=" O VAL C 911 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AB9, first strand: chain 'D' and resid 544 through 548 removed outlier: 4.182A pdb=" N ASP D 590 " --> pdb=" O PHE D 547 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE D 587 " --> pdb=" O ILE D 636 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR D 638 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE D 589 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE D 656 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N CYS D 520 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 689 through 690 removed outlier: 3.694A pdb=" N LYS D 690 " --> pdb=" O VAL D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 764 through 771 removed outlier: 5.975A pdb=" N SER D 799 " --> pdb=" O ILE D 840 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU D 842 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 877 through 879 removed outlier: 3.690A pdb=" N ILE D 910 " --> pdb=" O GLU D 932 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 882 through 883 Processing sheet with id=AC5, first strand: chain 'E' and resid 544 through 548 removed outlier: 6.996A pdb=" N PHE E 545 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASP E 590 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE E 587 " --> pdb=" O ILE E 636 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N THR E 638 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE E 589 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE E 518 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE E 656 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N CYS E 520 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 619 through 620 Processing sheet with id=AC7, first strand: chain 'E' and resid 689 through 691 Processing sheet with id=AC8, first strand: chain 'E' and resid 765 through 771 removed outlier: 5.933A pdb=" N SER E 799 " --> pdb=" O ILE E 840 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU E 842 " --> pdb=" O SER E 799 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 877 through 879 removed outlier: 6.907A pdb=" N ALA E 878 " --> pdb=" O VAL E 911 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 882 through 883 Processing sheet with id=AD2, first strand: chain 'F' and resid 544 through 548 removed outlier: 4.370A pdb=" N LEU F 519 " --> pdb=" O PHE F 635 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 518 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 619 through 620 Processing sheet with id=AD4, first strand: chain 'F' and resid 689 through 691 Processing sheet with id=AD5, first strand: chain 'F' and resid 764 through 766 removed outlier: 6.126A pdb=" N SER F 799 " --> pdb=" O ILE F 840 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU F 842 " --> pdb=" O SER F 799 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 769 through 771 Processing sheet with id=AD7, first strand: chain 'F' and resid 877 through 879 removed outlier: 6.953A pdb=" N ALA F 878 " --> pdb=" O VAL F 911 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE F 910 " --> pdb=" O GLU F 932 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 882 through 883 removed outlier: 3.553A pdb=" N GLU F 882 " --> pdb=" O LEU F 890 " (cutoff:3.500A) 1252 hydrogen bonds defined for protein. 3648 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: 5.08 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8592 1.34 - 1.46: 5024 1.46 - 1.58: 12399 1.58 - 1.69: 12 1.69 - 1.81: 196 Bond restraints: 26223 Sorted by residual: bond pdb=" C ASN E 584 " pdb=" N PRO E 585 " ideal model delta sigma weight residual 1.328 1.354 -0.026 1.26e-02 6.30e+03 4.31e+00 bond pdb=" CA VAL F 429 " pdb=" CB VAL F 429 " ideal model delta sigma weight residual 1.527 1.547 -0.020 1.31e-02 5.83e+03 2.44e+00 bond pdb=" CA VAL A 429 " pdb=" CB VAL A 429 " ideal model delta sigma weight residual 1.527 1.545 -0.019 1.31e-02 5.83e+03 2.03e+00 bond pdb=" CA VAL A 658 " pdb=" CB VAL A 658 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.31e-02 5.83e+03 1.72e+00 bond pdb=" CA LEU E 425 " pdb=" C LEU E 425 " ideal model delta sigma weight residual 1.519 1.533 -0.014 1.32e-02 5.74e+03 1.13e+00 ... (remaining 26218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 34947 1.72 - 3.44: 480 3.44 - 5.15: 81 5.15 - 6.87: 29 6.87 - 8.59: 1 Bond angle restraints: 35538 Sorted by residual: angle pdb=" N VAL D 434 " pdb=" CA VAL D 434 " pdb=" C VAL D 434 " ideal model delta sigma weight residual 113.53 108.90 4.63 9.80e-01 1.04e+00 2.23e+01 angle pdb=" N VAL B 549 " pdb=" CA VAL B 549 " pdb=" C VAL B 549 " ideal model delta sigma weight residual 111.91 109.21 2.70 8.90e-01 1.26e+00 9.22e+00 angle pdb=" N