Starting phenix.real_space_refine on Sun Aug 24 10:02:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c1r_16381/08_2025/8c1r_16381_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c1r_16381/08_2025/8c1r_16381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8c1r_16381/08_2025/8c1r_16381_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c1r_16381/08_2025/8c1r_16381_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c1r_16381/08_2025/8c1r_16381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c1r_16381/08_2025/8c1r_16381.map" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 S 124 5.16 5 C 12024 2.51 5 N 2880 2.21 5 O 3284 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18333 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 405, 3083 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Conformer: "B" Number of residues, atoms: 405, 3083 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 bond proxies already assigned to first conformer: 3127 Chain: "B" Number of atoms: 3068 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 406, 3057 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 Conformer: "B" Number of residues, atoms: 406, 3057 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 bond proxies already assigned to first conformer: 3114 Chain: "C" Number of atoms: 3063 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 405, 3052 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 55 Conformer: "B" Number of residues, atoms: 405, 3052 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 55 bond proxies already assigned to first conformer: 3109 Chain: "D" Number of atoms: 3076 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 406, 3065 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 60 Conformer: "B" Number of residues, atoms: 406, 3065 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 60 bond proxies already assigned to first conformer: 3122 Chain: "E" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1366 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1381 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 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: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 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: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1367 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {'OLC': 1, 'PLM': 2, 'ZK1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'OLC': 1, 'PLM': 1, 'ZK1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'PLM': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N APHE A 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 574 " occ=0.50 residue: pdb=" N APHE A 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 623 " occ=0.50 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 C 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 623 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.50 Time building chain proxies: 7.99, per 1000 atoms: 0.44 Number of scatterers: 18333 At special positions: 0 Unit cell: (118.944, 116.466, 137.116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 9 15.00 F 12 9.00 O 3284 8.00 N 2880 7.00 C 12024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.01 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.04 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.04 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.01 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.06 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 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: 1.61 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4264 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 27 sheets defined 59.6% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.700A pdb=" N ASP A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 488 removed outlier: 4.184A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.683A 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 629 Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.559A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (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 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 757 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 820 removed outlier: 3.528A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.686A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 482 through 489 removed outlier: 3.501A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.619A 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 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 removed outlier: 3.961A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 4.147A 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 715 removed outlier: 3.551A pdb=" N ARG B 715 " --> pdb=" O TYR