Starting phenix.real_space_refine on Sat Aug 8 05:42:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/31ep_58342/08_2026/31ep_58342.cif Found real_map, /net/cci-nas-00/data/ceres_data/31ep_58342/08_2026/31ep_58342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/31ep_58342/08_2026/31ep_58342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/31ep_58342/08_2026/31ep_58342.map" model { file = "/net/cci-nas-00/data/ceres_data/31ep_58342/08_2026/31ep_58342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/31ep_58342/08_2026/31ep_58342.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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: 8 Type Number sf(0) Gaussians Al 4 5.89 5 P 12 5.49 5 Mg 4 5.21 5 S 120 5.16 5 C 16056 2.51 5 N 4364 2.21 5 O 4850 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25422 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4185 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 25, 'TRANS': 511} Chain: "B" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4185 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 25, 'TRANS': 511} Chain: "C" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4185 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 25, 'TRANS': 511} Chain: "D" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4185 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 25, 'TRANS': 511} Chain: "E" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4185 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 25, 'TRANS': 511} Chain: "F" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4185 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 25, 'TRANS': 511} Chain: "G" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 26 residue: pdb=" N UNK G 74 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 74 " occ=0.50 residue: pdb=" N UNK G 75 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 75 " occ=0.50 residue: pdb=" N UNK G 76 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 76 " occ=0.50 residue: pdb=" N UNK G 77 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 77 " occ=0.50 residue: pdb=" N UNK G 78 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 78 " occ=0.50 residue: pdb=" N UNK G 79 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 79 " occ=0.50 residue: pdb=" N UNK G 80 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 80 " occ=0.50 residue: pdb=" N UNK G 81 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 81 " occ=0.50 residue: pdb=" N UNK G 82 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 82 " occ=0.50 residue: pdb=" N UNK G 83 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 83 " occ=0.50 residue: pdb=" N UNK G 84 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 84 " occ=0.50 residue: pdb=" N UNK G 85 " occ=0.50 ... (3 atoms not shown) pdb=" CB UNK G 85 " occ=0.50 ... (remaining 14 not shown) Time building chain proxies: 4.36, per 1000 atoms: 0.17 Number of scatterers: 25422 At special positions: 0 Unit cell: (132.86, 137.24, 138.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 120 16.00 P 12 15.00 Al 4 13.00 Mg 4 11.99 F 12 9.00 O 4850 8.00 N 4364 7.00 C 16056 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=1, symmetry=0 Links applied TRANS " UNK H 75 " - " UNK G 85 " " UNK H 78 " - " UNK G 82 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 762.5 milliseconds 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6028 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 31 sheets defined 51.1% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 412 through 424 Processing helix chain 'A' and resid 431 through 448 Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.535A pdb=" N ILE A 468 " --> pdb=" O TRP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 removed outlier: 3.533A pdb=" N GLU A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'A' and resid 530 through 541 removed outlier: 4.495A pdb=" N ARG A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 591 through 595 Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.820A pdb=" N ALA A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 removed outlier: 4.274A pdb=" N ALA A 617 " --> pdb=" O PRO A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.689A pdb=" N ARG A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET A 653 " --> pdb=" O LEU A 649 " (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 703 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 834 through 837 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 924 through 929 removed outlier: 3.506A pdb=" N THR A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 947 removed outlier: 3.881A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.237A pdb=" N GLU B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 448 Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.541A pdb=" N ILE B 468 " --> pdb=" O TRP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 Processing helix chain 'B' and resid 494 through 512 Processing helix chain 'B' and resid 530 through 541 removed outlier: 4.418A pdb=" N ARG B 534 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 558 Processing helix chain 'B' and resid 571 through 580 Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 603 through 611 removed outlier: 3.834A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.816A pdb=" N ALA B 617 " --> pdb=" O GLU B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 645 removed outlier: 3.769A pdb=" N THR B 644 " --> pdb=" O VAL B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.733A pdb=" N MET B 653 " --> pdb=" O LEU B 649 " (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 703 Processing helix chain 'B' and resid 709 through 729 Processing helix chain 'B' and resid 741 through 747 removed outlier: 3.951A pdb=" N PHE B 745 " --> pdb=" O ASN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 829 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: 3.506A pdb=" N THR B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 947 removed outlier: 3.942A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 425 removed outlier: 3.607A pdb=" N LEU C 425 " --> pdb=" O PHE C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 448 removed outlier: 3.739A pdb=" N VAL C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.589A pdb=" N ILE C 468 " --> pdb=" O TRP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 489 Processing helix chain 'C' and resid 494 through 512 removed outlier: 3.576A pdb=" N LYS C 498 " --> pdb=" O MET C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 541 removed outlier: 4.163A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 3.696A 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 580 Processing helix chain 'C' and resid 591 through 595 Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.949A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 618 removed outlier: 3.806A pdb=" N ALA C 617 " --> pdb=" O GLU C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.699A pdb=" N MET C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 673 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 730 removed outlier: 3.563A pdb=" N GLY C 730 " --> pdb=" O LYS C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 747 removed outlier: 4.095A pdb=" N PHE C 745 " --> pdb=" O ASN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 829 Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 856 through 870 Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 916 through 922 Processing helix chain 'C' and resid 924 through 929 Processing helix chain 'C' and resid 938 through 947 removed outlier: 3.853A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 425 removed outlier: 3.756A pdb=" N GLU D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 448 Processing helix chain 'D' and resid 452 through 468 removed outlier: 3.517A pdb=" N ASN D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 468 " --> pdb=" O TRP D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 489 removed outlier: 3.530A pdb=" N GLU D 488 " --> pdb=" O GLN D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 512 removed outlier: 3.572A pdb=" N LYS D 498 " --> pdb=" O MET D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 541 removed outlier: 4.026A pdb=" N ARG D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER D 535 " --> pdb=" O SER D 531 " (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 591 through 595 Processing helix chain 'D' and resid 602 through 611 removed outlier: 3.748A pdb=" N ALA D 606 " --> pdb=" O ASP D 602 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 608 " --> pdb=" O SER D 604 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 618 removed outlier: 3.720A pdb=" N ALA D 617 " --> pdb=" O GLU D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.642A pdb=" N ARG D 652 " --> pdb=" O PRO D 648 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET D 653 " --> pdb=" O LEU D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 673 Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 685 through 687 No H-bonds generated for 'chain 'D' and resid 685 through 687' Processing helix chain 'D' and resid 692 through 703 Processing helix chain 'D' and resid 709 through 729 Processing helix chain 'D' and resid 742 through 747 Processing helix chain 'D' and resid 807 through 829 Processing helix chain 'D' and