Starting phenix.real_space_refine on Thu Sep 18 16:56:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b64_44245/09_2025/9b64_44245.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b64_44245/09_2025/9b64_44245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b64_44245/09_2025/9b64_44245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b64_44245/09_2025/9b64_44245.map" model { file = "/net/cci-nas-00/data/ceres_data/9b64_44245/09_2025/9b64_44245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b64_44245/09_2025/9b64_44245.cif" } resolution = 3.56 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 12029 2.51 5 N 2984 2.21 5 O 3352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18493 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3140 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 404, 3140 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3190 Chain: "B" Number of atoms: 3177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3222 Chain: "A" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3133 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 3180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3215 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS C 435 " occ=0.25 ... (18 atoms not shown) pdb=" NE2BHIS C 435 " occ=0.75 residue: pdb=" N APHE B 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.57 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.43 Time building chain proxies: 5.25, per 1000 atoms: 0.28 Number of scatterers: 18493 At special positions: 0 Unit cell: (116.44, 110.7, 146.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3352 8.00 N 2984 7.00 C 12029 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.04 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " 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=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4366 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 24 sheets defined 61.6% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.552A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 128 removed outlier: 3.783A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.953A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 removed outlier: 3.642A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'F' and resid 105 through 126 removed outlier: 3.875A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.883A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 removed outlier: 3.665A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.907A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 424 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 488 removed outlier: 3.825A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.779A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 630 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.800A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 825 Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.870A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 489 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.853A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.800A 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 706 through 714 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 825 removed outlier: 3.534A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.682A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.890A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.767A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 630 Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.550A pdb=" N GLN A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.844A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 825 removed outlier: 3.558A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.772A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 489 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.813A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 825 Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.749A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.784A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 29 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 126 removed outlier: 3.560A pdb=" N ILE G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.701A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.720A pdb=" N TYR G 181 " --> pdb=" O GLY G 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AA4, first strand: chain 'C' and resid 406 through 408 Processing sheet with id=AA5, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AA6, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.564A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 646 through 648 removed outlier: 3.820A pdb=" N LEU C 703 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 439 through 444 removed outlier: 6.285A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA B 477 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASP B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 439 through 444 removed outlier: 6.285A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA B 477 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASP B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 407 through 408 removed outlier: 3.520A pdb=" N GLU B 422 " --> pdb=" O MET B 407 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.543A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.366A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 440 through 444 removed outlier: 3.699A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.661A pdb=" N ALA A 452 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AB7, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.665A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 646 through 648 removed outlier: 8.183A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.437A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 490 through 491 Processing sheet with id=AC3, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.608A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 648 removed outlier: 8.392A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC6, first strand: chain 'G' and resid 78 through 79 1216 hydrogen bonds defined for protein. 