VAL A 430 " pdb=" CA VAL A 430 " pdb=" C VAL A 430 " ideal model delta sigma weight residual 108.63 111.12 -2.49 8.60e-01 1.35e+00 8.36e+00 angle pdb=" C GLU F 583 " pdb=" N ASN F 584 " pdb=" CA ASN F 584 " ideal model delta sigma weight residual 122.89 119.81 3.08 1.12e+00 7.97e-01 7.58e+00 angle pdb=" CA VAL F 626 " pdb=" C VAL F 626 " pdb=" N PRO F 627 " ideal model delta sigma weight residual 116.57 119.17 -2.60 9.80e-01 1.04e+00 7.02e+00 ... (remaining 35533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.70: 14849 18.70 - 37.39: 944 37.39 - 56.09: 137 56.09 - 74.79: 29 74.79 - 93.48: 24 Dihedral angle restraints: 15983 sinusoidal: 6296 harmonic: 9687 Sorted by residual: dihedral pdb=" CA ARG E 424 " pdb=" C ARG E 424 " pdb=" N LEU E 425 " pdb=" CA LEU E 425 " ideal model delta harmonic sigma weight residual 180.00 -152.65 -27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" C5' ADP D1001 " pdb=" O5' ADP D1001 " pdb=" PA ADP D1001 " pdb=" O2A ADP D1001 " ideal model delta sinusoidal sigma weight residual -60.00 -153.48 93.48 1 2.00e+01 2.50e-03 2.55e+01 dihedral pdb=" CA ARG D 874 " pdb=" C ARG D 874 " pdb=" N GLN D 875 " pdb=" CA GLN D 875 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 15980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2564 0.030 - 0.059: 995 0.059 - 0.089: 361 0.089 - 0.118: 176 0.118 - 0.148: 22 Chirality restraints: 4118 Sorted by residual: chirality pdb=" CA ILE D 645 " pdb=" N ILE D 645 " pdb=" C ILE D 645 " pdb=" CB ILE D 645 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ILE E 645 " pdb=" N ILE E 645 " pdb=" C ILE E 645 " pdb=" CB ILE E 645 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE B 645 " pdb=" N ILE B 645 " pdb=" C ILE B 645 " pdb=" CB ILE B 645 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 4115 not shown) Planarity restraints: 4578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 738 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO E 739 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 739 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 739 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 761 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO A 762 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 762 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 762 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 738 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO F 739 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 739 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 739 " 0.023 5.00e-02 4.00e+02 ... (remaining 4575 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 228 2.63 - 3.20: 23583 3.20 - 3.77: 39598 3.77 - 4.33: 54110 4.33 - 4.90: 89486 Nonbonded interactions: 207005 Sorted by model distance: nonbonded pdb=" O3B ADP E1001 " pdb="MG MG E1002 " model vdw 2.068 2.170 nonbonded pdb=" O2A ADP E1001 " pdb="MG MG E1002 " model vdw 2.087 2.170 nonbonded pdb=" O2B ADP B1001 " pdb="MG MG B1002 " model vdw 2.120 2.170 nonbonded pdb=" OG1 THR B 530 " pdb="MG MG B1002 " model vdw 2.124 2.170 nonbonded pdb=" O2B ADP C1001 " pdb="MG MG C1002 " model vdw 2.188 2.170 ... (remaining 207000 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' and ((resid 396 through 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 through 410 or (resid 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 448 or (res \ id 449 and (name N or name CA or name C or name O or name CB )) or resid 450 thr \ ough 595 or resid 603 through 631 or (resid 632 and (name N or name CA or name C \ or name O or name CB )) or resid 633 through 685 or (resid 686 and (name N or n \ ame CA or name C or name O or name CB )) or resid 687 through 689 or (resid 690 \ and (name N or name CA or name C or name O or name CB )) or resid 691 through 77 \ 2 or (resid 773 and (name N or name CA or name C or name O or name CB )) or resi \ d 774 through 788 or resid 796 through 836 or (resid 837 and (name N or name CA \ or name C or name O or name CB )) or resid 838 through 948 or (resid 949 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 396 through 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 through 410 or (resid 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 448 or (resid 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 595 or resi \ d 603 through 631 or (resid 632 and (name N or name CA or name C or name O or na \ me CB )) or resid 633 through 685 or (resid 686 and (name N or name CA or name C \ or name O or name CB )) or resid 687 through 689 or (resid 690 and (name N or n \ ame CA or name C or name O or name CB )) or resid 691 through 772 or (resid 773 \ and (name N or name CA or name C or name O or name