Starting phenix.real_space_refine on Wed Mar 4 23:27:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lep_23292/03_2026/7lep_23292.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lep_23292/03_2026/7lep_23292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lep_23292/03_2026/7lep_23292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lep_23292/03_2026/7lep_23292.map" model { file = "/net/cci-nas-00/data/ceres_data/7lep_23292/03_2026/7lep_23292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lep_23292/03_2026/7lep_23292.cif" } resolution = 3.25 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= 0.020 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 S 106 5.16 5 Cl 2 4.86 5 C 10959 2.51 5 N 2586 2.21 5 O 2882 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16559 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2844 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 403, 2843 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 390} Chain breaks: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 6, 'ASP:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 87 Conformer: "B" Number of residues, atoms: 403, 2843 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 390} Chain breaks: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 6, 'ASP:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 87 bond proxies already assigned to first conformer: 2903 Chain: "B" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2929 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 112 Chain: "C" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2855 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 390} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 6, 'ASP:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 84 Chain: "D" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2921 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 119 Chain: "E" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1092 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 137} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "F" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1096 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 3, 'TRANS': 137} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "G" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1144 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain breaks: 3 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'ARG:plan': 7, 'GLU:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 81 Chain: "H" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1144 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain breaks: 3 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'ARG:plan': 7, 'GLU:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 94 Unusual residues: {'POV': 8, 'ZK1': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 349 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-1': 8, 'POV:plan-2': 8, 'POV:plan-3': 8} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 117 Unusual residues: {'C14': 1, 'POV': 5, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-1': 4, 'POV:plan-2': 4, 'POV:plan-3': 4} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 94 Unusual residues: {'D10': 1, 'POV': 7, 'ZK1': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 7, 'POV:plan-3': 7} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 111 Unusual residues: {'POV': 6, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 5, 'POV:plan-2': 5, 'POV:plan-3': 5} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'D12': 1, 'OCT': 1, 'POV': 1, 'XVD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'D12': 1, 'OCT': 1, 'POV': 1, 'XVD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 8 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 932 SG CYS A 524 77.862 74.417 62.979 1.00 23.71 S ATOM 6721 SG CYS C 524 39.034 47.071 62.900 1.00 23.98 S Time building chain proxies: 4.96, per 1000 atoms: 0.30 Number of scatterers: 16559 At special positions: 0 Unit cell: (119.178, 122.488, 147.869, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 106 16.00 P 6 15.00 F 18 9.00 O 2882 8.00 N 2586 7.00 C 10959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 100 " distance=2.04 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 100 " distance=2.04 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 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 802.7 milliseconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4084 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 16 sheets defined 59.0% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 412 through 415 Processing helix chain 'A' and resid 420 through 433 removed outlier: 4.316A pdb=" N ALA A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.636A pdb=" N VAL A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 485 removed outlier: 3.753A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.673A pdb=" N LEU A 514 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 541 removed outlier: 3.962A pdb=" N VAL A 526 " --> pdb=" O TRP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 625 removed outlier: 4.322A pdb=" N VAL A 597 " --> pdb=" O SER A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 660 through 672 removed outlier: 3.916A pdb=" N SER A 672 " --> pdb=" O ALA A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 693 Processing helix chain 'A' and resid 702 through 709 Processing helix chain 'A' and resid 739 through 752 removed outlier: 3.805A pdb=" N ASN A 743 " --> pdb=" O ARG A 739 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA A 745 " --> pdb=" O PRO A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 763 removed outlier: 3.694A pdb=" N LEU A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 813 removed outlier: 3.873A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.553A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 522 through 545 removed outlier: 3.555A pdb=" N VAL B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.511A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 626 removed outlier: 3.807A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 643 Processing helix chain 'B' and resid 653 through 661 removed outlier: 4.891A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.759A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 