3526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5691 1.34 - 1.46: 4848 1.46 - 1.58: 8161 1.58 - 1.70: 1 1.70 - 1.82: 208 Bond restraints: 18909 Sorted by residual: bond pdb=" CB PRO C 745 " pdb=" CG PRO C 745 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.88e+00 bond pdb=" CG LEU B 751 " pdb=" CD2 LEU B 751 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.42e+00 bond pdb=" CB GLU D 705 " pdb=" CG GLU D 705 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.33e+00 bond pdb=" CB GLU C 644 " pdb=" CG GLU C 644 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CB PRO C 737 " pdb=" CG PRO C 737 " ideal model delta sigma weight residual 1.492 1.546 -0.054 5.00e-02 4.00e+02 1.17e+00 ... (remaining 18904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 25303 2.58 - 5.15: 225 5.15 - 7.73: 21 7.73 - 10.31: 13 10.31 - 12.88: 3 Bond angle restraints: 25565 Sorted by residual: angle pdb=" CA PRO C 745 " pdb=" N PRO C 745 " pdb=" CD PRO C 745 " ideal model delta sigma weight residual 112.00 104.26 7.74 1.40e+00 5.10e-01 3.05e+01 angle pdb=" C LYS C 765 " pdb=" N TRP C 766 " pdb=" CA TRP C 766 " ideal model delta sigma weight residual 122.49 114.45 8.04 1.55e+00 4.16e-01 2.69e+01 angle pdb=" CG ARG F 99 " pdb=" CD ARG F 99 " pdb=" NE ARG F 99 " ideal model delta sigma weight residual 112.00 121.95 -9.95 2.20e+00 2.07e-01 2.04e+01 angle pdb=" CB MET C 408 " pdb=" CG MET C 408 " pdb=" SD MET C 408 " ideal model delta sigma weight residual 112.70 125.58 -12.88 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CA GLN E 207 " pdb=" CB GLN E 207 " pdb=" CG GLN E 207 " ideal model delta sigma weight residual 114.10 122.17 -8.07 2.00e+00 2.50e-01 1.63e+01 ... (remaining 25560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9443 17.86 - 35.72: 1281 35.72 - 53.57: 285 53.57 - 71.43: 33 71.43 - 89.29: 25 Dihedral angle restraints: 11067 sinusoidal: 4227 harmonic: 6840 Sorted by residual: dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 165.14 -72.14 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 157.65 -64.65 1 1.00e+01 1.00e-02 5.49e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 151.50 -58.50 1 1.00e+01 1.00e-02 4.58e+01 ... (remaining 11064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1964 0.036 - 0.072: 693 0.072 - 0.107: 177 0.107 - 0.143: 38 0.143 - 0.179: 5 Chirality restraints: 2877 Sorted by residual: chirality pdb=" CA PRO C 745 " pdb=" N PRO C 745 " pdb=" C PRO C 745 " pdb=" CB PRO C 745 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CB ILE A 812 " pdb=" CA ILE A 812 " pdb=" CG1 ILE A 812 " pdb=" CG2 ILE A 812 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA TRP C 766 " pdb=" N TRP C 766 " pdb=" C TRP C 766 " pdb=" CB TRP C 766 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 2874 not shown) Planarity restraints: 3155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 766 " -0.034 2.00e-02 2.50e+03 3.38e-02 2.86e+01 pdb=" CG TRP C 766 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 TRP C 766 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP C 766 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 766 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 766 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 766 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 766 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 766 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP C 766 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 671 " -0.039 2.00e-02 2.50e+03 3.14e-02 2.47e+01 pdb=" CG TRP B 671 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP B 671 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP B 671 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 671 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 671 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 671 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 671 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 671 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP B 671 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 403 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO C 404 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 404 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 404 " 0.050 5.00e-02 4.00e+02 ... (remaining 3152 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1628 2.74 - 3.28: 19039 3.28 - 3.82: 32205 3.82 - 4.36: 35342 4.36 - 4.90: 62298 Nonbonded interactions: 150512 Sorted by model distance: nonbonded pdb=" N LEU G 3 " pdb=" OE1 GLN G 9 " model vdw 2.201 3.120 nonbonded pdb=" O VAL C 681 " pdb=" OH TYR C 700 " model vdw 2.228 3.040 nonbonded pdb=" OG SER B 635 " pdb=" OD1 ASP B 638 " model vdw 2.242 3.040 nonbonded pdb=" OE1 GLU A 657 " pdb=" NH2 ARG A 660 " model vdw 2.255 3.120 nonbonded pdb=" NE2 GLN B 642 " pdb=" O ILE B 645 " model vdw 2.261 3.120 ... (remaining 150507 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 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 575 or (resid 576 and (name N or name CA or name C or name \ O or name CB )) or resid 577 through 622 or resid 624 