CB )) or resid 774 through 83 \ 6 or (resid 837 and (name N or name CA or name C or name O or name CB )) or resi \ d 838 through 948 or (resid 949 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'C' and (resid 396 through 410 or (resid 411 and (name N or name CA or na \ me C or name O or name CB )) or resid 412 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 448 or (resid \ 449 and (name N or name CA or name C or name O or name CB )) or resid 450 throug \ h 595 or resid 603 through 631 or (resid 632 and (name N or name CA or name C or \ name O or name CB )) or resid 633 through 685 or (resid 686 and (name N or name \ CA or name C or name O or name CB )) or resid 687 through 689 or (resid 690 and \ (name N or name CA or name C or name O or name CB )) or resid 691 through 772 o \ r (resid 773 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 74 through 788 or resid 790 or resid 797 through 836 or (resid 837 and (name N o \ r name CA or name C or name O or name CB )) or resid 838 through 948 or (resid 9 \ 49 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 396 through 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 through 410 or (resid 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 448 or (resid 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 595 or resi \ d 603 through 631 or (resid 632 and (name N or name CA or name C or name O or na \ me CB )) or resid 633 through 685 or (resid 686 and (name N or name CA or name C \ or name O or name CB )) or resid 687 through 788 or resid 796 through 948 or (r \ esid 949 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and ((resid 396 through 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 through 413 or (resid 414 and (name N or name CA or \ name C or name O or name CB )) or resid 415 through 448 or (resid 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 595 or resi \ d 603 through 631 or (resid 632 and (name N or name CA or name C or name O or na \ me CB )) or resid 633 through 689 or (resid 690 and (name N or name CA or name C \ or name O or name CB )) or resid 691 through 772 or (resid 773 and (name N or n \ ame CA or name C or name O or name CB )) or resid 774 through 788 or resid 796 t \ hrough 836 or (resid 837 and (name N or name CA or name C or name O or name CB ) \ ) or resid 838 through 949)) selection = (chain 'F' and ((resid 396 through 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 through 410 or (resid 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 595 or resi \ d 603 through 685 or (resid 686 and (name N or name CA or name C or name O or na \ me CB )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C \ or name O or name CB )) or resid 691 through 772 or (resid 773 and (name N or n \ ame CA or name C or name O or name CB )) or resid 774 through 788 or resid 796 t \ hrough 836 or (resid 837 and (name N or name CA or name C or name O or name CB ) \ ) or resid 838 through 948 or (resid 949 and (name N or name CA or name C or nam \ e O or name CB )))) } 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.770 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26223 Z= 0.113 Angle : 0.552 8.589 35538 Z= 0.301 Chirality : 0.040 0.148 4118 Planarity : 0.004 0.045 4578 Dihedral : 12.884 93.482 9729 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: 1.22 (0.15), residues: 3287 helix: 1.56 (0.14), residues: 1476 sheet: 0.52 (0.25), residues: 438 loop : 0.20 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 422 TYR 0.010 0.001 TYR A 939 PHE 0.010 0.001 PHE E 547 TRP 0.019 0.001 TRP F 464 HIS 0.003 0.001 HIS D 938 Details of bonding type rmsd covalent geometry : bond 0.00209 (26223) covalent geometry : angle 0.55228 (35538) hydrogen bonds : bond 0.16668 ( 1252) hydrogen bonds : angle 6.55918 ( 3648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.8946 (tpp) cc_final: 0.8136 (tpp) REVERT: A 439 ASP cc_start: 0.8870 (m-30) cc_final: 0.8229 (m-30) REVERT: D 756 MET cc_start: 0.8878 (ttm) cc_final: 0.8525 (ttp) REVERT: E 420 LYS cc_start: 0.8548 (tmtt) cc_final: 0.7685 (tmtt) REVERT: E 574 ILE cc_start: 0.8516 (mm) cc_final: 0.8282 (mm) REVERT: E 766 MET cc_start: 0.8499 (ttt) cc_final: 0.8219 (ttp) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1576 time to fit residues: 60.3833 Evaluate side-chains 168 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 451 HIS ** E 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.113130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.086783 restraints weight = 45653.572| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.56 r_work: 0.3139 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26223 Z= 0.123 Angle : 0.539 9.753 35538 Z= 0.270 Chirality : 0.041 0.163 4118 Planarity : 0.004 0.044 4578 Dihedral : 4.957 103.080 3647 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.48 % Allowed : 4.20 % Favored : 95.32 % 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: 1.31 (0.15), residues: 3287 helix: 1.61 (0.13), residues: 1531 sheet: 0.56 (0.25), residues: 433 loop : 0.23 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 546 TYR 0.012 0.001 TYR D 834 PHE 0.010 0.001 PHE D 547 TRP 0.020 0.001 TRP A 770 HIS 0.006 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00282 (26223) covalent geometry : angle 0.53892 (35538) hydrogen bonds : bond 0.03834 ( 1252) hydrogen bonds : angle 4.95552 ( 3648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.724 Fit side-chains REVERT: B 427 GLU cc_start: 0.7936 (pm20) cc_final: 0.7693 (pm20) REVERT: D 489 GLU cc_start: 0.8445 (tt0) cc_final: 0.8210 (tm-30) REVERT: D 756 MET cc_start: 0.8921 (ttm) cc_final: 0.8539 (ttp) REVERT: E 420 LYS cc_start: 0.8534 (tmtt) cc_final: 0.8314 (tmtt) REVERT: E 574 ILE cc_start: 0.8612 (mm) cc_final: 0.8387 (mm) REVERT: E 869 MET cc_start: 0.8711 (mtm) cc_final: 0.8504 (mtp) outliers start: 13 outliers final: 10 residues processed: 201 average time/residue: 0.1320 time to fit residues: 44.4425 Evaluate side-chains 179 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain F residue 620 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 297 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 59 optimal weight: 80.0000 chunk 149 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 841 HIS ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.110790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.084191 restraints weight = 46314.175| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.60 r_work: 0.3072 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26223 Z= 0.188 Angle : 0.566 9.947 35538 Z= 0.283 Chirality : 0.043 0.184 4118 Planarity : 0.004 0.049 4578 Dihedral : 5.170 104.677 3647 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.92 % Allowed : 6.19 % Favored : 92.89 % 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: 1.23 (0.15), residues: 3287 helix: 1.60 (0.13), residues: 1520 sheet: 0.48 (0.25), residues: 430 loop : 0.13 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 482 TYR 0.016 0.002 TYR C 544 PHE 0.013 0.002 PHE E 820 TRP 0.021 0.001 TRP A 770 HIS 0.005 0.001 HIS E 491 Details of bonding type rmsd covalent geometry : bond 0.00459 (26223) covalent geometry : angle 0.56642 (35538) hydrogen bonds : bond 0.03727 ( 1252) hydrogen bonds : angle 4.67693 ( 3648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: B 427 GLU cc_start: 0.8072 (pm20) cc_final: 0.7727 (pm20) REVERT: C 700 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8520 (mp) REVERT: C 756 MET cc_start: 0.8577 (ttm) cc_final: 0.8354 (ttm) REVERT: D 426 LYS cc_start: 0.8462 (pttm) cc_final: 0.8213 (pttm) REVERT: D 653 MET cc_start: 0.8603 (mtm) cc_final: 0.8335 (mtp) REVERT: D 756 MET cc_start: 0.8903 (ttm) cc_final: 0.8487 (ttm) REVERT: E 574 ILE cc_start: 0.8701 (mm) cc_final: 0.8483 (mm) REVERT: E 869 MET cc_start: 0.8793 (mtm) cc_final: 0.8572 (mtp) outliers start: 25 outliers final: 21 residues processed: 203 average time/residue: 0.1249 time to fit residues: 42.2234 Evaluate side-chains 188 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 620 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 117 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 320 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 265 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 788 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.110916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.084567 restraints weight = 45931.762| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.58 r_work: 0.3077 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26223 Z= 0.153 Angle : 0.539 10.671 35538 Z= 0.267 Chirality : 0.042 0.175 4118 Planarity : 0.004 0.050 4578 Dihedral : 5.123 104.683 3647 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.33 % Allowed : 7.30 % Favored : 91.37 % 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: 1.21 (0.15), residues: 3287 helix: 1.63 (0.13), residues: 1529 sheet: 0.43 (0.25), residues: 437 loop : 0.06 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 482 TYR 0.014 0.001 TYR B 939 PHE 0.013 0.001 PHE E 820 TRP 0.013 0.001 TRP F 464 HIS 0.004 0.001 HIS E 451 Details of bonding type rmsd covalent geometry : bond 0.00369 (26223) covalent geometry : angle 0.53897 (35538) hydrogen bonds : bond 0.03353 ( 1252) hydrogen bonds : angle 4.51078 ( 3648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.679 Fit side-chains REVERT: A 426 LYS cc_start: 