705 through 713 Processing helix chain 'B' and resid 743 through 756 removed outlier: 4.224A pdb=" N ASN B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU B 748 " --> pdb=" O ASN B 744 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 749 " --> pdb=" O ALA B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 769 removed outlier: 3.598A pdb=" N LYS B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 818 removed outlier: 3.917A pdb=" N VAL B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 798 " --> pdb=" O GLY B 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.535A pdb=" N ALA C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 420 through 433 removed outlier: 4.375A pdb=" N ALA C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 430 " --> pdb=" O ALA C 426 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 465 removed outlier: 3.612A pdb=" N GLY C 461 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 485 removed outlier: 3.789A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 518 through 541 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 625 removed outlier: 4.184A pdb=" N VAL C 597 " --> pdb=" O SER C 593 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 598 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN C 615 " --> pdb=" O SER C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 651 through 658 Processing helix chain 'C' and resid 660 through 672 removed outlier: 3.931A pdb=" N SER C 672 " --> pdb=" O ALA C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 693 removed outlier: 3.524A pdb=" N LYS C 693 " --> pdb=" O VAL C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 709 Processing helix chain 'C' and resid 739 through 752 Processing helix chain 'C' and resid 755 through 763 Processing helix chain 'C' and resid 788 through 813 removed outlier: 3.842A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 810 " --> pdb=" O ALA C 806 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 436 Processing helix chain 'D' and resid 464 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 522 through 547 removed outlier: 3.621A pdb=" N SER D 547 " --> pdb=" O VAL D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.757A pdb=" N PHE D 579 " --> pdb=" O ASN D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.774A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 643 removed outlier: 4.100A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.703A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 705 through 713 Processing helix chain 'D' and resid 743 through 756 removed outlier: 4.250A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU D 748 " --> pdb=" O ASN D 744 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA D 749 " --> pdb=" O ALA D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 769 removed outlier: 3.532A pdb=" N LYS D 761 " --> pdb=" O GLY D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 819 removed outlier: 3.865A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG D 819 " --> pdb=" O CYS D 815 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 36 removed outlier: 3.972A pdb=" N ALA E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 86 removed outlier: 4.288A pdb=" N VAL E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Proline residue: E 70 - end of helix removed outlier: 3.890A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 102 removed outlier: 3.836A pdb=" N LEU E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 125 through 159 removed outlier: 3.524A pdb=" N ASN E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 36 removed outlier: 4.073A pdb=" N ALA F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 86 removed outlier: 4.366A pdb=" N VAL F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Proline residue: F 70 - end of helix removed outlier: 3.859A pdb=" N HIS F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 102 removed outlier: 3.790A pdb=" N LEU F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 125 through 159 removed outlier: 3.696A pdb=" N ASN F 129 " --> pdb=" O ALA F 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 41 removed outlier: 3.958A pdb=" N ILE G 39 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER G 40 " --> pdb=" O THR G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 127 Processing helix chain 'G' and resid 128 through 150 removed outlier: 3.581A pdb=" N ILE G 132 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG G 149 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 184 removed outlier: 3.766A pdb=" N VAL G 166 " --> pdb=" O GLY G 162 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY G 169 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA G 184 " --> pdb=" O ILE G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 232 Processing helix chain 'H' and resid 20 through 41 removed outlier: 3.957A pdb=" N ILE H 39 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER H 40 " --> pdb=" O THR H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 127 Processing helix chain 'H' and resid 128 through 150 removed outlier: 3.581A pdb=" N ILE H 132 " --> pdb=" O SER H 128 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG H 149 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL H 150 " --> pdb=" O ALA H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 184 removed outlier: 3.766A pdb=" N VAL H 166 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY H 169 " --> pdb=" O PHE H 165 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA H 184 " --> pdb=" O ILE H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 232 Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 393 removed outlier: 7.137A pdb=" N ALA A 391 " --> pdb=" O ALA A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 402 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 476 removed outlier: 4.213A pdb=" N LEU A 475 " --> pdb=" O GLY A 729 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 698 through 701 Processing sheet with id=AA5, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.867A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 646 through 648 removed outlier: 8.627A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 391 through 395 removed outlier: 7.281A pdb=" N ALA C 391 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA C 439 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL C 393 " --> pdb=" O ALA C 439 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 402 through 404 Processing sheet with id=AA9, first strand: chain 'C' and resid 698 through 701 Processing sheet with id=AB1, first strand: chain 'D' and resid 397 through 398 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.863A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 646 through 648 removed outlier: 8.332A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 82 through 83 Processing sheet with id=AB5, first strand: chain 'G' and resid 88 through 89 Processing sheet with id=AB6, first strand: chain 'H' and resid 82 through 83 Processing sheet with id=AB7, first strand: chain 'H' and resid 88 through 89 947 hydrogen bonds defined for protein. 