through 626 or (resid 627 \ and (name N or name CA or name C or name O or name CB )) or resid 628 through 7 \ 63 or resid 765 through 812 or (resid 813 and (name N or name CA or name C or na \ me O or name CB )) or resid 814 through 818 or (resid 819 through 820 and (name \ N or name CA or name C or name O or name CB )) or resid 821 through 825)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 506 or (resid 511 and (name N or name CA or name C or name \ O or name CB )) or resid 512 through 575 or (resid 576 and (name N or name CA o \ r name C or name O or name CB )) or resid 577 through 593 or (resid 594 and (nam \ e N or name CA or name C or name O or name CB )) or resid 595 through 622 or res \ id 624 through 626 or (resid 627 and (name N or name CA or name C or name O or n \ ame CB )) or resid 628 through 763 or resid 765 through 773 or (resid 784 and (n \ ame N or name CA or name C or name O or name CB )) or resid 785 through 825)) selection = (chain 'C' and (resid 393 through 434 or resid 436 through 593 or (resid 594 and \ (name N or name CA or name C or name O or name CB )) or resid 595 through 622 o \ r resid 624 through 626 or (resid 627 and (name N or name CA or name C or name O \ or name CB )) or resid 628 through 666 or (resid 667 and (name N or name CA or \ name C or name O or name CB )) or resid 668 through 763 or resid 765 through 812 \ or (resid 813 and (name N or name CA or name C or name O or name CB )) or resid \ 814 through 818 or (resid 819 through 820 and (name N or name CA or name C or n \ ame O or name CB )) or resid 821 through 825)) selection = (chain 'D' and (resid 393 through 434 or resid 436 through 506 or (resid 511 and \ (name N or name CA or name C or name O or name CB )) or resid 512 through 575 o \ r (resid 576 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 77 through 593 or (resid 594 and (name N or name CA or name C or name O or name \ CB )) or resid 595 through 622 or resid 624 through 666 or (resid 667 and (name \ N or name CA or name C or name O or name CB )) or resid 668 through 763 or resid \ 765 through 773 or (resid 784 and (name N or name CA or name C or name O or nam \ e CB )) or resid 785 through 825)) } ncs_group { reference = (chain 'E' and resid 5 through 214) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 214)) selection = (chain 'G' and resid 5 through 214) selection = (chain 'H' and (resid 5 through 41 or resid 55 through 214)) } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.780 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.570 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.003 0.099 18921 Z= 0.136 Angle : 0.642 12.884 25589 Z= 0.337 Chirality : 0.039 0.179 2877 Planarity : 0.005 0.102 3155 Dihedral : 16.807 89.291 6665 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.15 % Allowed : 27.72 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.18), residues: 2337 helix: 2.44 (0.14), residues: 1393 sheet: -0.74 (0.37), residues: 192 loop : -0.91 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 594 TYR 0.019 0.001 TYR E 156 PHE 0.015 0.001 PHE D 658 TRP 0.086 0.002 TRP C 766 HIS 0.007 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00299 (18909) covalent geometry : angle 0.64008 (25565) SS BOND : bond 0.00430 ( 12) SS BOND : angle 1.64815 ( 24) hydrogen bonds : bond 0.12805 ( 1211) hydrogen bonds : angle 4.92658 ( 3526) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 346 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: H 115 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8597 (mp) REVERT: F 117 MET cc_start: 0.7842 (mmt) cc_final: 0.7639 (mmm) REVERT: F 178 TRP cc_start: 0.7586 (p-90) cc_final: 0.4641 (m100) REVERT: F 204 ARG cc_start: 0.6746 (ptm160) cc_final: 0.6542 (ptm160) REVERT: C 641 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7445 (mttt) REVERT: A 769 ASP cc_start: 0.7559 (m-30) cc_final: 0.7324 (t0) REVERT: D 816 TYR cc_start: 0.7431 (t80) cc_final: 0.7179 (t80) REVERT: E 5 ASP cc_start: 0.5721 (m-30) cc_final: 0.5263 (m-30) REVERT: E 78 LYS cc_start: 0.7427 (ptmt) cc_final: 0.6807 (pttt) outliers start: 3 outliers final: 2 residues processed: 348 average time/residue: 0.1302 time to fit residues: 68.4068 Evaluate side-chains 330 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 327 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain G residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS H 149 ASN F 149 ASN D 508 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN G 149 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.131906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.092183 restraints weight = 81992.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.096408 restraints weight = 30967.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099140 restraints weight = 18309.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.100673 restraints weight = 13771.