0.9344 (mmmm) cc_final: 0.8925 (mtmm) REVERT: A 552 MET cc_start: 0.7700 (tpt) cc_final: 0.7325 (tpt) REVERT: B 421 PHE cc_start: 0.8752 (m-80) cc_final: 0.8540 (m-80) REVERT: B 427 GLU cc_start: 0.8118 (pm20) cc_final: 0.7715 (pm20) REVERT: C 699 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7533 (mt) REVERT: C 700 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8517 (mp) REVERT: C 709 VAL cc_start: 0.7531 (OUTLIER) cc_final: 0.7242 (p) REVERT: C 939 TYR cc_start: 0.8331 (t80) cc_final: 0.8099 (t80) REVERT: D 489 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8495 (tm-30) REVERT: D 653 MET cc_start: 0.8672 (mtm) cc_final: 0.8428 (mtp) REVERT: D 756 MET cc_start: 0.8930 (ttm) cc_final: 0.8519 (ttp) REVERT: E 574 ILE cc_start: 0.8690 (mm) cc_final: 0.8477 (mm) REVERT: E 766 MET cc_start: 0.8814 (ttt) cc_final: 0.8566 (ttt) REVERT: E 869 MET cc_start: 0.8773 (mtm) cc_final: 0.8548 (mtp) outliers start: 36 outliers final: 20 residues processed: 207 average time/residue: 0.1318 time to fit residues: 45.8226 Evaluate side-chains 191 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 879 MET Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 880 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 620 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 270 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 242 optimal weight: 0.0570 chunk 161 optimal weight: 1.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 397 GLN ** E 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.107970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.081625 restraints weight = 45905.123| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.61 r_work: 0.3011 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26223 Z= 0.162 Angle : 0.541 10.722 35538 Z= 0.268 Chirality : 0.042 0.176 4118 Planarity : 0.004 0.050 4578 Dihedral : 5.117 103.912 3647 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.40 % Allowed : 8.81 % Favored : 89.79 % 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: 1.22 (0.15), residues: 3287 helix: 1.67 (0.13), residues: 1531 sheet: 0.43 (0.25), residues: 437 loop : 0.01 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 482 TYR 0.015 0.001 TYR B 939 PHE 0.013 0.001 PHE E 820 TRP 0.015 0.001 TRP F 464 HIS 0.004 0.001 HIS E 491 Details of bonding type rmsd covalent geometry : bond 0.00391 (26223) covalent geometry : angle 0.54120 (35538) hydrogen bonds : bond 0.03333 ( 1252) hydrogen bonds : angle 4.46166 ( 3648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 426 LYS cc_start: 0.9363 (mmmm) cc_final: 0.9010 (mtmm) REVERT: A 552 MET cc_start: 0.7582 (tpt) cc_final: 0.7247 (tpt) REVERT: A 654 GLU cc_start: 0.6672 (pm20) cc_final: 0.6381 (pm20) REVERT: B 421 PHE cc_start: 0.8733 (m-80) cc_final: 0.8483 (m-80) REVERT: B 427 GLU cc_start: 0.8274 (pm20) cc_final: 0.7815 (pm20) REVERT: C 653 MET cc_start: 0.8434 (mtm) cc_final: 0.8116 (mtm) REVERT: C 699 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7424 (mt) REVERT: C 700 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8455 (mp) REVERT: C 709 VAL cc_start: 0.7560 (OUTLIER) cc_final: 0.7265 (p) REVERT: C 808 GLU cc_start: 0.8070 (pm20) cc_final: 0.7582 (pt0) REVERT: D 653 MET cc_start: 0.8690 (mtm) cc_final: 0.8483 (mtp) REVERT: D 756 MET cc_start: 0.8982 (ttm) cc_final: 0.8560 (ttm) REVERT: E 432 LYS cc_start: 0.8712 (tppt) cc_final: 0.8394 (tppt) REVERT: E 574 ILE cc_start: 0.8689 (mm) cc_final: 0.8468 (mm) REVERT: E 766 MET cc_start: 0.8836 (ttt) cc_final: 0.8620 (ttt) REVERT: E 869 MET cc_start: 0.8785 (mtm) cc_final: 0.8536 (mtp) outliers start: 38 outliers final: 29 residues processed: 202 average time/residue: 0.1345 time to fit residues: 45.1870 Evaluate side-chains 198 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain C residue 456 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 773 MET Chi-restraints excluded: chain C residue 879 MET Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 880 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 810 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 29 optimal weight: 2.9990 chunk 259 optimal weight: 0.9990 chunk 325 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 281 optimal weight: 0.9980 chunk 305 optimal weight: 0.0470 chunk 40 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.109723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.083308 restraints weight = 45679.177| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.64 r_work: 0.3046 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26223 Z= 0.098 Angle : 0.507 11.343 35538 Z= 0.248 Chirality : 0.040 0.162 4118 Planarity : 0.004 0.048 4578 Dihedral : 4.931 100.483 3647 