2793 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: 2.56 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2536 1.32 - 1.45: 5346 1.45 - 1.59: 8836 1.59 - 1.73: 4 1.73 - 1.86: 168 Bond restraints: 16890 Sorted by residual: bond pdb=" CAT ZK1 D 901 " pdb=" OAA ZK1 D 901 " ideal model delta sigma weight residual 1.214 1.401 -0.187 2.00e-02 2.50e+03 8.75e+01 bond pdb=" CAT ZK1 C 901 " pdb=" OAA ZK1 C 901 " ideal model delta sigma weight residual 1.214 1.397 -0.183 2.00e-02 2.50e+03 8.36e+01 bond pdb=" CAT ZK1 A 901 " pdb=" OAA ZK1 A 901 " ideal model delta sigma weight residual 1.214 1.397 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" CAU ZK1 C 901 " pdb=" OAB ZK1 C 901 " ideal model delta sigma weight residual 1.215 1.398 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" CAU ZK1 A 901 " pdb=" OAB ZK1 A 901 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.31e+01 ... (remaining 16885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 22304 2.33 - 4.67: 493 4.67 - 7.00: 86 7.00 - 9.34: 11 9.34 - 11.67: 9 Bond angle restraints: 22903 Sorted by residual: angle pdb=" N PRO F 109 " pdb=" CA PRO F 109 " pdb=" CB PRO F 109 " ideal model delta sigma weight residual 103.25 110.14 -6.89 1.05e+00 9.07e-01 4.30e+01 angle pdb=" N PRO E 109 " pdb=" CA PRO E 109 " pdb=" CB PRO E 109 " ideal model delta sigma weight residual 103.25 110.12 -6.87 1.05e+00 9.07e-01 4.28e+01 angle pdb=" O11 POV B 902 " pdb=" P POV B 902 " pdb=" O12 POV B 902 " ideal model delta sigma weight residual 97.67 109.34 -11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" O11 POV D 902 " pdb=" P POV D 902 " pdb=" O12 POV D 902 " ideal model delta sigma weight residual 97.67 109.23 -11.56 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C14 POV B 902 " pdb=" N POV B 902 " pdb=" C15 POV B 902 " ideal model delta sigma weight residual 108.02 119.56 -11.54 3.00e+00 1.11e-01 1.48e+01 ... (remaining 22898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.47: 9418 29.47 - 58.94: 290 58.94 - 88.42: 21 88.42 - 117.89: 14 117.89 - 147.36: 8 Dihedral angle restraints: 9751 sinusoidal: 3371 harmonic: 6380 Sorted by residual: dihedral pdb=" CB CYS G 90 " pdb=" SG CYS G 90 " pdb=" SG CYS G 100 " pdb=" CB CYS G 100 " ideal model delta sinusoidal sigma weight residual 93.00 41.08 51.92 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" CB CYS H 90 " pdb=" SG CYS H 90 " pdb=" SG CYS H 100 " pdb=" CB CYS H 100 " ideal model delta sinusoidal sigma weight residual 93.00 41.13 51.87 1 1.00e+01 1.00e-02 3.67e+01 dihedral pdb=" CB CYS C 714 " pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " pdb=" CB CYS C 769 " ideal model delta sinusoidal sigma weight residual -86.00 -131.73 45.73 1 1.00e+01 1.00e-02 2.90e+01 ... (remaining 9748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1945 0.047 - 0.095: 572 0.095 - 0.142: 127 0.142 - 0.189: 9 0.189 - 0.237: 4 Chirality restraints: 2657 Sorted by residual: chirality pdb=" CA PRO F 109 " pdb=" N PRO F 109 " pdb=" C PRO F 109 " pdb=" CB PRO F 109 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO E 109 " pdb=" N PRO E 109 " pdb=" C PRO E 109 " pdb=" CB PRO E 109 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA PHE G 130 " pdb=" N PHE G 130 " pdb=" C PHE G 130 " pdb=" CB PHE G 130 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.44e-01 ... (remaining 2654 not shown) Planarity restraints: 2760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 766 " 0.018 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP B 766 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP B 766 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP B 766 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 766 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 766 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 766 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 766 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 766 " 0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP B 766 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 417 " 0.022 2.00e-02 2.50e+03 2.10e-02 8.86e+00 pdb=" CG TYR A 417 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR A 417 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 417 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 417 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 417 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 417 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 417 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 207 " -0.024 2.00e-02 2.50e+03 2.19e-02 8.36e+00 pdb=" CG PHE G 207 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE G 207 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE G 207 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE G 207 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 207 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE G 207 " -0.001 2.00e-02 2.50e+03 ... (remaining 2757 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 109 2.56 - 3.14: 13904 3.14 - 3.73: 24886 3.73 - 4.31: 33229 4.31 - 4.90: 56763 Nonbonded interactions: 128891 Sorted by model distance: nonbonded pdb=" NH1 ARG D 485 " pdb=" OAA ZK1 D 901 " model vdw 1.973 2.496 nonbonded pdb=" O SER C 543 " pdb=" OH TYR H 226 " model vdw 2.170 3.040 nonbonded pdb=" O ILE A 498 " pdb=" ND2 ASN A 705 " model vdw 2.190 3.120 nonbonded pdb=" O ILE C 498 " pdb=" ND2 ASN C 705 " model vdw 2.206 3.120 nonbonded pdb=" OG1 THR A 478 " pdb=" OE2 GLU D 755 " model vdw 2.216 3.040 ... (remaining 128886 