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.101473 restraints weight = 11894.928| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18921 Z= 0.152 Angle : 0.556 10.080 25589 Z= 0.288 Chirality : 0.040 0.186 2877 Planarity : 0.005 0.086 3155 Dihedral : 3.878 52.886 2568 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.49 % Allowed : 24.02 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.18), residues: 2337 helix: 2.66 (0.14), residues: 1403 sheet: -0.48 (0.39), residues: 180 loop : -0.91 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 594 TYR 0.019 0.001 TYR B 673 PHE 0.015 0.001 PHE C 814 TRP 0.074 0.002 TRP C 766 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00359 (18909) covalent geometry : angle 0.55473 (25565) SS BOND : bond 0.00590 ( 12) SS BOND : angle 1.12102 ( 24) hydrogen bonds : bond 0.03905 ( 1211) hydrogen bonds : angle 3.86379 ( 3526) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 346 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: H 115 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8548 (mp) REVERT: F 126 GLU cc_start: 0.6526 (mt-10) cc_final: 0.6075 (tm-30) REVERT: D 629 MET cc_start: 0.7626 (mmm) cc_final: 0.7385 (mmt) REVERT: D 816 TYR cc_start: 0.7498 (t80) cc_final: 0.7259 (t80) REVERT: E 5 ASP cc_start: 0.5884 (m-30) cc_final: 0.5458 (m-30) REVERT: E 58 MET cc_start: 0.7018 (mtp) cc_final: 0.6602 (mtp) REVERT: E 78 LYS cc_start: 0.7340 (ptmt) cc_final: 0.6715 (pttt) outliers start: 68 outliers final: 34 residues processed: 388 average time/residue: 0.1297 time to fit residues: 75.8922 Evaluate side-chains 352 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 317 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 197 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 211 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS B 756 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.092266 restraints weight = 66648.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.096268 restraints weight = 26868.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098739 restraints weight = 16453.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.100147 restraints weight = 12722.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.100748 restraints weight = 11121.259| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18921 Z= 0.179 Angle : 0.571 8.086 25589 Z= 0.298 Chirality : 0.041 0.204 2877 Planarity : 0.004 0.065 3155 Dihedral : 3.868 50.687 2566 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.06 % Allowed : 24.08 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.18), residues: 2337 helix: 2.53 (0.14), residues: 1401 sheet: -0.61 (0.38), residues: 176 loop : -0.81 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 594 TYR 0.022 0.002 TYR B 673 PHE 0.016 0.001 PHE C 814 TRP 0.090 0.002 TRP C 766 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00422 (18909) covalent geometry : angle 0.56994 (25565) SS BOND : bond 0.00825 ( 12) SS BOND : angle 1.23578 ( 24) hydrogen bonds : bond 0.04128 ( 1211) hydrogen bonds : angle 3.92959 ( 3526) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 348 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 GLN cc_start: 0.7724 (mt0) cc_final: 0.7503 (mt0) REVERT: H 86 ASP cc_start: -0.0278 (OUTLIER) cc_final: -0.0921 (t70) REVERT: H 117 MET cc_start: 0.7821 (mmm) cc_final: 0.7534 (mtp) REVERT: H 196 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7714 (tp) REVERT: H 199 HIS cc_start: 0.7921 (t70) cc_final: 0.7631 (t70) REVERT: F 126 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6292 (tm-30) REVERT: C 407 MET cc_start: 0.7116 (ptp) cc_final: 0.6596 (ptm) REVERT: C 641 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7377 (mttt) REVERT: C 814 PHE cc_start: 0.7985 (t80) cc_final: 0.7748 (t80) REVERT: B 634 GLU cc_start: 0.7189 (tp30) cc_final: 0.6815 (tp30) REVERT: B 702 TYR cc_start: 0.8281 (t80) cc_final: 0.7828 (t80) REVERT: A 416 GLU cc_start: 0.5809 (mp0) cc_final: 0.5518 (mp0) REVERT: A 634 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7276 (pt0) REVERT: A 708 MET cc_start: 0.7939 (tpp) cc_final: 0.7599 (tpt) REVERT: D 463 MET cc_start: 0.8341 (mmt) cc_final: 0.7129 (mmt) REVERT: D 816 TYR cc_start: 0.7591 (t80) cc_final: 0.7384 (t80) REVERT: E 10 MET cc_start: 0.8275 (mmm) cc_final: 0.8037 (mmm) REVERT: E 78 LYS cc_start: 0.7571 (ptmt) cc_final: 0.7364 (ptmm) outliers start: 79 outliers final: 51 residues processed: 405 average time/residue: 0.1249 time to fit residues: 76.4219 Evaluate side-chains 371 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 317 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 641 LYS Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 96 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 158 optimal weight: 0.0060 chunk 64 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 9 GLN H 132 HIS H 149 ASN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN G 72 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.134000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095180 restraints weight = 105212.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099966 restraints weight = 33955.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103000 restraints weight = 18734.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.104762 restraints weight = 13691.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105730 restraints weight = 11655.124| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18921 Z= 0.112 Angle : 0.523 13.375 25589 Z= 0.268 Chirality : 0.039 0.214 2877 Planarity : 0.004 0.059 3155 Dihedral : 3.544 22.582 2563 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.08 % Allowed : 25.51 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.18), residues: 2337 helix: 2.75 (0.14), residues: 1399 sheet: -0.59 (0.38), residues: 166 loop : -0.78 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 594 TYR 0.017 0.001 TYR E 156 PHE 0.010 0.001 PHE C 814 TRP 0.070 0.002 TRP C 766 HIS 0.004 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00255 (18909) covalent geometry : angle 0.52222 (25565) SS BOND : bond 0.00339 ( 12) SS BOND : angle 1.11289 ( 24) hydrogen bonds : bond 0.03467 ( 1211) hydrogen bonds : angle 3.71204 ( 3526) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 350 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.0025 (OUTLIER) cc_final: -0.0653 (t70) REVERT: H 115 