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.14 % Allowed : 9.66 % Favored : 89.20 % 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: 1.39 (0.15), residues: 3287 helix: 1.83 (0.13), residues: 1537 sheet: 0.52 (0.25), residues: 432 loop : 0.06 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 482 TYR 0.016 0.001 TYR C 939 PHE 0.013 0.001 PHE F 935 TRP 0.015 0.001 TRP F 464 HIS 0.004 0.001 HIS E 451 Details of bonding type rmsd covalent geometry : bond 0.00223 (26223) covalent geometry : angle 0.50688 (35538) hydrogen bonds : bond 0.02942 ( 1252) hydrogen bonds : angle 4.30648 ( 3648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.985 Fit side-chains REVERT: A 426 LYS cc_start: 0.9311 (mmmm) cc_final: 0.8965 (mtmm) REVERT: A 494 MET cc_start: 0.7604 (ptm) cc_final: 0.7306 (ptm) REVERT: A 552 MET cc_start: 0.7676 (tpt) cc_final: 0.7472 (tpt) REVERT: B 421 PHE cc_start: 0.8734 (m-80) cc_final: 0.8476 (m-80) REVERT: B 427 GLU cc_start: 0.8238 (pm20) cc_final: 0.7751 (pm20) REVERT: C 653 MET cc_start: 0.8383 (mtm) cc_final: 0.8105 (mtm) REVERT: C 700 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8460 (mp) REVERT: C 709 VAL cc_start: 0.7541 (OUTLIER) cc_final: 0.7299 (p) REVERT: D 756 MET cc_start: 0.8961 (ttm) cc_final: 0.8627 (ttp) REVERT: E 426 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8432 (mmmt) REVERT: E 432 LYS cc_start: 0.8738 (tppt) cc_final: 0.8421 (tppt) REVERT: E 574 ILE cc_start: 0.8648 (mm) cc_final: 0.8429 (mm) REVERT: E 766 MET cc_start: 0.8818 (ttt) cc_final: 0.8586 (ttt) REVERT: E 869 MET cc_start: 0.8741 (mtm) cc_final: 0.8472 (mtp) REVERT: F 588 LEU cc_start: 0.8697 (tp) cc_final: 0.8467 (tt) outliers start: 31 outliers final: 22 residues processed: 202 average time/residue: 0.1521 time to fit residues: 52.3537 Evaluate side-chains 189 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain C residue 456 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 773 MET Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 810 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 247 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 319 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 244 optimal weight: 0.9990 chunk 233 optimal weight: 8.9990 chunk 239 optimal weight: 0.9990 chunk 272 optimal weight: 2.9990 chunk 275 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.109570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.083263 restraints weight = 45711.215| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.63 r_work: 0.3051 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26223 Z= 0.103 Angle : 0.511 11.590 35538 Z= 0.249 Chirality : 0.040 0.215 4118 Planarity : 0.004 0.048 4578 Dihedral : 4.858 97.578 3647 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.44 % Allowed : 9.88 % Favored : 88.68 % 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: 1.44 (0.15), residues: 3287 helix: 1.88 (0.13), residues: 1538 sheet: 0.56 (0.25), residues: 430 loop : 0.08 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 482 TYR 0.016 0.001 TYR C 939 PHE 0.013 0.001 PHE E 635 TRP 0.015 0.001 TRP F 464 HIS 0.003 0.001 HIS E 451 Details of bonding type rmsd covalent geometry : bond 0.00240 (26223) covalent geometry : angle 0.51084 (35538) hydrogen bonds : bond 0.02916 ( 1252) hydrogen bonds : angle 4.25700 ( 3648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.901 Fit side-chains REVERT: A 426 LYS cc_start: 0.9289 (mmmm) cc_final: 0.8965 (mtmm) REVERT: A 494 MET cc_start: 0.7653 (ptm) cc_final: 0.7355 (ptm) REVERT: A 552 MET cc_start: 0.7692 (tpt) cc_final: 0.7468 (tpt) REVERT: B 427 GLU cc_start: 0.8211 (pm20) cc_final: 0.7755 (pm20) REVERT: C 699 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7427 (mt) REVERT: C 700 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8494 (mp) REVERT: C 709 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7293 (p) REVERT: C 808 GLU cc_start: 0.8166 (pm20) cc_final: 0.7711 (pt0) REVERT: D 756 MET cc_start: 0.8975 (ttm) cc_final: 0.8654 (ttp) REVERT: E 426 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8481 (mmmt) REVERT: E 432 LYS cc_start: 0.8731 (tppt) cc_final: 0.8414 (tppt) REVERT: E 574 ILE cc_start: 0.8685 (mm) cc_final: 0.8464 (mm) REVERT: E 766 MET cc_start: 0.8798 (ttt) cc_final: 0.8576 (ttt) REVERT: E 869 MET cc_start: 0.8749 (mtm) cc_final: 0.8472 (mtp) outliers start: 39 outliers final: 28 residues processed: 201 average time/residue: 0.1419 time to fit residues: 48.4189 Evaluate side-chains 192 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain C residue 456 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 773 MET Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 777 THR