resid 833 through 838 Processing helix chain 'D' and resid 856 through 870 Processing helix chain 'D' and resid 894 through 905 Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 924 through 929 Processing helix chain 'D' and resid 938 through 947 removed outlier: 3.930A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 425 Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.748A pdb=" N VAL E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 468 removed outlier: 3.853A pdb=" N ILE E 468 " --> pdb=" O TRP E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 491 Processing helix chain 'E' and resid 494 through 511 Processing helix chain 'E' and resid 528 through 541 Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 571 through 580 Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.636A pdb=" N ILE E 595 " --> pdb=" O VAL E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 611 removed outlier: 3.969A pdb=" N ALA E 606 " --> pdb=" O ASP E 602 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 610 " --> pdb=" O ALA E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 617 removed outlier: 4.062A pdb=" N ALA E 617 " --> pdb=" O PRO E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 652 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 Processing helix chain 'E' and resid 709 through 729 Processing helix chain 'E' and resid 742 through 747 Processing helix chain 'E' and resid 807 through 829 Processing helix chain 'E' and resid 856 through 870 Processing helix chain 'E' and resid 894 through 905 Processing helix chain 'E' and resid 916 through 922 Processing helix chain 'E' and resid 924 through 929 Processing helix chain 'E' and resid 938 through 947 removed outlier: 3.894A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 425 Processing helix chain 'F' and resid 432 through 447 removed outlier: 4.062A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 447 " --> pdb=" O SER F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 468 removed outlier: 3.746A pdb=" N ILE F 468 " --> pdb=" O TRP F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 490 removed outlier: 3.926A pdb=" N ASP F 490 " --> pdb=" O VAL F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 511 Processing helix chain 'F' and resid 528 through 540 Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 571 through 581 Processing helix chain 'F' and resid 603 through 612 removed outlier: 3.606A pdb=" N LEU F 607 " --> pdb=" O PRO F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 617 Processing helix chain 'F' and resid 646 through 651 Processing helix chain 'F' and resid 662 through 673 removed outlier: 3.613A pdb=" N ILE F 669 " --> pdb=" O GLU F 665 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 683 Processing helix chain 'F' and resid 692 through 703 Processing helix chain 'F' and resid 709 through 729 removed outlier: 3.507A pdb=" N SER F 729 " --> pdb=" O TYR F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 740 No H-bonds generated for 'chain 'F' and resid 738 through 740' Processing helix chain 'F' and resid 741 through 747 removed outlier: 3.969A 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 834 through 838 removed outlier: 4.181A pdb=" N SER F 838 " --> pdb=" O LEU F 835 " (cutoff:3.500A) 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 Processing helix chain 'F' and resid 938 through 947 removed outlier: 3.934A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 548 removed outlier: 6.562A pdb=" N ILE A 587 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR A 638 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE A 589 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 519 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ALA A 639 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE A 521 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE A 518 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE A 656 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N CYS A 520 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 689 through 690 Processing sheet with id=AA3, first strand: chain 'A' and resid 799 through 803 removed outlier: 6.061A pdb=" N SER A 799 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU A 842 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N LEU A 877 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N MET A 766 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA A 878 " --> pdb=" O VAL A 911 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 882 through 884 removed outlier: 4.285A pdb=" N LYS A 888 " --> pdb=" O SER A 884 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 544 through 548 removed outlier: 6.517A pdb=" N ILE B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR B 638 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE B 589 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LYS B 517 " --> pdb=" O PHE B 635 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS B 637 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 519 " --> pdb=" O CYS B 637 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA B 639 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE B 521 " --> pdb=" O ALA B 639 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE B 518 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE B 656 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N CYS B 520 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 765 through 770 removed outlier: 6.238A pdb=" N SER B 799 " --> pdb=" O ILE B 840 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU B 842 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 877 through 879 removed outlier: 6.883A pdb=" N ALA B 878 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AA9, first strand: chain 'C' and resid 544 through 546 removed outlier: 6.745A pdb=" N PHE C 545 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LYS C 517 " --> pdb=" O PHE C 635 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N CYS C 637 " --> pdb=" O LYS C 517 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 519 " --> pdb=" O CYS C 637 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ALA C 639 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE C 521 " --> pdb=" O ALA C 639 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE C 518 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE C 656 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS C 520 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 619 through 620 Processing sheet with id=AB2, first strand: chain 'C' and resid 689 through 690 removed outlier: 3.899A pdb=" N LYS C 690 " --> pdb=" O VAL C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 764 through 769 removed outlier: 6.035A pdb=" N SER C 799 " --> pdb=" O ILE C 840 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU C 842 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 805 through 806 removed outlier: 6.013A pdb=" N GLN C 805 " --> pdb=" O LYS C 851 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 877 through 879 removed outlier: 6.531A pdb=" N ILE C 910 " --> pdb=" O HIS C 934 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL C 936 " --> pdb=" O ILE C 910 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU C 912 " --> pdb=" O VAL C 936 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AB7, first strand: chain 'D' and resid 544 through 548 removed outlier: 6.858A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ASP D 590 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE D 547 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE D 587 " --> pdb=" O ILE D 636 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR D 638 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE D 589 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LYS D 517 " --> pdb=" O PHE D 635 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N CYS D 637 " --> pdb=" O LYS D 517 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU D 519 " --> pdb=" O CYS D 637 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ALA D 639 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE D 521 " --> pdb=" O ALA D 639 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE D 518 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE D 656 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N CYS D 520 " --> pdb=" O ILE D 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 619 through 620 Processing sheet with id=AB9, first strand: chain 'D' and resid 689 through 691 removed outlier: 3.611A pdb=" N LYS D 690 " --> pdb=" O VAL D 735 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL D 737 " --> pdb=" O LYS D 690 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 765 through 771 removed outlier: 6.045A pdb=" N SER D 799 " --> pdb=" O ILE D 840 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU D 842 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 877 through 879 Processing sheet with id=AC3, first strand: chain 'D' and resid 882 through 884 removed outlier: 4.365A pdb=" N LYS D 888 " --> pdb=" O SER D 884 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 544 through 548 removed outlier: 6.364A pdb=" N ILE E 587 " --> pdb=" O ILE E 636 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N THR E 638 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE E 589 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LYS E 517 " --> pdb=" O PHE E 635 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N CYS E 637 " --> pdb=" O LYS E 517 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU E 519 " --> pdb=" O CYS E 637 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ALA E 639 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE E 521 " --> pdb=" O ALA E 639 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE E 518 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE E 656 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS E 520 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 619 through 620 Processing sheet with id=AC6, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.773A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 800 through 803 removed outlier: 9.066A pdb=" N LEU E 877 " --> pdb=" O VAL E 764 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET E 766 " --> pdb=" O LEU E 877 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET E 879 " --> pdb=" O MET E 766 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 768 " --> pdb=" O MET E 879 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.431A pdb=" N LEU F 519 " --> pdb=" O CYS F 637 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ALA F 639 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE F 521 " --> pdb=" O ALA F 639 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE F 518 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 689 through 691 removed outlier: 6.863A pdb=" N LYS F 690 " --> pdb=" O VAL F 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 765 through 769 removed outlier: 5.977A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 877 through 879 Processing sheet with id=AD3, first strand: chain 'F' and resid 882 through 883 Processing sheet with id=AD4, first strand: chain 'G' and resid 76 through 83 1159 hydrogen bonds defined for protein. 3357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8443 1.34 - 1.46: 4440 1.46 - 1.58: 12769 1.58 - 1.69: 30 1.69 - 1.81: 198 Bond restraints: 25880 Sorted by residual: bond pdb=" CB ARG A 721 " pdb=" CG ARG A 721 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.94e+00 bond pdb=" C4 ADP C1001 " pdb=" C5 ADP C1001 " ideal model delta sigma weight residual 1.490 1.456 0.034 2.00e-02 2.50e+03 2.82e+00 bond pdb=" C4 ADP B1001 " pdb=" C5 ADP B1001 " ideal model delta sigma weight residual 1.490 1.457 0.033 2.00e-02 2.50e+03 2.74e+00 bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.458 0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" CA GLN F 515 " pdb=" C GLN F 515 " ideal model delta sigma weight residual 1.520 1.527 -0.008 4.80e-03 4.34e+04 2.49e+00 ... (remaining 25875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 34410 1.92 - 3.84: 547 3.84 - 5.76: 66 5.76 - 7.67: 17 7.67 - 9.59: 2 Bond angle restraints: 35042 Sorted by residual: angle pdb=" N GLU A 846 " pdb=" CA GLU A 846 " pdb=" C GLU A 846 " ideal model delta sigma weight residual 110.91 106.94 3.97 1.17e+00 7.31e-01 1.15e+01 angle pdb=" O2B ADP E1001 " pdb=" PB ADP E1001 " pdb=" O3A ADP E1001 " ideal model delta sigma weight residual 108.20 98.61 9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C HIS A 843 " pdb=" N VAL A 844 " pdb=" CA VAL A 844 " ideal model delta sigma weight residual 123.25 120.09 3.16 1.10e+00 8.26e-01 8.23e+00 angle pdb=" N VAL B 430 " pdb=" CA VAL B 430 " pdb=" C VAL B 430 " ideal model delta sigma weight residual 108.63 111.05 -2.42 8.60e-01 1.35e+00 7.92e+00 angle pdb=" C ARG F 562 " pdb=" N ARG F 563 " pdb=" CA ARG F 563 " ideal model delta sigma weight residual 121.54 126.67 -5.13 1.91e+00 2.74e-01 7.21e+00 ... (remaining 35037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.75: 15504 33.75 - 67.50: 255 67.50 - 101.25: 12 101.25 - 135.00: 11 135.00 - 168.74: 2 Dihedral angle restraints: 15784 sinusoidal: 6412 harmonic: 9372 Sorted by residual: dihedral pdb=" CA UNK G 85 " pdb=" N UNK G 85 " pdb=" C UNK H 75 " pdb=" CA UNK H 75 " ideal model delta harmonic sigma weight residual -180.00 -11.26 -168.74 0 5.00e+00 4.00e-02 1.14e+03 dihedral pdb=" CA UNK G 82 " pdb=" N UNK G 82 " pdb=" C UNK H 78 " pdb=" CA UNK H 78 " ideal model delta harmonic sigma weight residual -180.00 -15.81 -164.19 0 5.00e+00 4.00e-02 1.08e+03 dihedral pdb=" C5' ADP E1001 " pdb=" O5' ADP E1001 " pdb=" PA ADP E1001 " pdb=" O2A ADP E1001 " ideal model delta sinusoidal sigma weight residual 300.00 175.45 124.55 1 2.00e+01 2.50e-03 3.76e+01 ... (remaining 15781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2401 0.031 - 0.062: 1053 0.062 - 0.093: 357 0.093 - 0.124: 170 0.124 - 0.155: 17 Chirality restraints: 3998 Sorted by residual: chirality pdb=" CA ILE F 645 " pdb=" N ILE F 645 " pdb=" C ILE F 645 " pdb=" CB ILE F 645 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA PRO A 845 " pdb=" N PRO A 845 " pdb=" C PRO A 845 " pdb=" CB PRO A 845 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.72e-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 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 3995 not shown) Planarity restraints: 4508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N UNK G 85 " 0.049 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" CA UNK H 75 " 0.003 2.00e-02 2.50e+03 pdb=" C UNK H 75 " -0.074 2.00e-02 2.50e+03 pdb=" O UNK H 75 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 947 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO D 948 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 948 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 948 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 430 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO F 431 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO F 431 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 431 " -0.022 5.00e-02 4.00e+02 ... (remaining 4505 not shown) Histogram of nonbonded interaction distances: 0.15 - 1.10: 57 1.10 - 2.05: 157 2.05 - 3.00: 14427 3.00 - 3.95: 68509 3.95 - 4.90: 132020 Warning: very small nonbonded interaction distances. Nonbonded interactions: 215170 Sorted by model distance: nonbonded pdb=" CB UNK G 84 " pdb=" CB UNK H 76 " model vdw 0.148 3.840 nonbonded pdb=" CA UNK G 86 " pdb=" CA UNK H 74 " model vdw 0.353 3.900 nonbonded pdb=" CB UNK G 80 " pdb=" CB UNK H 80 " model vdw 0.429 3.840 nonbonded pdb=" CB UNK G 81 " pdb=" CB UNK H 79 " model vdw 0.435 3.840 nonbonded pdb=" CB UNK G 77 " pdb=" CB UNK H 83 " model vdw 0.451 3.840 ... (remaining 215165 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 412 through 1001) selection = (chain 'B' and resid 412 through 1001) selection = (chain 'C' and resid 412 through 1001) selection = (chain 'D' and resid 412 through 1001) selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.50 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: 10.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.070 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 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 : 0.008 0.809 25883 Z= 0.507 Angle : 0.911 79.344 35048 Z= 0.502 Chirality : 0.042 0.155 3998 Planarity : 0.005 0.047 4506 Dihedral : 12.912 124.554 9750 Min Nonbonded Distance : 0.148 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.11 % Favored : 95.30 % Rotamer: Outliers : 2.16 % Allowed : 5.99 % Favored : 91.85 % 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 are not related in a simple way. whole: -1.14 (0.14), residues: 3210 helix: -1.31 (0.10), residues: 1432 sheet: -1.47 (0.22), residues: 434 loop : 0.50 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 904 TYR 0.019 0.002 TYR A 939 PHE 0.027 0.002 PHE C 547 TRP 0.005 0.001 TRP F 770 HIS 0.005 0.001 HIS F 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (25880) covalent geometry : angle 0.64094 / 0.35 (35042) hydrogen bonds : bond 0.16068 / 10.52 ( 1159) hydrogen bonds : angle 8.89930 / 6.23 ( 3357) Misc. bond : bond 0.02681 / 1.41 ( 1) link_TRANS : bond 0.72047 / 35.68 ( 2) link_TRANS : angle 49.49826 / 29.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 355 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 ARG cc_start: 0.8134 (ttm-80) cc_final: 0.7870 (ttm110) REVERT: A 499 LYS cc_start: 0.8135 (mttm) cc_final: 0.7839 (mmtt) REVERT: A 793 LYS cc_start: 0.1805 (OUTLIER) cc_final: 0.1354 (tttm) REVERT: B 423 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7730 (mm-30) REVERT: B 563 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7987 (ptt180) REVERT: B 929 GLU cc_start: 0.8557 (tt0) cc_final: 0.8343 (pt0) REVERT: C 426 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8542 (mmtt) REVERT: C 488 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7901 (tp30) REVERT: C 547 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.7717 (p90) REVERT: C 569 MET cc_start: 0.8997 (ptm) cc_final: 0.8718 (ptt) REVERT: C 599 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.6405 (p90) REVERT: C 625 ASP cc_start: 0.8615 (m-30) cc_final: 0.8316 (m-30) REVERT: C 918 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8058 (pttt) REVERT: D 773 MET cc_start: 0.6988 (pp-130) cc_final: 0.6558 (pp-130) REVERT: D 793 LYS cc_start: 0.5744 (OUTLIER) cc_final: 0.4351 (mptt) REVERT: E 429 VAL cc_start: 0.7530 (t) cc_final: 0.7241 (m) REVERT: E 456 ASN cc_start: 0.7264 (t0) cc_final: 0.7006 (t0) REVERT: E 460 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7377 (m-40) REVERT: E 562 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7565 (ttm170) REVERT: E 583 GLU cc_start: 0.8012 (tp30) cc_final: 0.7748 (mm-30) REVERT: E 591 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8013 (mm-30) REVERT: E 602 ASP cc_start: 0.7412 (m-30) cc_final: 0.7028 (t0) REVERT: E 609 GLU cc_start: 0.8600 (tt0) cc_final: 0.8345 (tt0) REVERT: E 625 ASP cc_start: 0.7280 (m-30) cc_final: 0.6827 (t0) REVERT: E 896 LYS cc_start: 0.8726 (tppt) cc_final: 0.8414 (tptt) REVERT: F 449 ASP cc_start: 0.6888 (t70) cc_final: 0.6536 (t0) REVERT: F 499 LYS cc_start: 0.8327 (ptpt) cc_final: 0.8102 (ptmm) REVERT: F 549 VAL cc_start: 0.9013 (t) cc_final: 0.8788 (m) REVERT: F 562 ARG cc_start: 0.7115 (mmt90) cc_final: 0.6780 (mmm-85) REVERT: F 652 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7723 (ttm-80) REVERT: F 781 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8451 (pt0) outliers start: 59 outliers final: 11 residues processed: 402 average time/residue: 0.6730 time to fit residues: 306.2708 Evaluate side-chains 259 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 PHE Chi-restraints excluded: chain C residue 599 TYR Chi-restraints excluded: chain C residue 918 LYS Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 793 LYS Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 851 LYS Chi-restraints excluded: chain F residue 640 ASN Chi-restraints excluded: chain F residue 781 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 0.0670 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.0370 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 GLN B 433 HIS C 456 ASN ** C 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** F 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 451 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.108489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.075501 restraints weight = 38533.629| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.33 r_work: 0.2784 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 25883 Z= 0.173 Angle : 0.840 43.279 35048 Z= 0.408 Chirality : 0.044 0.476 3998 Planarity : 0.005 0.097 4506 Dihedral : 9.488 131.841 3632 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.41 % Allowed : 11.18 % Favored : 86.40 % 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 are not related in a simple way. whole: 0.12 (0.14), residues: 3210 helix: 0.59 (0.13), residues: 1452 sheet: -0.73 (0.24), residues: 409 loop : -0.02 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 786 TYR 0.038 0.002 TYR D 565 PHE 0.024 0.002 PHE D 947 TRP 0.010 0.001 TRP F 770 HIS 0.007 0.001 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (25880) covalent geometry : angle 0.79348 / 0.38 (35042) hydrogen bonds : bond 0.04621 / 3.14 ( 1159) hydrogen bonds : angle 6.25488 / 4.27 ( 3357) Misc. bond : bond 0.00024 / 0.01 ( 1) link_TRANS : bond 0.05947 / 3.12 ( 2) link_TRANS : angle 21.05714 / 9.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 264 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8356 (p0) REVERT: A 423 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8541 (tp30) REVERT: A 459 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.8080 (ttm110) REVERT: A 499 LYS cc_start: 0.8334 (mttm) cc_final: 0.8014 (mmmt) REVERT: A 846 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7740 (mm-30) REVERT: B 423 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7860 (mm-30) REVERT: B 426 LYS cc_start: 0.8455 (mtpp) cc_final: 0.8233 (mtmm) REVERT: B 482 ARG cc_start: 0.8065 (ttt-90) cc_final: 0.7749 (ttt-90) REVERT: B 563 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8721 (ptt-90) REVERT: B 929 GLU cc_start: 0.8653 (tt0) cc_final: 0.8425 (pt0) REVERT: C 426 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8610 (mmtt) REVERT: C 488 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7947 (tp30) REVERT: C 547 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7844 (p90) REVERT: D 435 MET cc_start: 0.8739 (tpt) cc_final: 0.8508 (tpt) REVERT: D 552 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7712 (ttm) REVERT: D 773 MET cc_start: 0.7022 (pp-130) cc_final: 0.6789 (pp-130) REVERT: D 793 LYS cc_start: 0.5696 (OUTLIER) cc_final: 0.4363 (mptt) REVERT: D 846 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: D 915 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8605 (mt-10) REVERT: E 591 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8312 (mm-30) REVERT: E 602 ASP cc_start: 0.7435 (m-30) cc_final: 0.6972 (t0) REVERT: E 609 GLU cc_start: 0.8698 (tt0) cc_final: 0.8490 (tt0) REVERT: E 851 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8415 (mttp) REVERT: E 896 LYS cc_start: 0.8943 (tppt) cc_final: 0.8626 (tptt) REVERT: F 449 ASP cc_start: 0.6724 (t70) cc_final: 0.6394 (t0) REVERT: F 499 LYS cc_start: 0.8431 (ptpt) cc_final: 0.8222 (ptmm) REVERT: F 781 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8383 (pt0) REVERT: F 826 MET cc_start: 0.8890 (tpp) cc_final: 0.8617 (tpp) REVERT: F 897 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8448 (mp0) outliers start: 66 outliers final: 21 residues processed: 303 average time/residue: 0.6757 time to fit residues: 232.9950 Evaluate side-chains 268 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 PHE Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 918 LYS Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 793 LYS Chi-restraints excluded: chain D residue 846 GLU Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 915 GLU Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 851 LYS Chi-restraints excluded: chain E residue 923 LEU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 641 VAL Chi-restraints excluded: chain F residue 781 GLU Chi-restraints excluded: chain F residue 846 GLU Chi-restraints excluded: chain F residue 897 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 269 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 233 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 255 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 143 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 HIS ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN E 451 HIS F 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.109692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.076819 restraints weight = 38731.965| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.31 r_work: 0.2825 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 25883 Z= 0.143 Angle : 0.769 48.812 35048 Z= 0.371 Chirality : 0.042 0.299 3998 Planarity : 0.005 0.091 4506 Dihedral : 8.870 128.025 3622 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 2.49 % Allowed : 12.46 % Favored : 85.05 % 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 are not related in a simple way. whole: 0.72 (0.15), residues: 3210 helix: 1.40 (0.13), residues: 1452 sheet: -0.24 (0.25), residues: 401 loop : -0.22 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 597 TYR 0.019 0.002 TYR C 599 PHE 0.020 0.001 PHE F 547 TRP 0.017 0.001 TRP F 770 HIS 0.005 0.001 HIS F 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (25880) covalent geometry : angle 0.71309 / 0.34 (35042) hydrogen bonds : bond 0.03830 / 2.66 ( 1159) hydrogen bonds : angle 5.61714 / 3.70 ( 3357) Misc. bond : bond 0.00013 / 0.01 ( 1) link_TRANS : bond 0.05023 / 2.61 ( 2) link_TRANS : angle 22.01510 / 9.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 260 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8349 (p0) REVERT: A 423 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8473 (tp30) REVERT: A 459 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8113 (ttm110) REVERT: A 499 LYS cc_start: 0.8294 (mttm) cc_final: 0.7956 (mmmt) REVERT: A 846 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7782 (mm-30) REVERT: B 423 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7853 (mm-30) REVERT: B 482 ARG cc_start: 0.8105 (ttt-90) cc_final: 0.7854 (ttt-90) REVERT: B 846 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7801 (mm-30) REVERT: C 426 LYS cc_start: 0.8965 (mtpp) cc_final: 0.8626 (mmtt) REVERT: C 435 MET cc_start: 0.9106 (tpt) cc_final: 0.8866 (mmm) REVERT: C 454 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7992 (mm-30) REVERT: C 547 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7953 (p90) REVERT: C 569 MET cc_start: 0.9093 (ptm) cc_final: 0.8837 (ptt) REVERT: C 846 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8016 (mp0) REVERT: D 440 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: D 590 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8516 (t0) REVERT: D 773 MET cc_start: 0.7010 (pp-130) cc_final: 0.6743 (pp-130) REVERT: D 776 SER cc_start: 0.8907 (p) cc_final: 0.8705 (m) REVERT: D 793 LYS cc_start: 0.5732 (OUTLIER) cc_final: 0.4463 (mptt) REVERT: D 846 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: D 915 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8595 (mt-10) REVERT: E 456 ASN cc_start: 0.7162 (OUTLIER) cc_final: 0.6880 (m-40) REVERT: E 591 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8325 (mm-30) REVERT: E 602 ASP cc_start: 0.7432 (m-30) cc_final: 0.6919 (t0) REVERT: E 620 LEU cc_start: 0.8850 (tp) cc_final: 0.8446 (tm) REVERT: E 710 ARG cc_start: 0.8019 (mmm160) cc_final: 0.7772 (mmm160) REVERT: E 896 LYS cc_start: 0.8933 (tppt) cc_final: 0.8601 (tptt) REVERT: E 922 ASP cc_start: 0.8268 (t70) cc_final: 0.8044 (OUTLIER) REVERT: F 449 ASP cc_start: 0.6598 (t70) cc_final: 0.6306 (t0) REVERT: F 499 LYS cc_start: 0.8435 (ptpt) cc_final: 0.8220 (ptmm) REVERT: F 632 LYS cc_start: 0.8259 (tppp) cc_final: 0.8035 (tptp) REVERT: F 897 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8408 (mp0) outliers start: 68 outliers final: 24 residues processed: 301 average time/residue: 0.6416 time to fit residues: 219.6616 Evaluate side-chains 269 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 599 TYR Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain C residue 547 PHE Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 918 LYS Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 793 LYS Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 846 GLU Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 915 GLU Chi-restraints excluded: chain E residue 456 ASN Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain F residue 456 ASN Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 640 ASN Chi-restraints excluded: chain F residue 641 VAL Chi-restraints excluded: chain F residue 897 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 68 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 HIS ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.107708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.074482 restraints weight = 38431.780| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.31 r_work: 0.2782 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 25883 Z= 0.193 Angle : 0.786 48.783 35048 Z= 0.378 Chirality : 0.043 0.266 3998 Planarity : 0.005 0.094 4506 Dihedral : 8.645 124.841 3604 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 2.85 % Allowed : 12.65 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.15), residues: 3210 helix: 1.58 (0.13), residues: 1453 sheet: 0.03 (0.25), residues: 405 loop : -0.38 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 597 TYR 0.021 0.002 TYR A 939 PHE 0.024 0.002 PHE C 547 TRP 0.023 0.001 TRP F 770 HIS 0.005 0.001 HIS F 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (25880) covalent geometry : angle 0.73244 / 0.35 (35042) hydrogen bonds : bond 0.04280 / 2.95 ( 1159) hydrogen bonds : angle 5.57323 / 3.65 ( 3357) Misc. bond : bond 0.00024 / 0.01 ( 1) link_TRANS : bond 0.05350 / 2.78 ( 2) link_TRANS : angle 21.84129 / 9.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 250 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8353 (p0) REVERT: A 423 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8458 (tp30) REVERT: A 459 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.8193 (ttm110) REVERT: A 499 LYS cc_start: 0.8354 (mttm) cc_final: 0.8014 (mmtt) REVERT: A 846 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7873 (mm-30) REVERT: B 412 ASP cc_start: 0.4938 (OUTLIER) cc_final: 0.4557 (m-30) REVERT: B 423 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7866 (mm-30) REVERT: B 482 ARG cc_start: 0.8117 (ttt-90) cc_final: 0.7732 (ttt-90) REVERT: B 597 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7603 (ttm170) REVERT: B 647 GLU cc_start: 0.8824 (tp30) cc_final: 0.8555 (tt0) REVERT: C 426 LYS cc_start: 0.8984 (mtpp) cc_final: 0.8686 (mmtt) REVERT: C 454 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8054 (mm-30) REVERT: C 547 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8064 (p90) REVERT: D 440 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: D 552 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7668 (ttm) REVERT: D 773 MET cc_start: 0.7048 (pp-130) cc_final: 0.6749 (pp-130) REVERT: D 793 LYS cc_start: 0.5743 (OUTLIER) cc_final: 0.4523 (mptt) REVERT: D 846 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: D 915 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8614 (mt-10) REVERT: E 456 ASN cc_start: 0.7070 (OUTLIER) cc_final: 0.6788 (m-40) REVERT: E 462 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6467 (mm) REVERT: E 489 GLU cc_start: 0.8862 (pp20) cc_final: 0.8476 (pp20) REVERT: E 557 GLU cc_start: 0.7402 (mp0) cc_final: 0.7162 (mp0) REVERT: E 591 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8291 (mm-30) REVERT: E 602 ASP cc_start: 0.7547 (m-30) cc_final: 0.7017 (t0) REVERT: E 620 LEU cc_start: 0.8870 (tp) cc_final: 0.8502 (tm) REVERT: E 624 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6657 (pp) REVERT: E 710 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7816 (mmm160) REVERT: F 449 ASP cc_start: 0.6641 (t70) cc_final: 0.6343 (t0) REVERT: F 499 LYS cc_start: 0.8451 (ptpt) cc_final: 0.8220 (ptmm) REVERT: F 632 LYS cc_start: 0.8269 (tppp) cc_final: 0.7867 (tptt) REVERT: F 826 MET cc_start: 0.8977 (tpp) cc_final: 0.8694 (tpp) REVERT: F 846 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: F 897 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8403 (mp0) outliers start: 78 outliers final: 28 residues processed: 301 average time/residue: 0.6094 time to fit residues: 209.8810 Evaluate side-chains 284 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 599 TYR Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 547 PHE Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 918 LYS Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 793 LYS Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 846 GLU Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 915 GLU Chi-restraints excluded: chain E residue 456 ASN Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain F residue 456 ASN Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 641 VAL Chi-restraints excluded: chain F residue 846 GLU Chi-restraints excluded: chain F residue 897 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 94 optimal weight: 0.2980 chunk 252 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 chunk 219 optimal weight: 0.6980 chunk 126 optimal weight: 0.4980 chunk 207 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 315 optimal weight: 2.9990 chunk 124 optimal weight: 0.0570 chunk 173 optimal weight: 0.8980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 HIS ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN D 561 HIS E 451 HIS F 451 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.110646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.077697 restraints weight = 38360.646| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.32 r_work: 0.2833 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 25883 Z= 0.124 Angle : 0.729 42.775 35048 Z= 0.352 Chirality : 0.040 0.269 3998 Planarity : 0.004 0.095 4506 Dihedral : 8.098 129.334 3604 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 2.45 % Allowed : 13.82 % Favored : 83.74 % 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 are not related in a simple way. whole: 1.10 (0.15), residues: 3210 helix: 1.85 (0.14), residues: 1458 sheet: 0.38 (0.26), residues: 394 loop : -0.36 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 562 TYR 0.014 0.001 TYR A 939 PHE 0.020 0.001 PHE F 547 TRP 0.024 0.001 TRP F 770 HIS 0.002 0.001 HIS F 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (25880) covalent geometry : angle 0.67756 / 0.32 (35042) hydrogen bonds : bond 0.03420 / 2.38 ( 1159) hydrogen bonds : angle 5.31150 / 3.43 ( 3357) Misc. bond : bond 0.00027 / 0.01 ( 1) link_TRANS : bond 0.05853 / 3.03 ( 2) link_TRANS : angle 20.52115 / 8.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 269 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8344 (p0) REVERT: A 423 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8408 (tp30) REVERT: A 459 ARG cc_start: 0.8384 (ttm-80) cc_final: 0.8148 (ttm110) REVERT: A 499 LYS cc_start: 0.8284 (mttm) cc_final: 0.7947 (mmmt) REVERT: A 846 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7780 (mm-30) REVERT: B 423 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7976 (mm-30) REVERT: B 482 ARG cc_start: 0.8111 (ttt-90) cc_final: 0.7594 (ttt-90) REVERT: B 597 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7625 (ttm170) REVERT: B 647 GLU cc_start: 0.8800 (tp30) cc_final: 0.8546 (tt0) REVERT: C 426 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8603 (mmtt) REVERT: C 435 MET cc_start: 0.9104 (tpt) cc_final: 0.8861 (mmm) REVERT: C 454 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7983 (mm-30) REVERT: C 741 ASN cc_start: 0.7525 (t0) cc_final: 0.7303 (t0) REVERT: C 846 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7874 (mp0) REVERT: D 479 ASP cc_start: 0.8158 (p0) cc_final: 0.7931 (p0) REVERT: D 552 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7580 (ttm) REVERT: D 647 GLU cc_start: 0.8726 (tp30) cc_final: 0.8486 (tp30) REVERT: D 741 ASN cc_start: 0.8057 (t0) cc_final: 0.7793 (t0) REVERT: D 773 MET cc_start: 0.6957 (pp-130) cc_final: 0.6670 (pp-130) REVERT: D 915 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8655 (mt-10) REVERT: D 918 LYS cc_start: 0.8609 (tptt) cc_final: 0.8381 (tppt) REVERT: E 456 ASN cc_start: 0.7113 (OUTLIER) cc_final: 0.6831 (m-40) REVERT: E 462 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6382 (mm) REVERT: E 489 GLU cc_start: 0.8861 (pp20) cc_final: 0.8425 (pp20) REVERT: E 492 TYR cc_start: 0.8406 (t80) cc_final: 0.8165 (t80) REVERT: E 577 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8190 (mm) REVERT: E 591 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8214 (mm-30) REVERT: E 602 ASP cc_start: 0.7556 (m-30) cc_final: 0.6984 (t0) REVERT: E 620 LEU cc_start: 0.8894 (tp) cc_final: 0.8553 (tm) REVERT: E 624 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6601 (pp) REVERT: F 449 