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8468 (mp) REVERT: F 110 LEU cc_start: 0.8130 (tt) cc_final: 0.7876 (tt) REVERT: F 126 GLU cc_start: 0.6565 (mt-10) cc_final: 0.6230 (tm-30) REVERT: C 407 MET cc_start: 0.6969 (ptp) cc_final: 0.6653 (ptm) REVERT: C 441 LYS cc_start: 0.8357 (tmtt) cc_final: 0.7938 (mmmt) REVERT: C 641 LYS cc_start: 0.7867 (ttpp) cc_final: 0.7401 (mttt) REVERT: C 814 PHE cc_start: 0.7962 (t80) cc_final: 0.7636 (t80) REVERT: B 549 TYR cc_start: 0.6302 (m-80) cc_final: 0.6097 (m-80) REVERT: B 702 TYR cc_start: 0.8219 (t80) cc_final: 0.7860 (t80) REVERT: A 416 GLU cc_start: 0.5664 (mp0) cc_final: 0.5439 (mp0) REVERT: A 634 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7311 (pt0) REVERT: A 638 ASP cc_start: 0.8043 (m-30) cc_final: 0.7697 (m-30) REVERT: D 463 MET cc_start: 0.8304 (mmt) cc_final: 0.7089 (mmt) REVERT: E 33 TRP cc_start: 0.8826 (m100) cc_final: 0.8554 (m100) REVERT: E 58 MET cc_start: 0.7186 (mtp) cc_final: 0.6833 (mtp) REVERT: G 37 ARG cc_start: 0.5169 (ptt-90) cc_final: 0.4542 (ptt-90) REVERT: G 72 ASN cc_start: 0.6913 (OUTLIER) cc_final: 0.6544 (p0) outliers start: 60 outliers final: 40 residues processed: 388 average time/residue: 0.1201 time to fit residues: 72.1667 Evaluate side-chains 364 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 321 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 642 GLN Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 122 optimal weight: 0.0980 chunk 191 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 218 optimal weight: 20.0000 chunk 220 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 208 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 9 GLN H 132 HIS H 149 ASN D 642 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.131767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.095528 restraints weight = 70694.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099274 restraints weight = 27797.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.101770 restraints weight = 16637.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.101735 restraints weight = 15468.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.101626 restraints weight = 13499.873| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18921 Z= 0.156 Angle : 0.542 10.017 25589 Z= 0.282 Chirality : 0.040 0.219 2877 Planarity : 0.004 0.058 3155 Dihedral : 3.657 22.977 2563 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.11 % Allowed : 24.08 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.18), residues: 2337 helix: 2.64 (0.14), residues: 1399 sheet: -0.54 (0.38), residues: 176 loop : -0.82 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 594 TYR 0.017 0.001 TYR E 156 PHE 0.023 0.001 PHE D 546 TRP 0.076 0.002 TRP B 671 HIS 0.006 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00368 (18909) covalent geometry : angle 0.54073 (25565) SS BOND : bond 0.00300 ( 12) SS BOND : angle 1.37314 ( 24) hydrogen bonds : bond 0.03817 ( 1211) hydrogen bonds : angle 3.81806 ( 3526) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 334 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LEU cc_start: 0.8077 (mp) cc_final: 0.7716 (mp) REVERT: H 24 MET cc_start: 0.6998 (tpt) cc_final: 0.6790 (tpp) REVERT: H 86 ASP cc_start: 0.0062 (OUTLIER) cc_final: -0.0617 (t0) REVERT: H 115 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8431 (mp) REVERT: F 110 LEU cc_start: 0.8129 (tt) cc_final: 0.7928 (tt) REVERT: F 126 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6316 (tm-30) REVERT: C 407 MET cc_start: 0.6994 (ptp) cc_final: 0.6599 (ptm) REVERT: C 641 LYS cc_start: 0.7883 (ttpp) cc_final: 0.7415 (mttt) REVERT: C 814 PHE cc_start: 0.8002 (t80) cc_final: 0.7737 (t80) REVERT: B 702 TYR cc_start: 0.8296 (t80) cc_final: 0.7951 (t80) REVERT: A 634 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7359 (pt0) REVERT: D 412 HIS cc_start: 0.6756 (p-80) cc_final: 0.6541 (p90) REVERT: D 463 MET cc_start: 0.8364 (mmt) cc_final: 0.7103 (mmt) REVERT: D 816 TYR cc_start: 0.7524 (t80) cc_final: 0.7305 (t80) REVERT: E 33 TRP cc_start: 0.8744 (m100) cc_final: 0.8420 (m100) REVERT: E 151 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8480 (mt) REVERT: G 149 ASN cc_start: 0.8662 (t0) cc_final: 0.8086 (t0) outliers start: 80 outliers final: 61 residues processed: 389 average time/residue: 0.1272 time to fit residues: 75.6418 Evaluate side-chains 384 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 320 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 642 GLN Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 88 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN ** D 747 ASN ** 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 = 0.3802 r_free = 0.3802 target = 0.133196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.094797 restraints weight = 103216.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100352 restraints weight = 34316.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.101595 restraints weight = 19576.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.102326 restraints weight = 15126.