Chi-restraints excluded: chain F residue 810 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 44 optimal weight: 0.3980 chunk 182 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 308 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 244 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.110465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.084246 restraints weight = 45663.389| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.65 r_work: 0.3057 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26223 Z= 0.098 Angle : 0.513 13.336 35538 Z= 0.248 Chirality : 0.040 0.226 4118 Planarity : 0.004 0.070 4578 Dihedral : 4.796 94.431 3647 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.25 % Allowed : 10.54 % Favored : 88.20 % 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: 1.47 (0.15), residues: 3287 helix: 1.93 (0.13), residues: 1538 sheet: 0.57 (0.25), residues: 430 loop : 0.06 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 482 TYR 0.017 0.001 TYR C 939 PHE 0.018 0.001 PHE D 820 TRP 0.017 0.001 TRP F 464 HIS 0.003 0.001 HIS E 451 Details of bonding type rmsd covalent geometry : bond 0.00227 (26223) covalent geometry : angle 0.51282 (35538) hydrogen bonds : bond 0.02878 ( 1252) hydrogen bonds : angle 4.22544 ( 3648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.837 Fit side-chains REVERT: A 426 LYS cc_start: 0.9295 (mmmm) cc_final: 0.8985 (mtmm) REVERT: A 494 MET cc_start: 0.7675 (ptm) cc_final: 0.7367 (ptm) REVERT: B 427 GLU cc_start: 0.8199 (pm20) cc_final: 0.7743 (pm20) REVERT: C 590 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8584 (m-30) REVERT: C 700 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8502 (mp) REVERT: C 709 VAL cc_start: 0.7558 (OUTLIER) cc_final: 0.7329 (p) REVERT: D 756 MET cc_start: 0.9016 (ttm) cc_final: 0.8690 (ttp) REVERT: D 820 PHE cc_start: 0.8613 (t80) cc_final: 0.8198 (t80) REVERT: E 426 LYS cc_start: 0.8753 (mmmt) cc_final: 0.8476 (mmmt) REVERT: E 432 LYS cc_start: 0.8749 (tppt) cc_final: 0.8445 (tppt) REVERT: E 574 ILE cc_start: 0.8658 (mm) cc_final: 0.8431 (mm) REVERT: E 766 MET cc_start: 0.8772 (ttt) cc_final: 0.8549 (ttt) outliers start: 34 outliers final: 27 residues processed: 198 average time/residue: 0.1486 time to fit residues: 49.2165 Evaluate side-chains 195 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain C residue 456 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 773 MET Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 777 THR Chi-restraints excluded: chain F residue 810 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 38 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 59 optimal weight: 80.0000 chunk 291 optimal weight: 6.9990 chunk 115 optimal weight: 30.0000 chunk 319 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 477 ASN F 876 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.107670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.081232 restraints weight = 46190.367| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.62 r_work: 0.3009 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26223 Z= 0.179 Angle : 0.565 12.067 35538 Z= 0.276 Chirality : 0.042 0.228 4118 Planarity : 0.004 0.062 4578 Dihedral : 4.989 95.039 3647 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.44 % Allowed : 10.58 % Favored : 87.98 % 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: 1.30 (0.15), residues: 3287 helix: 1.80 (0.13), residues: 1539 sheet: 0.51 (0.25), residues: 434 loop : -0.05 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 482 TYR 0.019 0.002 TYR C 939 PHE 0.014 0.001 PHE D 820 TRP 0.018 0.001 TRP F 464 HIS 0.004 0.001 HIS E 491 Details of bonding type rmsd covalent geometry : bond 0.00437 (26223) covalent geometry : angle 0.56512 (35538) hydrogen bonds : bond 0.03281 ( 1252) hydrogen bonds : angle 4.34000 ( 3648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 1.058 Fit side-chains REVERT: A 426 LYS cc_start: 0.9325 (mmmm) cc_final: 0.8940 (mtmm) REVERT: A 552 MET cc_start: 0.7806 (tpt) cc_final: 0.7438 (tpt) REVERT: B 427 GLU cc_start: 0.8280 (pm20) cc_final: 0.7819 (pm20) REVERT: B 808 GLU cc_start: 0.7727 (pm20) cc_final: 0.7523 (pm20) REVERT: C 590 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8588 (m-30) REVERT: C 700 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8463 (mp) REVERT: C 709 VAL cc_start: 0.7552 (OUTLIER) cc_final: 0.7259 (p) REVERT: C 808 GLU cc_start: 0.8102 (pm20) cc_final: 0.7528 (pt0) REVERT: D 820 PHE cc_start: 0.8711 (t80) cc_final: 0.8146 (t80) REVERT: E 426 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8459 (mmmt) REVERT: E 432 LYS cc_start: 0.8769 (tppt) cc_final: 0.8459 (tppt) REVERT: E 440 GLU cc_start: 0.8701 (mp0) cc_final: 0.8490 (mp0) REVERT: E 574 ILE cc_start: 0.8720 (mm) cc_final: 0.8498 (mm) REVERT: E 766 MET cc_start: 0.8843 (ttt) cc_final: 0.8637 (ttt) REVERT: E 869 MET cc_start: 0.8794 (mtm) cc_final: 0.8563 (mtp) REVERT: F 876 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7876 (t0) outliers start: 39 outliers final: 28 residues processed: 193 average time/residue: 0.1381 time to fit residues: 45.0961 Evaluate side-chains 191 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 773 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 699 LEU Chi-restraints excluded: chain F residue 810 MET Chi-restraints excluded: chain F residue 876 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 279 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 chunk 273 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 98 optimal weight: 0.0870 chunk 72 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.107794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.081300 restraints weight = 46032.446| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.64 r_work: 0.3012 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 26223 Z= 0.173 Angle : 0.684 59.187 35538 Z= 0.366 Chirality : 0.042 0.576 4118 Planarity : 0.004 0.079 4578 Dihedral : 4.988 95.021 3647 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.25 % Allowed : 10.73 % Favored : 88.02 % Cbeta Deviations : 0.03 % 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: 1.30 (0.15), residues: 3287 helix: 1.81 (0.13), residues: 1539 sheet: 0.49 (0.25), residues: 434 loop : -0.06 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 482 TYR 0.017 0.001 TYR C 939 PHE 0.013 0.001 PHE D 820 TRP 0.016 0.001 TRP F 464 HIS 0.004 0.001 HIS E 491 Details of bonding type rmsd covalent geometry : bond 0.00409 (26223) covalent geometry : angle 0.68416 (35538) hydrogen bonds : bond 0.03255 ( 1252) hydrogen bonds : angle 4.33903 ( 3648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.999 Fit side-chains REVERT: A 426 LYS cc_start: 0.9313 (mmmm) cc_final: 0.8952 (mtmm) REVERT: A 552 MET cc_start: 0.7822 (tpt) cc_final: 0.7465 (tpt) REVERT: B 427 GLU cc_start: 0.8252 (pm20) cc_final: 0.7801 (pm20) REVERT: C 590 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8600 (m-30) REVERT: C 700 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8483 (mp) REVERT: C 709 VAL cc_start: 0.7586 (OUTLIER) cc_final: 0.7292 (p) REVERT: C 808 GLU cc_start: 0.8086 (pm20) cc_final: 0.7531 (pt0) REVERT: D 820 PHE cc_start: 0.8713 (t80) cc_final: 0.8165 (t80) REVERT: E 426 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8490 (mmmt) REVERT: E 432 LYS cc_start: 0.8760 (tppt) cc_final: 0.8461 (tppt) REVERT: E 440 GLU cc_start: 0.8695 (mp0) cc_final: 0.8483 (mp0) REVERT: E 574 ILE cc_start: 0.8728 (mm) cc_final: 0.8508 (mm) REVERT: E 766 MET cc_start: 0.8829 (ttt) cc_final: 0.8622 (ttt) REVERT: E 869 MET cc_start: 0.8800 (mtm) cc_final: 0.8557 (mtp) outliers start: 34 outliers final: 31 residues processed: 184 average time/residue: 0.1240 time to fit residues: 38.7677 Evaluate side-chains 193 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain C residue 456 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 773 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 699 LEU Chi-restraints excluded: chain F residue 810 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 92 optimal weight: 0.7980 chunk 228 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 180 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 280 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.107793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.081316 restraints weight = 45885.583| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.63 r_work: 0.3013 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 26223 Z= 0.173 Angle : 0.684 59.187 35538 Z= 0.366 Chirality : 0.042 0.576 4118 Planarity : 0.004 0.079 4578 Dihedral : 4.988 95.021 3647 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.25 % Allowed : 10.69 % Favored : 88.06 % Cbeta Deviations : 0.03 % 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: 1.30 (0.15), residues: 3287 helix: 1.81 (0.13), residues: 1539 sheet: 0.49 (0.25), residues: 434 loop : -0.06 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 482 TYR 0.017 0.001 TYR C 939 PHE 0.013 0.001 PHE D 820 TRP 0.016 0.001 TRP F 464 HIS 0.004 0.001 HIS E 491 Details of bonding type rmsd covalent geometry : bond 0.00409 (26223) covalent geometry : angle 0.68416 (35538) hydrogen bonds : bond 0.03255 ( 1252) hydrogen bonds : angle 4.33903 ( 3648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4096.22 seconds wall clock time: 71 minutes 34.72 seconds (4294.72 seconds total)