ASP cc_start: 0.6573 (t70) cc_final: 0.6270 (t0) REVERT: F 451 HIS cc_start: 0.7272 (m90) cc_final: 0.7059 (m-70) REVERT: F 499 LYS cc_start: 0.8389 (ptpt) cc_final: 0.8157 (ptmm) REVERT: F 554 ASP cc_start: 0.7463 (t0) cc_final: 0.7218 (t0) REVERT: F 557 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7691 (pm20) REVERT: F 632 LYS cc_start: 0.8209 (tppp) cc_final: 0.7842 (tptt) REVERT: F 826 MET cc_start: 0.8925 (tpp) cc_final: 0.8667 (tpp) REVERT: F 846 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: F 897 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8358 (mp0) outliers start: 67 outliers final: 29 residues processed: 311 average time/residue: 0.6887 time to fit residues: 244.4257 Evaluate side-chains 285 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 599 TYR Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 776 SER Chi-restraints excluded: chain C residue 918 LYS Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 915 GLU Chi-restraints excluded: chain E residue 456 ASN Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 630 LEU Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain F residue 456 ASN Chi-restraints excluded: chain F residue 557 GLU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 640 ASN Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 846 GLU Chi-restraints excluded: chain F residue 897 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 243 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.0470 chunk 260 optimal weight: 0.9990 chunk 301 optimal weight: 4.9990 chunk 140 optimal weight: 0.0570 chunk 138 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 HIS ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.109480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.076435 restraints weight = 38735.238| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.39 r_work: 0.2818 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 25883 Z= 0.146 Angle : 0.639 17.590 35048 Z= 0.313 Chirality : 0.041 0.257 3998 Planarity : 0.004 0.096 4506 Dihedral : 7.967 133.151 3598 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.80 % Favored : 97.17 % Rotamer: Outliers : 2.27 % Allowed : 14.55 % Favored : 83.19 % 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 are not related in a simple way. whole: 1.15 (0.15), residues: 3210 helix: 1.89 (0.14), residues: 1465 sheet: 0.39 (0.25), residues: 403 loop : -0.34 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 597 TYR 0.018 0.001 TYR A 939 PHE 0.021 0.001 PHE F 547 TRP 0.023 0.001 TRP F 770 HIS 0.004 0.001 HIS F 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (25880) covalent geometry : angle 0.62796 / 0.31 (35042) hydrogen bonds : bond 0.03721 / 2.65 ( 1159) hydrogen bonds : angle 5.26765 / 3.43 ( 3357) Misc. bond : bond 0.00035 / 0.02 ( 1) link_TRANS : bond 0.05620 / 2.90 ( 2) link_TRANS : angle 9.18679 / 3.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 261 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8347 (p0) REVERT: A 423 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8474 (tp30) REVERT: A 459 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.8192 (ttm110) REVERT: A 499 LYS cc_start: 0.8292 (mttm) cc_final: 0.7958 (mmmt) REVERT: A 846 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7844 (mm-30) REVERT: B 412 ASP cc_start: 0.4921 (OUTLIER) cc_final: 0.4565 (m-30) REVERT: B 423 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7989 (mm-30) REVERT: B 482 ARG cc_start: 0.8102 (ttt-90) cc_final: 0.7536 (ttt-90) REVERT: B 597 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7870 (ttm170) REVERT: B 647 GLU cc_start: 0.8848 (tp30) cc_final: 0.8608 (tt0) REVERT: C 415 ASP cc_start: 0.7409 (p0) cc_final: 0.7124 (t0) REVERT: C 426 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8643 (mttp) REVERT: C 435 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8884 (mmm) REVERT: C 454 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8134 (mm-30) REVERT: C 741 ASN cc_start: 0.7600 (t0) cc_final: 0.7353 (t0) REVERT: C 846 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8006 (mp0) REVERT: D 426 LYS cc_start: 0.8235 (mtpp) cc_final: 0.8031 (ptpp) REVERT: D 440 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: D 552 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7588 (ttm) REVERT: D 647 GLU cc_start: 0.8732 (tp30) cc_final: 0.8469 (tp30) REVERT: D 741 ASN cc_start: 0.8072 (t0) cc_final: 0.7761 (t0) REVERT: D 773 MET cc_start: 0.6986 (pp-130) cc_final: 0.6697 (pp-130) REVERT: D 915 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8668 (mt-10) REVERT: D 918 LYS cc_start: 0.8627 (tptt) cc_final: 0.8390 (tppt) REVERT: E 456 ASN cc_start: 0.7064 (OUTLIER) cc_final: 0.6773 (m-40) REVERT: E 462 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6436 (mm) REVERT: E 489 GLU cc_start: 0.8870 (pp20) cc_final: 0.8403 (pp20) REVERT: E 577 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8178 (mm) REVERT: E 591 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8209 (mm-30) REVERT: E 602 ASP cc_start: 0.7599 (m-30) cc_final: 0.6955 (t0) REVERT: E 620 LEU cc_start: 0.8960 (tp) cc_final: 0.8613 (tm) REVERT: E 624 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6717 (pt) REVERT: E 710 ARG cc_start: 0.8003 (mmm160) cc_final: 0.7674 (tpm-80) REVERT: F 449 ASP cc_start: 0.6670 (t70) cc_final: 0.6374 (t0) REVERT: F 451 HIS cc_start: 0.7226 (m90) cc_final: 0.6996 (m-70) REVERT: F 499 LYS cc_start: 0.8395 (ptpt) cc_final: 0.8165 (ptmm) REVERT: F 557 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7780 (pm20) REVERT: F 632 LYS cc_start: 0.8204 (tppp) cc_final: 0.7852 (tptt) REVERT: F 826 MET cc_start: 0.8934 (tpp) cc_final: 0.8691 (tpp) REVERT: F 846 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: F 897 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8386 (mp0) outliers start: 62 outliers final: 24 residues processed: 296 average time/residue: 0.6490 time to fit residues: 219.8624 Evaluate side-chains 280 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 243 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 599 TYR Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 918 LYS Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 477 ASN Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 915 GLU Chi-restraints excluded: chain E residue 456 ASN Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain F residue 557 GLU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 641 VAL Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 846 GLU Chi-restraints excluded: chain F residue 897 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 225 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 280 optimal weight: 0.0070 chunk 317 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 300 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 HIS ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.110025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.077093 restraints weight = 38188.108| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.30 r_work: 0.2828 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 25883 Z= 0.139 Angle : 0.635 16.955 35048 Z= 0.310 Chirality : 0.041 0.262 3998 Planarity : 0.004 0.096 4506 Dihedral : 7.921 136.097 3598 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 2.01 % Allowed : 15.28 % Favored : 82.71 % 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 are not related in a simple way. whole: 1.21 (0.15), residues: 3210 helix: 1.93 (0.14), residues: 1466 sheet: 0.49 (0.26), residues: 402 loop : -0.33 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 511 TYR 0.019 0.001 TYR E 565 PHE 0.021 0.001 PHE F 547 TRP 0.026 0.001 TRP F 770 HIS 0.003 0.001 HIS C 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (25880) covalent geometry : angle 0.62579 / 0.30 (35042) hydrogen bonds : bond 0.03678 / 2.64 ( 1159) hydrogen bonds : angle 5.21102 / 3.39 ( 3357) Misc. bond : bond 0.00034 / 0.02 ( 1) link_TRANS : bond 0.05678 / 2.93 ( 2) link_TRANS : angle 8.46536 / 3.