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102419 restraints weight = 14125.473| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18921 Z= 0.119 Angle : 0.519 9.214 25589 Z= 0.269 Chirality : 0.039 0.215 2877 Planarity : 0.004 0.057 3155 Dihedral : 3.557 21.807 2563 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.80 % Allowed : 24.33 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.18), residues: 2337 helix: 2.76 (0.14), residues: 1399 sheet: -0.51 (0.39), residues: 166 loop : -0.78 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 204 TYR 0.018 0.001 TYR E 156 PHE 0.023 0.001 PHE D 546 TRP 0.057 0.002 TRP B 671 HIS 0.006 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00274 (18909) covalent geometry : angle 0.51685 (25565) SS BOND : bond 0.00280 ( 12) SS BOND : angle 1.65553 ( 24) hydrogen bonds : bond 0.03486 ( 1211) hydrogen bonds : angle 3.71290 ( 3526) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 340 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LEU cc_start: 0.8049 (mp) cc_final: 0.7714 (mp) REVERT: H 86 ASP cc_start: 0.0180 (OUTLIER) cc_final: -0.0523 (t0) REVERT: H 127 PHE cc_start: 0.5463 (OUTLIER) cc_final: 0.5135 (m-10) REVERT: H 131 ARG cc_start: 0.5106 (mmp-170) cc_final: 0.4865 (mmm160) REVERT: H 204 ARG cc_start: 0.7051 (ttm-80) cc_final: 0.6219 (ttp80) REVERT: F 126 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6337 (tm-30) REVERT: C 407 MET cc_start: 0.7009 (ptp) cc_final: 0.6587 (ptm) REVERT: C 441 LYS cc_start: 0.8271 (tmtt) cc_final: 0.7845 (tptp) REVERT: C 641 LYS cc_start: 0.7910 (ttpp) cc_final: 0.7471 (mttt) REVERT: C 814 PHE cc_start: 0.7987 (t80) cc_final: 0.7680 (t80) REVERT: B 702 TYR cc_start: 0.8285 (t80) cc_final: 0.7946 (t80) REVERT: A 634 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7389 (pt0) REVERT: D 463 MET cc_start: 0.8314 (mmt) cc_final: 0.7108 (mmt) REVERT: D 816 TYR cc_start: 0.7478 (t80) cc_final: 0.7272 (t80) REVERT: E 30 THR cc_start: 0.7200 (p) cc_final: 0.6964 (p) REVERT: G 56 GLU cc_start: 0.6340 (tm-30) cc_final: 0.6099 (tm-30) outliers start: 74 outliers final: 60 residues processed: 386 average time/residue: 0.1331 time to fit residues: 77.7457 Evaluate side-chains 387 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 325 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 642 GLN Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 155 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 199 optimal weight: 8.9990 chunk 209 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS H 149 ASN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.095509 restraints weight = 89973.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.099713 restraints weight = 30981.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.100902 restraints weight = 17872.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.101284 restraints weight = 18222.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101336 restraints weight = 15334.603| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18921 Z= 0.137 Angle : 0.546 11.472 25589 Z= 0.279 Chirality : 0.039 0.218 2877 Planarity : 0.004 0.056 3155 Dihedral : 3.566 21.474 2563 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.00 % Allowed : 24.08 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.18), residues: 2337 helix: 2.73 (0.14), residues: 1399 sheet: -0.57 (0.37), residues: 186 loop : -0.80 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 6 TYR 0.016 0.001 TYR E 156 PHE 0.023 0.001 PHE D 546 TRP 0.056 0.002 TRP B 671 HIS 0.006 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00323 (18909) covalent geometry : angle 0.54328 (25565) SS BOND : bond 0.00317 ( 12) SS BOND : angle 1.76569 ( 24) hydrogen bonds : bond 0.03589 ( 1211) hydrogen bonds : angle 3.74353 ( 3526) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 337 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LEU cc_start: 0.8047 (mp) cc_final: 0.7705 (mp) REVERT: H 24 MET cc_start: 0.7027 (tpt) cc_final: 0.6803 (tpp) REVERT: H 86 ASP cc_start: 0.0221 (OUTLIER) cc_final: -0.0493 (t0) REVERT: H 127 PHE cc_start: 0.5494 (OUTLIER) cc_final: 0.5161 (m-10) REVERT: H 131 ARG cc_start: 0.5226 (mmp-170) cc_final: 0.4986 (mmm160) REVERT: H 204 ARG cc_start: 0.6685 (ttm-80) cc_final: 0.6329 (mtm110) REVERT: F 126 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6341 (tm-30) REVERT: C 407 MET cc_start: 0.7078 (ptp) cc_final: 0.6615 (ptm) REVERT: C 441 LYS cc_start: 0.8279 (tmtt) cc_final: 0.7836 (tptp) REVERT: C 641 LYS cc_start: 0.7949 (ttpp) cc_final: 0.7498 (mttt) REVERT: C 814 PHE cc_start: 0.7987 (t80) cc_final: 0.7728 (t80) REVERT: B 702 TYR cc_start: 0.8306 (t80) cc_final: 0.8012 (t80) REVERT: A 634 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7404 (pt0) REVERT: A 756 GLN cc_start: 0.8279 (mm110) cc_final: 0.8041 (mm110) REVERT: D 463 MET cc_start: 0.8356 (mmt) cc_final: 0.7127 (mmt) REVERT: D 816 TYR cc_start: 0.7492 (t80) cc_final: 0.7278 (t80) REVERT: E 30 THR cc_start: 0.7232 (p) cc_final: 0.7012 (p) REVERT: G 37 ARG cc_start: 0.5356 (ptt-90) cc_final: 0.4828 (ptt-90) REVERT: G 40 CYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7218 (p) REVERT: G 56 GLU cc_start: 0.6384 (tm-30) cc_final: 0.6139 (tm-30) outliers start: 78 outliers final: 68 residues processed: 387 average time/residue: 0.1262 time to fit residues: 74.6938 Evaluate side-chains 398 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 327 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 642 GLN Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 131 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 167 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 82 HIS ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.131525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.093654 restraints weight = 104129.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.099359 restraints weight = 33979.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100018 restraints weight = 16797.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.099983 restraints weight = 16825.