B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.626A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 792 through 823 removed outlier: 3.526A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 removed outlier: 3.724A pdb=" N GLU C 550 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TRP C 551 " --> pdb=" O PRO C 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 547 through 551' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 629 Processing helix chain 'C' and resid 636 through 642 removed outlier: 4.063A pdb=" N GLN C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 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 757 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 792 through 821 removed outlier: 3.691A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 4.066A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.725A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 545 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 removed outlier: 3.592A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.708A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.600A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 757 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 823 removed outlier: 3.550A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 30 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 132 through 160 removed outlier: 3.570A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 210 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 93 through 105 removed outlier: 3.653A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 127 removed outlier: 3.891A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 160 Processing helix chain 'F' and resid 177 through 209 Processing helix chain 'G' and resid 7 through 30 removed outlier: 3.938A pdb=" N LEU G 11 " --> pdb=" O GLY G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 104 Processing helix chain 'G' and resid 105 through 127 removed outlier: 4.098A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.709A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER G 137 " --> pdb=" O ASN G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 210 Processing helix chain 'H' and resid 6 through 30 removed outlier: 4.058A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 105 through 128 removed outlier: 4.271A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 161 removed outlier: 3.545A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 209 removed outlier: 4.001A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.770A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.282A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.403A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 441 through 444 removed outlier: 3.547A pdb=" N THR B 443 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.757A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.689A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.770A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N ALA C 475 " --> pdb=" O PRO C 737 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.770A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N ALA C 475 " --> pdb=" O PRO C 737 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.714A pdb=" N ALA C 452 " --> pdb=" O ASN C 461 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.394A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 395 through 397 removed outlier: 6.290A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 451 through 453 Processing sheet with id=AC1, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.619A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.619A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.660A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 34 through 38 removed outlier: 3.554A pdb=" N LEU E 34 " --> pdb=" O SER E 61 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AC6, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AC7, first strand: chain 'G' and resid 65 through 67 Processing sheet with id=AC8, first strand: chain 'H' and resid 36 through 38 Processing sheet with id=AC9, first strand: chain 'H' and resid 65 through 67 1112 hydrogen bonds defined for protein. 