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8340 (p0) REVERT: A 423 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8433 (tp30) REVERT: A 459 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.8181 (ttm110) REVERT: A 499 LYS cc_start: 0.8307 (mttm) cc_final: 0.7971 (mmmt) REVERT: A 846 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7827 (mm-30) REVERT: B 412 ASP cc_start: 0.4915 (OUTLIER) cc_final: 0.4593 (m-30) REVERT: B 423 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7974 (mm-30) REVERT: B 482 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.7544 (ttt-90) REVERT: B 490 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7500 (m-30) REVERT: B 597 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7834 (ttm170) REVERT: B 647 GLU cc_start: 0.8826 (tp30) cc_final: 0.8582 (tt0) REVERT: B 846 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7868 (mm-30) REVERT: C 415 ASP cc_start: 0.7426 (p0) cc_final: 0.7061 (t0) REVERT: C 426 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8691 (mmtm) REVERT: C 435 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8810 (mmm) REVERT: C 454 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8114 (mm-30) REVERT: C 741 ASN cc_start: 0.7529 (t0) cc_final: 0.7297 (t0) REVERT: C 786 ARG cc_start: 0.8526 (mtm110) cc_final: 0.8096 (mtp180) REVERT: C 846 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7901 (mp0) REVERT: D 440 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: D 552 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7605 (ttm) REVERT: D 647 GLU cc_start: 0.8735 (tp30) cc_final: 0.8520 (tp30) REVERT: D 741 ASN cc_start: 0.8096 (t0) cc_final: 0.7772 (t0) REVERT: D 773 MET cc_start: 0.6992 (pp-130) cc_final: 0.6707 (pp-130) REVERT: D 915 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8641 (mt-10) REVERT: E 456 ASN cc_start: 0.7034 (OUTLIER) cc_final: 0.6752 (m-40) REVERT: E 462 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6408 (mm) REVERT: E 489 GLU cc_start: 0.8873 (pp20) cc_final: 0.8395 (pp20) REVERT: E 577 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8156 (mm) REVERT: E 591 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8177 (mm-30) REVERT: E 602 ASP cc_start: 0.7622 (m-30) cc_final: 0.6992 (t0) REVERT: E 620 LEU cc_start: 0.8950 (tp) cc_final: 0.8625 (tm) REVERT: E 624 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6688 (pt) REVERT: E 710 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7705 (tpm-80) REVERT: F 449 ASP cc_start: 0.6671 (t70) cc_final: 0.6381 (t0) REVERT: F 451 HIS cc_start: 0.7230 (m90) cc_final: 0.7000 (m-70) REVERT: F 499 LYS cc_start: 0.8411 (ptpt) cc_final: 0.8171 (ptmm) REVERT: F 632 LYS cc_start: 0.8222 (tppp) cc_final: 0.7804 (tptt) REVERT: F 826 MET cc_start: 0.8925 (tpp) cc_final: 0.8684 (tpp) REVERT: F 846 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: F 897 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8377 (mp0) outliers start: 55 outliers final: 25 residues processed: 280 average time/residue: 0.6802 time to fit residues: 217.8798 Evaluate side-chains 279 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 599 TYR Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 776 SER Chi-restraints excluded: chain C residue 918 LYS Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 915 GLU Chi-restraints excluded: chain E residue 456 ASN Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 641 VAL Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 846 GLU Chi-restraints excluded: chain F residue 897 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 96 optimal weight: 0.0980 chunk 144 optimal weight: 8.9990 chunk 295 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 129 optimal weight: 0.0470 chunk 54 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN D 561 HIS F 743 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.110748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.077927 restraints weight = 38475.765| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.37 r_work: 0.2846 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 25883 Z= 0.128 Angle : 0.621 16.830 35048 Z= 0.302 Chirality : 0.040 0.284 3998 Planarity : 0.004 0.096 4506 Dihedral : 7.795 137.148 3598 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 1.75 % Allowed : 15.50 % Favored : 82.75 % 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 are not related in a simple way. whole: 1.31 (0.15), residues: 3210 helix: 2.01 (0.14), residues: 1461 sheet: 0.56 (0.26), residues: 402 loop : -0.26 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 511 TYR 0.026 0.001 TYR E 565 PHE 0.020 0.001 PHE F 547 TRP 0.028 0.001 TRP F 770 HIS 0.002 0.001 HIS F 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (25880) covalent geometry : angle 0.61283 / 0.30 (35042) hydrogen bonds : bond 0.03586 / 2.61 ( 1159) hydrogen bonds : angle 5.14541 / 3.34 ( 3357) Misc. bond : bond 0.00030 / 0.02 ( 1) link_TRANS : bond 0.06123 / 3.16 ( 2) link_TRANS : angle 7.66142 / 3.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8336 (p0) REVERT: A 423 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8449 (tp30) REVERT: A 459 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.8196 (ttm110) REVERT: A 499 LYS cc_start: 0.8303 (mttm) cc_final: 0.7976 (mmmt) REVERT: A 846 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7837 (mm-30) REVERT: B 412 ASP cc_start: 0.5023 (OUTLIER) cc_final: 0.4699 (m-30) REVERT: B 423 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7869 (mm-30) REVERT: B 490 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: B 597 ARG cc_start: 0.8096 (ttm110) cc_final: 0.7883 (ttm170) REVERT: B 647 GLU cc_start: 0.8859 (tp30) cc_final: 0.8618 (tt0) REVERT: B 733 GLU cc_start: 0.8362 (tt0) cc_final: 0.8152 (tp30) REVERT: B 846 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7860 (mm-30) REVERT: C 415 ASP cc_start: 0.7373 (p0) cc_final: 0.6983 (t0) REVERT: C 426 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8678 (mmtm) REVERT: C 435 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8835 (mmm) REVERT: C 454 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8095 (mm-30) REVERT: C 741 ASN cc_start: 0.7523 (t0) cc_final: 0.7281 (t0) REVERT: C 846 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7944 (mp0) REVERT: D 511 ARG cc_start: 0.8490 (ptm-80) cc_final: 0.8131 (ttt-90) REVERT: D 552 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7466 (ttm) REVERT: D 647 GLU cc_start: 0.8717 (tp30) cc_final: 0.8494 (tp30) REVERT: D 741 ASN cc_start: 0.8028 (t0) cc_final: 0.7708 (t0) REVERT: D 773 MET cc_start: 0.7029 (pp-130) cc_final: 0.6682 (pp-130) REVERT: D 915 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8686 (mt-10) REVERT: E 456 ASN cc_start: 0.7050 (OUTLIER) cc_final: 0.6768 (m-40) REVERT: E 462 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6560 (mm) REVERT: E 482 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7717 (ttp-110) REVERT: E 489 GLU cc_start: 0.8847 (pp20) cc_final: 0.8339 (pp20) REVERT: E 577 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8152 (mm) REVERT: E 591 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8204 (mm-30) REVERT: E 602 ASP cc_start: 0.7650 (m-30) cc_final: 0.6984 (t0) REVERT: E 620 LEU cc_start: 0.8982 (tp) cc_final: 0.8674 (tm) REVERT: E 624 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6715 (pt) REVERT: E 710 ARG cc_start: 0.8035 (mmm160) cc_final: 0.7690 (tpm-80) REVERT: E 846 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8162 (mm-30) REVERT: F 449 ASP cc_start: 0.6692 (t70) cc_final: 0.6406 (t0) REVERT: F 451 HIS cc_start: 0.7185 (m90) cc_final: 0.6965 (m-70) REVERT: F 499 LYS cc_start: 0.8389 (ptpt) cc_final: 0.8159 (ptmm) REVERT: F 632 LYS cc_start: 0.8156 (tppp) cc_final: 0.7798 (tptt) REVERT: F 826 MET cc_start: 0.8909 (tpp) cc_final: 0.8676 (tpp) REVERT: F 846 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: F 897 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8362 (mp0) outliers start: 48 outliers final: 22 residues processed: 291 average time/residue: 0.6598 time to fit residues: 219.8638 Evaluate side-chains 281 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 599 TYR Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 776 SER Chi-restraints excluded: chain C residue 918 LYS Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 915 GLU Chi-restraints excluded: chain E residue 456 ASN Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 641 VAL Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 846 GLU Chi-restraints excluded: chain F residue 897 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 303 optimal weight: 5.9990 chunk 301 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 chunk 276 optimal weight: 0.6980 chunk 186 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 HIS ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3479 r_free = 0.3479 target = 0.109566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.076416 restraints weight = 38515.261| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.42 r_work: 0.2811 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 25883 Z= 0.148 Angle : 0.636 16.352 35048 Z= 0.311 Chirality : 0.041 0.256 3998 Planarity : 0.004 0.096 4506 Dihedral : 7.833 142.168 3594 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 1.54 % Allowed : 16.05 % Favored : 82.42 % 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 are not related in a simple way. whole: 1.27 (0.15), residues: 3210 helix: 1.98 (0.14), residues: 1467 sheet: 0.55 (0.26), residues: 403 loop : -0.31 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 705 TYR 0.019 0.001 TYR A 939 PHE 0.021 0.001 PHE F 547 TRP 0.028 0.001 TRP F 770 HIS 0.004 0.001 HIS F 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (25880) covalent geometry : angle 0.62777 / 0.31 (35042) hydrogen bonds : bond 0.03806 / 2.74 ( 1159) hydrogen bonds : angle 5.15129 / 3.34 ( 3357) Misc. bond : bond 0.00034 / 0.02 ( 1) link_TRANS : bond 0.05986 / 3.09 ( 2) link_TRANS : angle 7.86942 / 3.