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.100281 restraints weight = 15394.811| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18921 Z= 0.154 Angle : 0.562 11.792 25589 Z= 0.288 Chirality : 0.040 0.220 2877 Planarity : 0.004 0.056 3155 Dihedral : 3.641 21.664 2563 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.21 % Allowed : 23.97 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.18), residues: 2337 helix: 2.69 (0.14), residues: 1395 sheet: -0.62 (0.38), residues: 176 loop : -0.85 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 6 TYR 0.015 0.001 TYR E 156 PHE 0.023 0.001 PHE D 546 TRP 0.064 0.002 TRP B 671 HIS 0.006 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00364 (18909) covalent geometry : angle 0.56049 (25565) SS BOND : bond 0.00342 ( 12) SS BOND : angle 1.57825 ( 24) hydrogen bonds : bond 0.03730 ( 1211) hydrogen bonds : angle 3.80775 ( 3526) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 335 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LEU cc_start: 0.8024 (mp) cc_final: 0.7678 (mp) REVERT: H 24 MET cc_start: 0.7041 (tpt) cc_final: 0.6827 (tpp) REVERT: H 86 ASP cc_start: 0.0489 (OUTLIER) cc_final: -0.0265 (t0) REVERT: H 127 PHE cc_start: 0.5389 (OUTLIER) cc_final: 0.5111 (m-10) REVERT: H 204 ARG cc_start: 0.6676 (ttm-80) cc_final: 0.6280 (mtm110) REVERT: F 126 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6383 (tm-30) REVERT: F 203 ASP cc_start: 0.8106 (t0) cc_final: 0.7888 (t0) REVERT: F 209 ARG cc_start: 0.4893 (OUTLIER) cc_final: 0.4329 (tmm160) REVERT: C 407 MET cc_start: 0.7013 (ptp) cc_final: 0.6580 (ptm) REVERT: C 441 LYS cc_start: 0.8287 (tmtt) cc_final: 0.7840 (tptp) REVERT: C 641 LYS cc_start: 0.7883 (ttpp) cc_final: 0.7426 (mttt) REVERT: C 814 PHE cc_start: 0.7993 (t80) cc_final: 0.7738 (t80) REVERT: B 702 TYR cc_start: 0.8318 (t80) cc_final: 0.8027 (t80) REVERT: A 634 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7385 (pt0) REVERT: A 756 GLN cc_start: 0.8235 (mm110) cc_final: 0.8013 (mm110) REVERT: D 463 MET cc_start: 0.8375 (mmt) cc_final: 0.7148 (mmt) REVERT: D 816 TYR cc_start: 0.7503 (t80) cc_final: 0.7281 (t80) REVERT: E 30 THR cc_start: 0.7130 (p) cc_final: 0.6868 (p) REVERT: G 10 MET cc_start: 0.7614 (tpp) cc_final: 0.7115 (tpp) REVERT: G 37 ARG cc_start: 0.5366 (ptt-90) cc_final: 0.4859 (ptt-90) REVERT: G 40 CYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7205 (p) REVERT: G 56 GLU cc_start: 0.6494 (tm-30) cc_final: 0.6261 (tm-30) outliers start: 82 outliers final: 70 residues processed: 388 average time/residue: 0.1327 time to fit residues: 77.8674 Evaluate side-chains 398 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 324 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 209 ARG Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 642 GLN Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 137 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 203 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 149 ASN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN E 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.133053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094568 restraints weight = 89824.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099250 restraints weight = 30337.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.102203 restraints weight = 17171.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103917 restraints weight = 12702.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.104604 restraints weight = 10900.986| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18921 Z= 0.116 Angle : 0.550 11.990 25589 Z= 0.279 Chirality : 0.039 0.214 2877 Planarity : 0.004 0.054 3155 Dihedral : 3.554 21.833 2563 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.75 % Allowed : 24.74 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.18), residues: 2337 helix: 2.77 (0.14), residues: 1399 sheet: -0.57 (0.37), residues: 186 loop : -0.77 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 6 TYR 0.019 0.001 TYR A 647 PHE 0.023 0.001 PHE D 546 TRP 0.058 0.002 TRP B 671 HIS 0.006 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00264 (18909) covalent geometry : angle 0.54889 (25565) SS BOND : bond 0.00293 ( 12) SS BOND : angle 1.34174 ( 24) hydrogen bonds : bond 0.03408 ( 1211) hydrogen bonds : angle 3.69804 ( 3526) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 337 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LEU cc_start: 0.8116 (mp) cc_final: 0.7782 (mp) REVERT: H 24 MET cc_start: 0.7038 (tpt) cc_final: 0.6814 (tpp) REVERT: H 86 ASP cc_start: 0.0220 (OUTLIER) cc_final: -0.0349 (t0) REVERT: F 65 ARG cc_start: 0.6273 (ptp-110) cc_final: 0.5958 (ptp-110) REVERT: F 209 ARG cc_start: 0.4942 (OUTLIER) cc_final: 0.4418 (tmm160) REVERT: C 407 MET cc_start: 0.6840 (ptp) cc_final: 0.6558 (ptm) REVERT: C 441 LYS cc_start: 0.8264 (tmtt) cc_final: 0.7826 (tptp) REVERT: C 641 LYS cc_start: 0.7923 (ttpp) cc_final: 0.7475 (mttt) REVERT: C 814 PHE cc_start: 0.7982 (t80) cc_final: 0.7765 (t80) REVERT: B 702 TYR cc_start: 0.8319 (t80) cc_final: 0.8016 (t80) REVERT: B 732 TYR cc_start: 0.8492 (m-10) cc_final: 0.8174 (m-10) REVERT: A 399 THR cc_start: 0.8766 (p) cc_final: 0.8374 (m) REVERT: A 634 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7362 (pt0) REVERT: D 463 MET cc_start: 0.8369 (mmt) cc_final: 0.7143 (mmt) REVERT: D 633 ILE cc_start: 0.8766 (mm) cc_final: 0.8536 (tp) REVERT: D 816 TYR cc_start: 0.7526 (t80) cc_final: 0.7305 (t80) REVERT: E 30 THR cc_start: 0.6965 (p) cc_final: 0.6732 (p) REVERT: E 58 MET cc_start: 0.7288 (mtp) cc_final: 0.7067 (mtp) REVERT: G 10 MET cc_start: 0.7515 (tpp) cc_final: 0.7061 (tpp) REVERT: G 37 ARG cc_start: 0.5251 (ptt-90) cc_final: 0.4749 (ptt-90) REVERT: G 99 ARG cc_start: 0.5207 (ttm110) cc_final: 0.4250 (ptm160) outliers start: 73 outliers final: 62 residues processed: 382 average time/residue: 0.1336 time to fit residues: 77.6739 Evaluate side-chains 389 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 325 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 209 ARG Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 642 GLN Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 225 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 143 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 149 ASN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN ** D 747 ASN ** 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 = 0.3806 r_free = 0.3806 target = 0.133306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095375 restraints weight = 80982.