3244 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: 3.73 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2850 1.31 - 1.45: 5429 1.45 - 1.58: 10240 1.58 - 1.72: 13 1.72 - 1.85: 201 Bond restraints: 18733 Sorted by residual: bond pdb=" CAO ZK1 A 901 " pdb=" PBA ZK1 A 901 " ideal model delta sigma weight residual 1.896 1.785 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" CAO ZK1 B 901 " pdb=" PBA ZK1 B 901 " ideal model delta sigma weight residual 1.896 1.797 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CAO ZK1 C 901 " pdb=" PBA ZK1 C 901 " ideal model delta sigma weight residual 1.896 1.799 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C LEU C 581 " pdb=" N GLY C 582 " ideal model delta sigma weight residual 1.335 1.273 0.061 1.26e-02 6.30e+03 2.35e+01 bond pdb=" CG MET B 585 " pdb=" SD MET B 585 " ideal model delta sigma weight residual 1.803 1.686 0.117 2.50e-02 1.60e+03 2.18e+01 ... (remaining 18728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 24443 2.66 - 5.32: 812 5.32 - 7.97: 47 7.97 - 10.63: 7 10.63 - 13.29: 3 Bond angle restraints: 25312 Sorted by residual: angle pdb=" N ASP A 590 " pdb=" CA ASP A 590 " pdb=" C ASP A 590 " ideal model delta sigma weight residual 113.23 107.12 6.11 1.24e+00 6.50e-01 2.42e+01 angle pdb=" N LEU C 639 " pdb=" CA LEU C 639 " pdb=" C LEU C 639 " ideal model delta sigma weight residual 112.23 106.07 6.16 1.26e+00 6.30e-01 2.39e+01 angle pdb=" O11 POV G1103 " pdb=" P POV G1103 " pdb=" O12 POV G1103 " ideal model delta sigma weight residual 97.67 110.96 -13.29 3.00e+00 1.11e-01 1.96e+01 angle pdb=" CA TYR C 673 " pdb=" CB TYR C 673 " pdb=" CG TYR C 673 " ideal model delta sigma weight residual 113.90 121.77 -7.87 1.80e+00 3.09e-01 1.91e+01 angle pdb=" N GLY D 653 " pdb=" CA GLY D 653 " pdb=" C GLY D 653 " ideal model delta sigma weight residual 110.56 117.75 -7.19 1.66e+00 3.63e-01 1.88e+01 ... (remaining 25307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.07: 10404 29.07 - 58.13: 480 58.13 - 87.20: 65 87.20 - 116.26: 14 116.26 - 145.33: 5 Dihedral angle restraints: 10968 sinusoidal: 4283 harmonic: 6685 Sorted by residual: dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual 93.00 6.09 86.91 1 1.00e+01 1.00e-02 9.08e+01 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 6.74 86.26 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual -86.00 -12.88 -73.12 1 1.00e+01 1.00e-02 6.81e+01 ... (remaining 10965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1865 0.069 - 0.137: 780 0.137 - 0.206: 150 0.206 - 0.274: 24 0.274 - 0.343: 6 Chirality restraints: 2825 Sorted by residual: chirality pdb=" CB VAL A 604 " pdb=" CA VAL A 604 " pdb=" CG1 VAL A 604 " pdb=" CG2 VAL A 604 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA SER D 615 " pdb=" N SER D 615 " pdb=" C SER D 615 " pdb=" CB SER D 615 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CB ILE A 612 " pdb=" CA ILE A 612 " pdb=" CG1 ILE A 612 " pdb=" CG2 ILE A 612 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 2822 not shown) Planarity restraints: 3073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 571 " 0.064 2.00e-02 2.50e+03 4.10e-02 2.94e+01 pdb=" CG PHE A 571 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A 571 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 571 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE A 571 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 571 " 0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 571 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " 0.052 2.00e-02 2.50e+03 3.20e-02 2.56e+01 pdb=" CG TRP A 606 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP A 606 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP A 606 " -0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 606 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 606 " 0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 606 " -0.050 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 176 " -0.053 2.00e-02 2.50e+03 2.91e-02 1.69e+01 pdb=" CG TYR H 176 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR H 176 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR H 176 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR H 176 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR H 176 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR H 176 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR H 176 " -0.029 2.00e-02 2.50e+03 ... (remaining 3070 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 221 2.63 - 3.20: 17470 3.20 - 3.77: 28237 3.77 - 4.33: 39474 4.33 - 4.90: 65572 Nonbonded interactions: 150974 Sorted by model distance: nonbonded pdb=" OG SER C 547 " pdb=" OE2 GLU C 550 " model vdw 2.068 3.040 nonbonded pdb=" O VAL B 681 " pdb=" OH TYR B 700 " model vdw 2.120 3.040 nonbonded pdb=" OD1 ASP A 651 " pdb=" N SER A 652 " model vdw 2.226 3.120 nonbonded pdb=" O GLU H 70 " pdb=" OE1 GLU H 70 " model vdw 2.226 3.040 nonbonded pdb=" NH2 ARG B 715 " pdb=" O LYS B 770 " model vdw 2.262 3.120 ... (remaining 150969 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 394 through 433 or (resid 434 and (name N or name CA or na \ me C or name O or name CB )) or resid 435 through 440 or (resid 441 and (name N \ or name CA or name C or name O or name CB )) or resid 442 through 453 or (resid \ 454 through 456 and (name N or name CA or name C or name O or name CB )) or resi \ d 457 or (resid 458 and (name N or name CA or name C or name O or name CB )) or \ resid 459 