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 248 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8334 (p0) REVERT: A 423 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8446 (tp30) REVERT: A 459 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8180 (ttm110) REVERT: A 499 LYS cc_start: 0.8287 (mttm) cc_final: 0.7948 (mmmt) REVERT: A 846 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7843 (mm-30) REVERT: B 412 ASP cc_start: 0.5240 (OUTLIER) cc_final: 0.4936 (m-30) REVERT: B 423 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7842 (mm-30) REVERT: B 482 ARG cc_start: 0.8083 (ttt-90) cc_final: 0.7576 (ttt-90) REVERT: B 490 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: B 647 GLU cc_start: 0.8855 (tp30) cc_final: 0.8620 (tt0) REVERT: B 733 GLU cc_start: 0.8430 (tt0) cc_final: 0.8169 (tp30) REVERT: B 846 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7893 (mm-30) REVERT: C 415 ASP cc_start: 0.7319 (p0) cc_final: 0.6859 (t0) REVERT: C 423 GLU cc_start: 0.8463 (pp20) cc_final: 0.8183 (mm-30) REVERT: C 426 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8676 (mmtm) REVERT: C 435 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8783 (mmm) REVERT: C 579 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8272 (tttp) REVERT: C 741 ASN cc_start: 0.7570 (t0) cc_final: 0.7337 (t0) REVERT: C 846 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8005 (mp0) REVERT: D 426 LYS cc_start: 0.8527 (ptmt) cc_final: 0.8293 (ptpp) REVERT: D 511 ARG cc_start: 0.8492 (ptm-80) cc_final: 0.8124 (ttt-90) REVERT: D 552 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7519 (ttm) REVERT: D 647 GLU cc_start: 0.8715 (tp30) cc_final: 0.8430 (tp30) REVERT: D 741 ASN cc_start: 0.8056 (t0) cc_final: 0.7751 (t0) REVERT: D 773 MET cc_start: 0.7049 (pp-130) cc_final: 0.6749 (pp-130) REVERT: D 915 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8669 (mt-10) REVERT: E 456 ASN cc_start: 0.6974 (OUTLIER) cc_final: 0.6708 (m-40) REVERT: E 462 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6641 (mm) REVERT: E 489 GLU cc_start: 0.8828 (pp20) cc_final: 0.8241 (pp20) REVERT: E 577 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8183 (mm) REVERT: E 591 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8194 (mm-30) REVERT: E 602 ASP cc_start: 0.7660 (m-30) cc_final: 0.6960 (t0) REVERT: E 620 LEU cc_start: 0.8951 (tp) cc_final: 0.8657 (tm) REVERT: E 624 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6589 (pp) REVERT: E 710 ARG cc_start: 0.8028 (mmm160) cc_final: 0.7656 (tpm-80) REVERT: E 846 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8022 (mp0) REVERT: F 449 ASP cc_start: 0.6738 (t70) cc_final: 0.6447 (t0) REVERT: F 451 HIS cc_start: 0.7221 (m90) cc_final: 0.6989 (m-70) REVERT: F 499 LYS cc_start: 0.8393 (ptpt) cc_final: 0.8155 (ptmm) REVERT: F 632 LYS cc_start: 0.8182 (tppp) cc_final: 0.7846 (tptt) REVERT: F 826 MET cc_start: 0.8913 (tpp) cc_final: 0.8688 (tpp) REVERT: F 897 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8368 (mp0) outliers start: 42 outliers final: 24 residues processed: 274 average time/residue: 0.6958 time to fit residues: 218.4348 Evaluate side-chains 278 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 599 TYR Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 776 SER Chi-restraints excluded: chain C residue 918 LYS Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 915 GLU Chi-restraints excluded: chain E residue 456 ASN Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 641 VAL Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 897 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 122 optimal weight: 0.5980 chunk 314 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 253 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 302 optimal weight: 0.0170 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3477 r_free = 0.3477 target = 0.109458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.076550 restraints weight = 38446.197| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.37 r_work: 0.2819 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 25883 Z= 0.146 Angle : 0.634 16.376 35048 Z= 0.309 Chirality : 0.041 0.262 3998 Planarity : 0.004 0.096 4506 Dihedral : 7.898 154.964 3594 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 1.57 % Allowed : 16.23 % Favored : 82.20 % 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 are not related in a simple way. whole: 1.29 (0.15), residues: 3210 helix: 1.98 (0.14), residues: 1462 sheet: 0.60 (0.26), residues: 403 loop : -0.29 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 705 TYR 0.019 0.001 TYR A 939 PHE 0.021 0.001 PHE F 547 TRP 0.030 0.001 TRP F 770 HIS 0.003 0.001 HIS F 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (25880) covalent geometry : angle 0.62511 / 0.30 (35042) hydrogen bonds : bond 0.03757 / 2.71 ( 1159) hydrogen bonds : angle 5.11688 / 3.32 ( 3357) Misc. bond : bond 0.00031 / 0.02 ( 1) link_TRANS : bond 0.06053 / 3.13 ( 2) link_TRANS : angle 7.91741 / 3.44 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8345 (p0) REVERT: A 423 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8440 (tp30) REVERT: A 459 ARG cc_start: 0.8410 (ttm-80) cc_final: 0.8201 (ttm110) REVERT: A 499 LYS cc_start: 0.8327 (mttm) cc_final: 0.7999 (mmmt) REVERT: A 846 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7831 (mm-30) REVERT: B 412 ASP cc_start: 0.5289 (OUTLIER) cc_final: 0.5015 (m-30) REVERT: B 419 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8089 (mm-30) REVERT: B 423 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7852 (mm-30) REVERT: B 482 ARG cc_start: 0.8084 (ttt-90) cc_final: 0.7802 (ttt-90) REVERT: B 490 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7559 (m-30) REVERT: B 647 GLU cc_start: 0.8866 (tp30) cc_final: 0.8633 (tt0) REVERT: B 733 GLU cc_start: 0.8367 (tt0) cc_final: 0.8158 (tp30) REVERT: B 846 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7866 (mm-30) REVERT: C 415 ASP cc_start: 0.7259 (p0) cc_final: 0.6818 (t0) REVERT: C 423 GLU cc_start: 0.8471 (pp20) cc_final: 0.8154 (mm-30) REVERT: C 426 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8694 (mmtm) REVERT: C 435 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8826 (mmm) REVERT: C 846 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8016 (mp0) REVERT: D 426 LYS cc_start: 0.8583 (ptmt) cc_final: 0.8346 (ptpp) REVERT: D 511 ARG cc_start: 0.8503 (ptm-80) cc_final: 0.8139 (ttt-90) REVERT: D 552 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7541 (ttm) REVERT: D 647 GLU cc_start: 0.8721 (tp30) cc_final: 0.8447 (tp30) REVERT: D 741 ASN cc_start: 0.8079 (t0) cc_final: 0.7769 (t0) REVERT: D 773 MET cc_start: 0.7103 (pp-130) cc_final: 0.6813 (pp-130) REVERT: D 915 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8678 (mt-10) REVERT: E 456 ASN cc_start: 0.6996 (OUTLIER) cc_final: 0.6731 (m-40) REVERT: E 462 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6631 (mm) REVERT: E 489 GLU cc_start: 0.8814 (pp20) cc_final: 0.8224 (pp20) REVERT: E 577 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8157 (mm) REVERT: E 591 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8220 (mm-30) REVERT: E 602 ASP cc_start: 0.7682 (m-30) cc_final: 0.6970 (t0) REVERT: E 620 LEU cc_start: 0.8942 (tp) cc_final: 0.8665 (tm) REVERT: E 624 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6492 (pp) REVERT: E 710 ARG cc_start: 0.8045 (mmm160) cc_final: 0.7679 (tpm-80) REVERT: E 846 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8032 (mp0) REVERT: F 449 ASP cc_start: 0.6740 (t70) cc_final: 0.6459 (t0) REVERT: F 451 HIS cc_start: 0.7245 (m90) cc_final: 0.7001 (m-70) REVERT: F 499 LYS cc_start: 0.8410 (ptpt) cc_final: 0.8178 (ptmm) REVERT: F 826 MET cc_start: 0.8940 (tpp) cc_final: 0.8711 (tpp) REVERT: F 897 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8393 (mp0) outliers start: 43 outliers final: 25 residues processed: 270 average time/residue: 0.6620 time to fit residues: 204.7409 Evaluate side-chains 274 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 599 TYR Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 776 SER Chi-restraints excluded: chain C residue 918 LYS Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 826 MET Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 915 GLU Chi-restraints excluded: chain E residue 456 ASN Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 641 VAL Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 897 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 124 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 138 optimal weight: 0.0980 chunk 251 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 211 optimal weight: 0.5980 chunk 271 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 741 ASN ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3486 r_free = 0.3486 target = 0.110092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.077118 restraints weight = 38345.140| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.41 r_work: 0.2826 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 25883 Z= 0.135 Angle : 0.629 16.272 35048 Z= 0.307 Chirality : 0.041 0.262 3998 Planarity : 0.004 0.096 4506 Dihedral : 7.823 154.560 3594 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 1.72 % Allowed : 16.19 % Favored : 82.09 % 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 are not related in a simple way. whole: 1.32 (0.15), residues: 3210 helix: 2.02 (0.14), residues: 1462 sheet: 0.65 (0.26), residues: 402 loop : -0.29 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 705 TYR 0.017 0.001 TYR A 939 PHE 0.019 0.001 PHE F 547 TRP 0.028 0.001 TRP F 770 HIS 0.003 0.001 HIS F 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (25880) covalent geometry : angle 0.62049 / 0.30 (35042) hydrogen bonds : bond 0.03632 / 2.63 ( 1159) hydrogen bonds : angle 5.07140 / 3.28 ( 3357) Misc. bond : bond 0.00028 / 0.01 ( 1) link_TRANS : bond 0.06060 / 3.14 ( 2) link_TRANS : angle 8.04691 / 3.50 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9313.79 seconds wall clock time: 158 minutes 58.89 seconds (9538.89 seconds total)