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 394 or (resid 395 and (name N or name CA or na \ me C or name O or name CB )) or resid 396 or resid 398 or resid 400 through 403 \ or (resid 405 through 407 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 414 or resid 417 through 422 or resid 424 through 429 or \ (resid 430 and (name N or name CA or name C or name O or name CB )) or resid 43 \ 1 or resid 436 or resid 440 through 441 or resid 443 through 451 or resid 453 th \ rough 454 or resid 456 through 461 or (resid 462 and (name N or name CA or name \ C or name O or name CB )) or resid 463 through 466 or resid 468 or resid 471 or \ resid 473 through 481 or (resid 482 through 483 and (name N or name CA or name C \ or name O or name CB )) or resid 484 through 506 or (resid 507 and (name N or n \ ame CA or name C or name O or name CB )) or resid 508 through 509 or (resid 510 \ and (name N or name CA or name C or name O or name CB or name CG1)) or resid 511 \ through 543 or (resid 565 and (name N or name CA or name C or name O or name CB \ )) or resid 566 through 581 or resid 583 through 629 or (resid 630 and (name N \ or name CA or name C or name O or name CB )) or resid 631 through 635 or (resid \ 637 through 640 and (name N or name CA or name C or name O or name CB )) or resi \ d 641 through 646 or resid 649 or resid 651 through 661 or (resid 662 and (name \ N or name CA or name C or name O or name CB )) or resid 665 through 667 or resid \ 669 or (resid 670 and (name N or name CA or name C or name O or name CB )) or r \ esid 672 through 675 or (resid 676 and (name N or name CA or name C or name O or \ name CB )) or resid 677 through 678 or resid 681 through 683 or resid 685 or re \ sid 687 through 689 or (resid 690 through 691 and (name N or name CA or name C o \ r name O or name CB )) or resid 693 through 695 or resid 697 or resid 699 throug \ h 729 or resid 731 through 736 or resid 738 or resid 742 through 749 or resid 75 \ 1 or resid 753 or resid 755 through 759 or resid 761 through 770 or (resid 776 t \ hrough 777 and (name N or name CA or name C or name O or name CB )) or resid 779 \ through 795 or resid 797 through 803 or resid 805 through 811 or (resid 812 thr \ ough 813 and (name N or name CA or name C or name O or name CB )) or resid 907 o \ r resid 909)) selection = (chain 'B' and (resid 397 through 400 or (resid 402 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 407 or resid 409 through 411 o \ r resid 416 through 418 or resid 421 through 426 or resid 428 through 435 or res \ id 440 or resid 444 through 445 or resid 447 through 452 or (resid 453 through 4 \ 55 and (name N or name CA or name C or name O or name CB )) or (resid 457 throug \ h 458 and (name N or name CA or name C or name O or name CB )) or resid 460 thro \ ugh 470 or resid 472 or resid 475 or resid 477 through 486 or (resid 487 and (na \ me N or name CA or name C or name O or name CB )) or resid 488 through 489 or (r \ esid 490 and (name N or name CA or name C or name O or name CB )) or resid 491 t \ hrough 507 or (resid 508 through 509 and (name N or name CA or name C or name O \ or name CB )) or resid 510 through 513 or (resid 514 and (name N or name CA or n \ ame C or name O or name CB or name CG1)) or resid 515 through 585 or resid 587 t \ hrough 639 or resid 641 through 650 or resid 653 or resid 655 through 659 or (re \ sid 660 through 661 and (name N or name CA or name C or name O or name CB )) or \ resid 662 through 665 or (resid 666 and (name N or name CA or name C or name O o \ r name CB )) or (resid 669 and (name N or name CA or name C or name O or name CB \ )) or resid 670 through 671 or resid 673 through 674 or resid 676 through 682 o \ r (resid 685 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 86 through 687 or resid 689 or (resid 691 through 692 and (name N or name CA or \ name C or name O or name CB )) or resid 693 through 695 or resid 697 through 699 \ or resid 701 or resid 703 through 714 or (resid 715 through 716 and (name N or \ name CA or name C or name O or name CB )) or resid 717 through 733 or resid 735 \ through 740 or resid 742 or resid 746 through 753 or resid 755 or resid 757 or r \ esid 759 through 763 or resid 765 through 768 or (resid 769 and (name N or name \ CA or name C or name O or name CB )) or resid 770 through 774 or resid 780 throu \ gh 781 or (resid 783 through 784 and (name N or name CA or name C or name O or n \ ame CB )) or resid 785 through 799 or resid 801 through 807 or resid 809 through \ 815 or (resid 816 through 817 and (name N or name CA or name C or name O or nam \ e CB )) or resid 905 or (resid 907 and (name C21 or name C22 or name C23 or name \ C24 or name C25)))) selection = (chain 'C' and (resid 393 through 394 or (resid 395 and (name N or name CA or na \ me C or name O or name CB )) or resid 396 or resid 398 or resid 400 through 403 \ or (resid 405 through 407 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 414 or resid 417 through 422 or resid 424 through 429 or \ (resid 430 and (name N or name CA or name C or name O or name CB )) or resid 43 \ 1 or resid 436 or resid 440 through 441 or resid 443 through 451 or resid 453 th \ rough 454 or resid 456 through 461 or (resid 462 and (name N or name CA or name \ C or name O or name CB )) or resid 463 through 466 or resid 468 or resid 471 or \ resid 473 through 481 or (resid 482 through 483 and (name N or name CA or name C \ or name O or name CB )) or resid 484 through 506 or (resid 507 and (name N or n \ ame CA or name C or name O or name CB )) or resid 508 through 509 or (resid 510 \ and (name N or name CA or name C or name O or name CB or name CG1)) or resid 511 \ through 543 or (resid 565 and (name N or name CA or name C or name O or name CB \ )) or resid 566 through 581 or resid 583 through 629 or (resid 630 and (name N \ or name CA or name C or name O or name CB )) or resid 631 through 635 or (resid \ 637 through 640 and (name N or name CA or name C or name O or name CB )) or resi \ d 641 through 646 or resid 649 or resid 651 through 662 or resid 665 through 667 \ or resid 669 or (resid 670 and (name N or name CA or name C or name O or name C \ B )) or resid 672 through 675 or (resid 676 and (name N or name CA or name C or \ name O or name CB )) or resid 677 through 678 or resid 681 through 683 or resid \ 685 or resid 687 through 689 or (resid 