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099743 restraints weight = 29743.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.102500 restraints weight = 17543.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.104118 restraints weight = 13304.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104777 restraints weight = 11517.156| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18921 Z= 0.116 Angle : 0.565 12.144 25589 Z= 0.286 Chirality : 0.039 0.214 2877 Planarity : 0.004 0.054 3155 Dihedral : 3.574 21.801 2563 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.34 % Allowed : 25.26 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.18), residues: 2337 helix: 2.76 (0.14), residues: 1399 sheet: -0.57 (0.37), residues: 186 loop : -0.80 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 6 TYR 0.018 0.001 TYR A 647 PHE 0.023 0.001 PHE D 546 TRP 0.071 0.002 TRP B 671 HIS 0.006 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00265 (18909) covalent geometry : angle 0.56269 (25565) SS BOND : bond 0.00272 ( 12) SS BOND : angle 1.66122 ( 24) hydrogen bonds : bond 0.03414 ( 1211) hydrogen bonds : angle 3.70352 ( 3526) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 324 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LEU cc_start: 0.8134 (mp) cc_final: 0.7800 (mp) REVERT: H 58 MET cc_start: 0.6028 (tpt) cc_final: 0.5684 (mmm) REVERT: H 86 ASP cc_start: 0.0178 (OUTLIER) cc_final: -0.0367 (t0) REVERT: F 65 ARG cc_start: 0.6276 (ptp-110) cc_final: 0.5984 (ptp-110) REVERT: F 102 ARG cc_start: 0.6373 (tpt90) cc_final: 0.5958 (tpt170) REVERT: F 178 TRP cc_start: 0.7508 (p-90) cc_final: 0.4350 (m100) REVERT: F 209 ARG cc_start: 0.4919 (OUTLIER) cc_final: 0.4430 (tmm160) REVERT: C 407 MET cc_start: 0.6794 (ptp) cc_final: 0.6559 (ptm) REVERT: C 441 LYS cc_start: 0.8247 (tmtt) cc_final: 0.7806 (tptp) REVERT: C 641 LYS cc_start: 0.7915 (ttpp) cc_final: 0.7477 (mttt) REVERT: C 692 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.6816 (tpp80) REVERT: C 814 PHE cc_start: 0.7991 (t80) cc_final: 0.7697 (t80) REVERT: B 549 TYR cc_start: 0.6252 (m-80) cc_final: 0.6026 (m-80) REVERT: B 702 TYR cc_start: 0.8307 (t80) cc_final: 0.8039 (t80) REVERT: B 732 TYR cc_start: 0.8453 (m-10) cc_final: 0.8155 (m-10) REVERT: A 399 THR cc_start: 0.8755 (p) cc_final: 0.8336 (m) REVERT: A 634 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7365 (pt0) REVERT: D 463 MET cc_start: 0.8348 (mmt) cc_final: 0.7140 (mmt) REVERT: D 816 TYR cc_start: 0.7527 (t80) cc_final: 0.7307 (t80) REVERT: E 30 THR cc_start: 0.6905 (p) cc_final: 0.6662 (p) REVERT: G 37 ARG cc_start: 0.5490 (ptt-90) cc_final: 0.4975 (ptt-90) REVERT: G 40 CYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7318 (p) REVERT: G 99 ARG cc_start: 0.5187 (ttm110) cc_final: 0.3846 (ptm160) outliers start: 65 outliers final: 57 residues processed: 366 average time/residue: 0.1346 time to fit residues: 74.3274 Evaluate side-chains 383 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 322 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 209 ARG Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 642 GLN Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 88 optimal weight: 0.0020 chunk 202 optimal weight: 4.9990 chunk 61 optimal weight: 0.0570 chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 overall best weight: 0.5710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 149 ASN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN ** D 747 ASN ** 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 = 0.3804 r_free = 0.3804 target = 0.133132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.095014 restraints weight = 73698.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.099241 restraints weight = 28198.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.101842 restraints weight = 16858.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.103330 restraints weight = 12888.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.103866 restraints weight = 11239.485| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18921 Z= 0.107 Angle : 0.567 11.945 25589 Z= 0.285 Chirality : 0.039 0.210 2877 Planarity : 0.004 0.054 3155 Dihedral : 3.534 22.080 2563 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.41 % Allowed : 26.28 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.18), residues: 2337 helix: 2.78 (0.14), residues: 1401 sheet: -0.59 (0.37), residues: 186 loop : -0.75 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 6 TYR 0.015 0.001 TYR A 647 PHE 0.023 0.001 PHE D 546 TRP 0.077 0.002 TRP B 671 HIS 0.006 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00235 (18909) covalent geometry : angle 0.56486 (25565) SS BOND : bond 0.00279 ( 12) SS BOND : angle 1.59500 ( 24) hydrogen bonds : bond 0.03284 ( 1211) hydrogen bonds : angle 3.69099 ( 3526) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3654.72 seconds wall clock time: 63 minutes 37.21 seconds (3817.21 seconds total)