690 through 691 and (name N or name CA or \ name C or name O or name CB )) or resid 693 through 695 or resid 697 or resid 6 \ 99 through 729 or resid 731 through 736 or resid 738 or resid 742 through 749 or \ resid 751 or resid 753 or resid 755 through 759 or resid 761 through 770 or (re \ sid 776 through 777 and (name N or name CA or name C or name O or name CB )) or \ resid 779 through 795 or resid 797 through 803 or resid 805 through 811 or (resi \ d 812 through 813 and (name N or name CA or name C or name O or name CB )) or re \ sid 907 or (resid 909 and (name C21 or name C22 or name C23 or name C24 or name \ C25)))) selection = (chain 'D' and (resid 397 through 400 or (resid 402 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 407 or resid 409 through 411 o \ r resid 416 through 418 or resid 421 through 426 or resid 428 through 435 or res \ id 440 or resid 444 through 445 or resid 447 through 452 or (resid 453 through 4 \ 55 and (name N or name CA or name C or name O or name CB )) or (resid 457 throug \ h 458 and (name N or name CA or name C or name O or name CB )) or resid 460 thro \ ugh 470 or resid 472 or resid 475 or resid 477 through 486 or (resid 487 and (na \ me N or name CA or name C or name O or name CB )) or resid 488 through 489 or (r \ esid 490 and (name N or name CA or name C or name O or name CB )) or resid 491 t \ hrough 507 or (resid 508 through 509 and (name N or name CA or name C or name O \ or name CB )) or resid 510 or (resid 511 and (name N or name CA or name C or nam \ e O or name CB )) or resid 512 through 585 or resid 587 through 639 or resid 641 \ through 650 or resid 653 or resid 655 through 659 or (resid 660 through 661 and \ (name N or name CA or name C or name O or name CB )) or resid 662 through 665 o \ r (resid 666 and (name N or name CA or name C or name O or name CB )) or (resid \ 669 and (name N or name CA or name C or name O or name CB )) or resid 670 throug \ h 671 or resid 673 through 674 or resid 676 through 682 or (resid 685 and (name \ N or name CA or name C or name O or name CB )) or resid 686 through 687 or resid \ 689 or (resid 691 through 692 and (name N or name CA or name C or name O or nam \ e CB )) or resid 693 through 695 or resid 697 through 699 or resid 701 or resid \ 703 through 714 or (resid 715 through 716 and (name N or name CA or name C or na \ me O or name CB )) or resid 717 through 733 or resid 735 through 740 or resid 74 \ 2 or resid 746 through 753 or resid 755 or resid 757 or resid 759 through 763 or \ resid 765 through 768 or (resid 769 and (name N or name CA or name C or name O \ or name CB )) or resid 770 through 774 or resid 780 through 781 or (resid 783 th \ rough 784 and (name N or name CA or name C or name O or name CB )) or resid 785 \ through 799 or resid 801 through 807 or resid 809 through 817 or (resid 905 and \ (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28)) or (resid 907 and (name C21 or name C22 or name C23 or name C24 \ or name C25)))) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 2 through 57 or (resid 58 through 59 and (name N or name C \ A or name C or name O or name CB )) or resid 60 through 201)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.420 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.970 Find NCS groups from input model: 0.420 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: 0.010 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.011 0.439 16897 Z= 0.556 Angle : 0.859 11.671 22915 Z= 0.421 Chirality : 0.046 0.237 2657 Planarity : 0.004 0.046 2760 Dihedral : 15.516 147.361 5649 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.28 % Favored : 94.58 % Rotamer: Outliers : 0.40 % Allowed : 0.67 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.48 (0.18), residues: 2178 helix: 0.84 (0.15), residues: 1267 sheet: -1.64 (0.53), residues: 115 loop : -2.03 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 624 TYR 0.051 0.002 TYR A 417 PHE 0.049 0.003 PHE G 207 TRP 0.058 0.002 TRP B 766 HIS 0.005 0.002 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.01006 (16890) covalent geometry : angle 0.85874 (22903) SS BOND : bond 0.00454 ( 6) SS BOND : angle 0.65115 ( 12) hydrogen bonds : bond 0.14979 ( 947) hydrogen bonds : angle 5.73868 ( 2793) Misc. bond : bond 0.43883 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 228 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: B 766 TRP cc_start: 0.6971 (m-10) cc_final: 0.6507 (m-10) REVERT: B 769 ASP cc_start: 0.8275 (m-30) cc_final: 0.7957 (m-30) REVERT: D 482 THR cc_start: 0.8483 (t) cc_final: 0.8232 (m) REVERT: D 769 ASP cc_start: 0.8351 (m-30) cc_final: 0.8049 (m-30) REVERT: E 132 GLN cc_start: 0.6977 (tp40) cc_final: 0.6722 (tp40) REVERT: H 103 ILE cc_start: 0.8519 (mm) cc_final: 0.8255 (mm) outliers start: 4 outliers final: 0 residues processed: 229 average time/residue: 0.1272 time to fit residues: 45.2209 Evaluate side-chains 183 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 ASN D 435 HIS H 172 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.189191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.148307 restraints weight = 22111.293| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.87 r_work: 0.3871 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16897 Z= 0.178 Angle : 0.582 9.639 22915 Z= 0.299 Chirality : 0.040 0.164 2657 Planarity : 0.004 0.041 2760 Dihedral : 11.063 124.743 2703 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.21 % Allowed : 8.58 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.02 (0.18), residues: 2178 helix: 1.21 (0.15), residues: 1293 sheet: -1.29 (0.54), residues: 114 loop : -1.97 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 715 TYR 0.027 0.002 TYR C 446 PHE 0.022 0.002 PHE G 207 TRP 0.020 0.001 TRP B 766 HIS 0.003 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00430 (16890) covalent geometry : angle 0.58191 (22903) SS BOND : bond 0.00275 ( 6) SS BOND : angle 0.55943 ( 12) hydrogen bonds : bond 0.05143 ( 947) hydrogen bonds : angle 4.05703 ( 2793) Misc. bond : bond 0.00274 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: B 427 ASP cc_start: 0.7951 (t0) cc_final: 0.7661 (t0) REVERT: B 766 TRP cc_start: 0.7225 (m100) cc_final: 0.6522 (m-10) REVERT: C 469 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7658 (t0) REVERT: C 515 ASP cc_start: 0.8500 (m-30) cc_final: 0.8247 (m-30) REVERT: D 769 ASP cc_start: 0.8665 (m-30) cc_final: 0.8106 (m-30) REVERT: E 132 GLN cc_start: 0.7092 (tp40) cc_final: 0.6776 (tp40) outliers start: 16 outliers final: 12 residues processed: 220 average time/residue: 0.1303 time to fit residues: 44.5474 Evaluate side-chains 196 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 176 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 154 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN B 744 ASN ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS G 183 ASN H 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.187143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.147643 restraints weight = 22318.499| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.46 r_work: 0.3803 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16897 Z= 0.232 Angle : 0.602 7.129 22915 Z= 0.310 Chirality : 0.042 0.165 2657 Planarity : 0.004 0.075 2760 Dihedral : 9.919 106.627 2703 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.48 % Allowed : 11.46 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.01 (0.18), residues: 2178 helix: 1.26 (0.15), residues: 1292 sheet: -1.34 (0.53), residues: 114 loop : -1.99 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 660 TYR 0.029 0.002 TYR C 446 PHE 0.025 0.002 PHE A 491 TRP 0.013 0.002 TRP B 766 HIS 0.003 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00578 (16890) covalent geometry : angle 0.60186 (22903) SS BOND : bond 0.00312 ( 6) SS BOND : angle 0.57610 ( 12) hydrogen bonds : bond 0.05412 ( 947) hydrogen bonds : angle 4.05749 ( 2793) Misc. bond : bond 0.00217 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.616 Fit side-chains REVERT: A 404 LEU cc_start: 0.7554 (mm) cc_final: 0.7337 (mt) REVERT: B 508 GLN cc_start: 0.7715 (pm20) cc_final: 0.7478 (pm20) REVERT: B 629 MET cc_start: 0.7998 (mmm) cc_final: 0.7714 (mmt) REVERT: B 766 TRP cc_start: 0.7566 (m100) cc_final: 0.6828 (m-10) REVERT: B 769 ASP cc_start: 0.8525 (m-30) cc_final: 0.7882 (m-30) REVERT: C 469 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7666 (t0) REVERT: D 769 ASP cc_start: 0.8662 (m-30) cc_final: 0.8129 (m-30) outliers start: 35 outliers final: 22 residues processed: 223 average time/residue: 0.1246 time to fit residues: 43.3631 Evaluate side-chains 200 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 816 TYR Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 80 optimal weight: 0.9990 chunk 179 optimal weight: 0.0770 chunk 193 optimal weight: 0.0970 chunk 117 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 136 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 208 optimal weight: 0.1980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN D 435 HIS G 172 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.193474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.153402 restraints weight = 22009.363| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.23 r_work: 0.3925 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16897 Z= 0.105 Angle : 0.482 7.232 22915 Z= 0.252 Chirality : 0.037 0.166 2657 Planarity : 0.003 0.065 2760 Dihedral : 8.807 94.278 2703 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.14 % Allowed : 14.81 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.57 (0.19), residues: 2178 helix: 1.76 (0.15), residues: 1291 sheet: -1.50 (0.52), residues: 116 loop : -1.78 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 660 TYR 0.022 0.001 TYR C 446 PHE 0.013 0.001 PHE G 205 TRP 0.016 0.001 TRP A 762 HIS 0.001 0.000 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00228 (16890) covalent geometry : angle 0.48190 (22903) SS BOND : bond 0.00274 ( 6) SS BOND : angle 0.60420 ( 12) hydrogen bonds : bond 0.03978 ( 947) hydrogen bonds : angle 3.63629 ( 2793) Misc. bond : bond 0.00092 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.597 Fit side-chains REVERT: B 427 ASP cc_start: 0.8075 (t0) cc_final: 0.7865 (t0) REVERT: B 629 MET cc_start: 0.7900 (mmm) cc_final: 0.7601 (mmt) REVERT: B 766 TRP cc_start: 0.7450 (m100) cc_final: 0.6823 (m-10) REVERT: B 769 ASP cc_start: 0.8457 (m-30) cc_final: 0.7824 (m-30) REVERT: D 427 ASP cc_start: 0.8041 (m-30) cc_final: 0.7516 (m-30) REVERT: D 766 TRP cc_start: 0.8477 (m100) cc_final: 0.7719 (m100) REVERT: D 769 ASP cc_start: 0.8634 (m-30) cc_final: 0.8078 (m-30) outliers start: 15 outliers final: 8 residues processed: 222 average time/residue: 0.1241 time to fit residues: 42.8263 Evaluate side-chains 187 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain H residue 220 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 47 optimal weight: 0.0470 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN D 435 HIS G 183 ASN H 183 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.192051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.152067 restraints weight = 22060.904| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.18 r_work: 0.3903 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16897 Z= 0.129 Angle : 0.495 6.996 22915 Z= 0.256 Chirality : 0.038 0.166 2657 Planarity : 0.003 0.052 2760 Dihedral : 8.392 95.598 2703 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.74 % Allowed : 16.15 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.66 (0.19), residues: 2178 helix: 1.80 (0.15), residues: 1296 sheet: -1.52 (0.50), residues: 116 loop : -1.71 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 660 TYR 0.015 0.001 TYR A 446 PHE 0.015 0.001 PHE C 491 TRP 0.009 0.001 TRP A 762 HIS 0.002 0.000 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00306 (16890) covalent geometry : angle 0.49511 (22903) SS BOND : bond 0.00266 ( 6) SS BOND : angle 0.57868 ( 12) hydrogen bonds : bond 0.04141 ( 947) hydrogen bonds : angle 3.61828 ( 2793) Misc. bond : bond 0.00109 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.604 Fit side-chains REVERT: B 427 ASP cc_start: 0.8166 (t0) cc_final: 0.7917 (t0) REVERT: B 629 MET cc_start: 0.7846 (mmm) cc_final: 0.7588 (mmt) REVERT: B 766 TRP cc_start: 0.7509 (m100) cc_final: 0.6853 (m-10) REVERT: B 769 ASP cc_start: 0.8396 (m-30) cc_final: 0.7756 (m-30) REVERT: D 427 ASP cc_start: 0.8064 (m-30) cc_final: 0.7572 (m-30) REVERT: D 766 TRP cc_start: 0.8483 (m100) cc_final: 0.7739 (m100) REVERT: D 769 ASP cc_start: 0.8647 (m-30) cc_final: 0.8072 (m-30) REVERT: F 136 TRP cc_start: 0.6700 (m100) cc_final: 0.6415 (m100) outliers start: 24 outliers final: 18 residues processed: 212 average time/residue: 0.1196 time to fit residues: 40.3408 Evaluate side-chains 201 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 220 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 219 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN D 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.186923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.146686 restraints weight = 22273.379| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.76 r_work: 0.3837 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16897 Z= 0.236 Angle : 0.593 7.772 22915 Z= 0.306 Chirality : 0.042 0.171 2657 Planarity : 0.004 0.048 2760 Dihedral : 8.960 97.503 2703 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.08 % Allowed : 15.55 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.32 (0.18), residues: 2178 helix: 1.49 (0.15), residues: 1292 sheet: -1.39 (0.51), residues: 114 loop : -1.80 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 660 TYR 0.020 0.002 TYR C 434 PHE 0.024 0.002 PHE A 491 TRP 0.027 0.002 TRP A 762 HIS 0.003 0.001 HIS H 105 Details of bonding type rmsd covalent geometry : bond 0.00587 (16890) covalent geometry : angle 0.59320 (22903) SS BOND : bond 0.00323 ( 6) SS BOND : angle 0.62128 ( 12) hydrogen bonds : bond 0.05211 ( 947) hydrogen bonds : angle 3.89307 ( 2793) Misc. bond : bond 0.00158 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.612 Fit side-chains REVERT: B 427 ASP cc_start: 0.8264 (t0) cc_final: 0.8039 (t0) REVERT: B 766 TRP cc_start: 0.7793 (m100) cc_final: 0.7176 (m-10) REVERT: B 769 ASP cc_start: 0.8547 (m-30) cc_final: 0.7909 (m-30) REVERT: C 670 MET cc_start: 0.6764 (mtp) cc_final: 0.6454 (mtm) REVERT: D 769 ASP cc_start: 0.8616 (m-30) cc_final: 0.7984 (m-30) REVERT: F 136 TRP cc_start: 0.6651 (m100) cc_final: 0.6382 (m100) outliers start: 44 outliers final: 35 residues processed: 221 average time/residue: 0.1258 time to fit residues: 43.4841 Evaluate side-chains 212 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 220 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 41 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 184 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 128 optimal weight: 0.1980 chunk 138 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 189 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN D 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.191677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.152541 restraints weight = 22011.964| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 2.38 r_work: 0.3903 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3952 r_free = 0.3952 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3952 r_free = 0.3952 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16897 Z= 0.121 Angle : 0.498 8.583 22915 Z= 0.257 Chirality : 0.038 0.169 2657 Planarity : 0.003 0.046 2760 Dihedral : 8.220 93.858 2703 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.14 % Allowed : 16.89 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.71 (0.19), residues: 2178 helix: 1.89 (0.15), residues: 1284 sheet: -1.58 (0.49), residues: 116 loop : -1.69 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 660 TYR 0.014 0.001 TYR C 669 PHE 0.015 0.001 PHE E 31 TRP 0.021 0.001 TRP A 762 HIS 0.002 0.000 HIS G 83 Details of bonding type rmsd covalent geometry : bond 0.00283 (16890) covalent geometry : angle 0.49833 (22903) SS BOND : bond 0.00249 ( 6) SS BOND : angle 0.53300 ( 12) hydrogen bonds : bond 0.04102 ( 947) hydrogen bonds : angle 3.60021 ( 2793) Misc. bond : bond 0.00102 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.632 Fit side-chains REVERT: B 427 ASP cc_start: 0.8182 (t0) cc_final: 0.7929 (t0) REVERT: B 766 TRP cc_start: 0.7596 (m100) cc_final: 0.6981 (m-10) REVERT: B 769 ASP cc_start: 0.8534 (m-30) cc_final: 0.7935 (m-30) REVERT: C 469 ASP cc_start: 0.7185 (t0) cc_final: 0.6953 (t0) REVERT: C 670 MET cc_start: 0.6645 (mtp) cc_final: 0.6327 (mtm) REVERT: D 427 ASP cc_start: 0.7962 (m-30) cc_final: 0.7356 (m-30) REVERT: D 766 TRP cc_start: 0.8437 (m100) cc_final: 0.7652 (m100) REVERT: D 769 ASP cc_start: 0.8609 (m-30) cc_final: 0.8000 (m-30) REVERT: F 136 TRP cc_start: 0.6688 (m100) cc_final: 0.6426 (m100) outliers start: 30 outliers final: 21 residues processed: 220 average time/residue: 0.1228 time to fit residues: 42.6637 Evaluate side-chains 202 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 220 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 122 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 63 optimal weight: 0.0970 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN C 565 ASN D 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.187917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.147395 restraints weight = 22145.508| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.16 r_work: 0.3854 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16897 Z= 0.202 Angle : 0.573 7.740 22915 Z= 0.294 Chirality : 0.040 0.185 2657 Planarity : 0.004 0.043 2760 Dihedral : 8.597 97.054 2703 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.82 % Allowed : 17.29 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.53 (0.18), residues: 2178 helix: 1.68 (0.15), residues: 1290 sheet: -1.53 (0.53), residues: 104 loop : -1.71 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 660 TYR 0.017 0.002 TYR C 434 PHE 0.021 0.002 PHE A 491 TRP 0.017 0.002 TRP A 762 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00501 (16890) covalent geometry : angle 0.57329 (22903) SS BOND : bond 0.00292 ( 6) SS BOND : angle 0.57901 ( 12) hydrogen bonds : bond 0.04832 ( 947) hydrogen bonds : angle 3.76776 ( 2793) Misc. bond : bond 0.00144 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.612 Fit side-chains REVERT: B 427 ASP cc_start: 0.8271 (t0) cc_final: 0.8015 (t0) REVERT: B 508 GLN cc_start: 0.7735 (pm20) cc_final: 0.7508 (pm20) REVERT: B 766 TRP cc_start: 0.7784 (m100) cc_final: 0.7101 (m-10) REVERT: B 769 ASP cc_start: 0.8615 (m-30) cc_final: 0.8009 (m-30) REVERT: C 670 MET cc_start: 0.6673 (mtp) cc_final: 0.6352 (mtm) REVERT: D 427 ASP cc_start: 0.8047 (m-30) cc_final: 0.7599 (m-30) REVERT: D 766 TRP cc_start: 0.8514 (m100) cc_final: 0.7727 (m100) REVERT: D 769 ASP cc_start: 0.8671 (m-30) cc_final: 0.8071 (m-30) REVERT: F 136 TRP cc_start: 0.6703 (m100) cc_final: 0.6448 (m100) outliers start: 40 outliers final: 34 residues processed: 212 average time/residue: 0.1172 time to fit residues: 39.8816 Evaluate side-chains 215 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 816 TYR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 565 ASN Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 220 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 166 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 180 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN C 565 ASN D 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.191225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.150987 restraints weight = 22038.072| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.16 r_work: 0.3898 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3948 r_free = 0.3948 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3948 r_free = 0.3948 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16897 Z= 0.130 Angle : 0.515 7.889 22915 Z= 0.265 Chirality : 0.038 0.177 2657 Planarity : 0.003 0.042 2760 Dihedral : 8.168 96.309 2703 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.68 % Allowed : 17.49 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.78 (0.19), residues: 2178 helix: 1.91 (0.15), residues: 1287 sheet: -1.42 (0.52), residues: 104 loop : -1.64 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 660 TYR 0.014 0.001 TYR C 669 PHE 0.015 0.001 PHE C 491 TRP 0.018 0.001 TRP A 762 HIS 0.002 0.000 HIS G 83 Details of bonding type rmsd covalent geometry : bond 0.00308 (16890) covalent geometry : angle 0.51541 (22903) SS BOND : bond 0.00252 ( 6) SS BOND : angle 0.52731 ( 12) hydrogen bonds : bond 0.04173 ( 947) hydrogen bonds : angle 3.59892 ( 2793) Misc. bond : bond 0.00100 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.643 Fit side-chains REVERT: B 427 ASP cc_start: 0.8336 (t0) cc_final: 0.8069 (t0) REVERT: B 766 TRP cc_start: 0.7740 (m100) cc_final: 0.7067 (m-10) REVERT: B 769 ASP cc_start: 0.8600 (m-30) cc_final: 0.8011 (m-30) REVERT: C 469 ASP cc_start: 0.7157 (t0) cc_final: 0.6943 (t0) REVERT: C 670 MET cc_start: 0.6640 (mtp) cc_final: 0.6315 (mtm) REVERT: D 769 ASP cc_start: 0.8676 (m-30) cc_final: 0.8070 (m-30) REVERT: F 136 TRP cc_start: 0.6679 (m100) cc_final: 0.6430 (m100) outliers start: 38 outliers final: 33 residues processed: 220 average time/residue: 0.1236 time to fit residues: 42.9469 Evaluate side-chains 219 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 565 ASN Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 200 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 163 optimal weight: 0.0060 chunk 171 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN C 565 ASN ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.190105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.149886 restraints weight = 21974.029| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.19 r_work: 0.3887 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3936 r_free = 0.3936 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3936 r_free = 0.3936 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16897 Z= 0.159 Angle : 0.544 9.020 22915 Z= 0.278 Chirality : 0.039 0.179 2657 Planarity : 0.004 0.041 2760 Dihedral : 8.192 96.644 2703 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.61 % Allowed : 18.10 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.77 (0.19), residues: 2178 helix: 1.90 (0.15), residues: 1286 sheet: -1.41 (0.52), residues: 104 loop : -1.65 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 628 TYR 0.015 0.001 TYR C 793 PHE 0.017 0.002 PHE A 491 TRP 0.016 0.001 TRP A 762 HIS 0.002 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00391 (16890) covalent geometry : angle 0.54365 (22903) SS BOND : bond 0.00256 ( 6) SS BOND : angle 0.53249 ( 12) hydrogen bonds : bond 0.04362 ( 947) hydrogen bonds : angle 3.63660 ( 2793) Misc. bond : bond 0.00116 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 0.602 Fit side-chains REVERT: B 427 ASP cc_start: 0.8315 (t0) cc_final: 0.8062 (t0) REVERT: B 762 LEU cc_start: 0.8965 (tp) cc_final: 0.8580 (tp) REVERT: B 766 TRP cc_start: 0.7751 (m100) cc_final: 0.6974 (m-10) REVERT: B 769 ASP cc_start: 0.8591 (m-30) cc_final: 0.8014 (m-30) REVERT: C 670 MET cc_start: 0.6635 (mtp) cc_final: 0.6318 (mtm) REVERT: D 405 TYR cc_start: 0.7012 (m-10) cc_final: 0.6795 (m-10) REVERT: D 427 ASP cc_start: 0.8017 (m-30) cc_final: 0.7811 (m-30) REVERT: F 136 TRP cc_start: 0.6709 (m100) cc_final: 0.6465 (m100) outliers start: 37 outliers final: 35 residues processed: 211 average time/residue: 0.1207 time to fit residues: 40.6494 Evaluate side-chains 216 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 49 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 120 optimal weight: 0.0060 chunk 197 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 202 optimal weight: 0.5980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN C 565 ASN ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.192741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.154524 restraints weight = 21990.168| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.69 r_work: 0.3904 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3952 r_free = 0.3952 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3952 r_free = 0.3952 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16897 Z= 0.117 Angle : 0.515 9.643 22915 Z= 0.263 Chirality : 0.037 0.172 2657 Planarity : 0.003 0.041 2760 Dihedral : 7.650 95.670 2703 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.41 % Allowed : 18.57 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.98 (0.19), residues: 2178 helix: 2.14 (0.15), residues: 1281 sheet: -1.80 (0.43), residues: 140 loop : -1.55 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 628 TYR 0.016 0.001 TYR C 669 PHE 0.014 0.001 PHE H 205 TRP 0.016 0.001 TRP A 762 HIS 0.002 0.000 HIS G 83 Details of bonding type rmsd covalent geometry : bond 0.00271 (16890) covalent geometry : angle 0.51522 (22903) SS BOND : bond 0.00238 ( 6) SS BOND : angle 0.57439 ( 12) hydrogen bonds : bond 0.03871 ( 947) hydrogen bonds : angle 3.50697 ( 2793) Misc. bond : bond 0.00088 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4218.79 seconds wall clock time: 72 minutes 59.06 seconds (4379.06 seconds total)