through 507 or (resid 508 through 509 and (name N or name CA or name C \ or name O or name CB )) or resid 510 through 573 or resid 575 through 593 or (r \ esid 594 and (name N or name CA or name C or name O or name CB )) or resid 595 t \ hrough 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 633 or (resid 634 and (name N or \ name CA or name C or name O or name CB )) or resid 635 through 637 or (resid 63 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 639 through \ 642 or (resid 643 through 644 and (name N or name CA or name C or name O or name \ CB )) or resid 645 through 650 or (resid 651 through 652 and (name N or name CA \ or name C or name O or name CB )) or resid 653 through 674 or (resid 675 and (n \ ame N or name CA or name C or name O or name CB )) or resid 676 through 687 or ( \ resid 688 and (name N or name CA or name C or name O or name CB )) or resid 689 \ through 715 or (resid 716 and (name N or name CA or name C or name O or name CB \ )) or resid 717 through 737 or (resid 738 and (name N or name CA or name C or na \ me O or name CB )) or resid 739 through 751 or (resid 752 and (name N or name CA \ or name C or name O or name CB )) or resid 753 through 754 or (resid 755 throug \ h 756 and (name N or name CA or name C or name O or name CB )) or resid 757 thro \ ugh 759 or (resid 760 through 761 and (name N or name CA or name C or name O or \ name CB )) or resid 762 through 764 or (resid 765 and (name N or name CA or name \ C or name O or name CB )) or resid 766 through 768 or (resid 769 and (name N or \ name CA or name C or name O or name CB )) or resid 770 through 774 or resid 784 \ through 812 or (resid 813 and (name N or name CA or name C or name O or name CB \ )) or resid 814 through 816 or (resid 817 and (name N or name CA or name C or n \ ame O or name CB )) or resid 818 or (resid 819 through 823 and (name N or name C \ A or name C or name O or name CB )) or resid 901)) selection = (chain 'B' and (resid 394 through 448 or (resid 449 and (name N or name CA or na \ me C or name O or name CB )) or resid 450 through 457 or (resid 458 and (name N \ or name CA or name C or name O or name CB )) or resid 459 through 507 or (resid \ 508 through 509 and (name N or name CA or name C or name O or name CB )) or resi \ d 510 or (resid 511 and (name N or name CA or name C or name O or name CB )) or \ resid 512 through 551 or (resid 569 and (name N or name CA or name C or name O o \ r name CB )) or resid 570 through 573 or resid 575 or (resid 576 and (name N or \ name CA or name C or name O or name CB )) or resid 577 through 593 or (resid 594 \ and (name N or name CA or name C or name O or name CB )) or resid 595 through 6 \ 22 or resid 624 through 637 or (resid 638 and (name N or name CA or name C or na \ me O or name CB )) or resid 639 through 650 or (resid 651 through 652 and (name \ N or name CA or name C or name O or name CB )) or resid 653 through 662 or (resi \ d 663 and (name N or name CA or name C or name O or name CB )) or resid 664 thro \ ugh 674 or (resid 675 and (name N or name CA or name C or name O or name CB )) o \ r resid 676 through 687 or (resid 688 and (name N or name CA or name C or name O \ or name CB )) or resid 689 through 694 or (resid 695 and (name N or name CA or \ name C or name O or name CB )) or resid 696 or (resid 697 and (name N or name CA \ or name C or name O or name CB )) or resid 698 through 755 or (resid 756 and (n \ ame N or name CA or name C or name O or name CB )) or resid 757 through 759 or ( \ resid 760 through 761 and (name N or name CA or name C or name O or name CB )) o \ r resid 762 through 771 or (resid 772 and (name N or name CA or name C or name O \ or name CB )) or resid 773 through 774 or (resid 784 and (name N or name CA or \ name C or name O or name CB )) or resid 785 through 816 or (resid 817 and (name \ N or name CA or name C or name O or name CB )) or resid 818 through 901)) selection = (chain 'C' and (resid 394 through 433 or (resid 434 and (name N or name CA or na \ me C or name O or name CB )) or resid 435 through 448 or (resid 449 and (name N \ or name CA or name C or name O or name CB )) or resid 450 through 453 or (resid \ 454 through 456 and (name N or name CA or name C or name O or name CB )) or resi \ d 457 through 573 or resid 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 (resi \ d 627 and (name N or name CA or name C or name O or name CB )) or resid 628 thro \ ugh 633 or (resid 634 and (name N or name CA or name C or name O or name CB )) o \ r resid 635 through 642 or (resid 643 through 644 and (name N or name CA or name \ C or name O or name CB )) or resid 645 through 674 or (resid 675 and (name N or \ name CA or name C or name O or name CB )) or resid 676 through 715 or (resid 71 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 717 through \ 751 or (resid 752 and (name N or name CA or name C or name O or name CB )) or re \ sid 753 through 754 or (resid 755 through 756 and (name N or name CA or name C o \ r name O or name CB )) or resid 757 through 760 or (resid 761 and (name N or nam \ e CA or name C or name O or name CB )) or resid 762 through 764 or (resid 765 an \ d (name N or name CA or name C or name O or name CB )) or resid 766 through 768 \ or (resid 769 and (name N or name CA or name C or name O or name CB )) or resid \ 770 through 774 or resid 784 through 812 or (resid 813 and (name N or name CA or \ name C or name O or name CB )) or resid 814 through 816 or (resid 817 and (name \ N or name CA or name C or name O or name CB )) or resid 818 or (resid 819 throu \ gh 823 and (name N or name CA or name C or name O or name CB )) or resid 901)) selection = (chain 'D' and (resid 394 through 433 or (resid 434 and (name N or name CA or na \ me C or name O or name CB )) or resid 435 through 448 or (resid 449 and (name N \ or name CA or name C or name O or name CB )) or resid 450 through 507 or (resid \ 508 through 509 and (name N or name CA or name C or name O or name CB )) or resi \ d 510 or (resid 511 and (name N or name CA or name C or name O or name CB )) or \ resid 512 through 551 or (resid 569 and (name N or name CA or name C or name O o \ r name CB )) or resid 570 through 573 or resid 575 or (resid 576 and (name N or \ name CA or name C or name O or name CB )) or resid 577 through 593 or (resid 594 \ and (name N or name CA or name C or name O or name CB )) or resid 595 through 6 \ 22 or resid 624 through 626 or (resid 627 and (name N or name CA or name C or na \ me O or name CB )) or resid 628 through 637 or (resid 638 and (name N or name CA \ or name C or name O or name CB )) or resid 639 through 650 or (resid 651 throug \ h 652 and (name N or name CA or name C or name O or name CB )) or resid 653 thro \ ugh 660 or (resid 661 and (name N or name CA or name C or name O or name CB )) o \ r resid 662 or (resid 663 and (name N or name CA or name C or name O or name CB \ )) or resid 664 through 687 or (resid 688 and (name N or name CA or name C or na \ me O or name CB )) or resid 689 through 694 or (resid 695 and (name N or name CA \ or name C or name O or name CB )) or resid 696 or (resid 697 and (name N or nam \ e CA or name C or name O or name CB )) or resid 698 through 737 or (resid 738 an \ d (name N or name CA or name C or name O or name CB )) or resid 739 through 754 \ or (resid 755 through 756 and (name N or name CA or name C or name O or name CB \ )) or resid 757 through 759 or (resid 760 through 761 and (name N or name CA or \ name C or name O or name CB )) or resid 762 through 764 or (resid 765 and (name \ N or name CA or name C or name O or name CB )) or resid 766 through 771 or (resi \ d 772 and (name N or name CA or name C or name O or name CB )) or resid 773 thro \ ugh 774 or (resid 784 and (name N or name CA or name C or name O or name CB )) o \ r resid 785 through 901)) } ncs_group { reference = (chain 'E' and (resid 5 through 84 or resid 93 through 210)) selection = (chain 'F' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 42 or resid 55 through 84 or resid 93 through 21 \ 0)) selection = (chain 'G' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 84 or resid 93 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 210)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.960 Find NCS groups from input model: 0.570 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: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.117 18745 Z= 0.654 Angle : 1.151 13.289 25336 Z= 0.704 Chirality : 0.075 0.343 2825 Planarity : 0.009 0.082 3073 Dihedral : 17.108 145.329 6668 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.16 % Rotamer: Outliers : 3.23 % Allowed : 3.94 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2290 helix: 1.64 (0.14), residues: 1334 sheet: -1.27 (0.41), residues: 168 loop : -2.37 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG D 661 TYR 0.059 0.008 TYR D 616 PHE 0.068 0.010 PHE A 571 TRP 0.052 0.010 TRP A 606 HIS 0.012 0.004 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.01087 (18733) covalent geometry : angle 1.14936 (25312) SS BOND : bond 0.01444 ( 12) SS BOND : angle 2.25425 ( 24) hydrogen bonds : bond 0.13635 ( 1107) hydrogen bonds : angle 5.01802 ( 3244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 328 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 768 TYR cc_start: 0.7836 (m-10) cc_final: 0.7229 (m-10) REVERT: B 422 GLU cc_start: 0.6327 (pt0) cc_final: 0.6089 (pm20) REVERT: B 473 ASP cc_start: 0.7455 (m-30) cc_final: 0.7202 (m-30) REVERT: B 590 ASP cc_start: 0.8378 (m-30) cc_final: 0.8065 (t0) REVERT: B 766 TRP cc_start: 0.7168 (m100) cc_final: 0.6960 (m100) REVERT: B 816 TYR cc_start: 0.7173 (t80) cc_final: 0.6917 (t80) REVERT: C 756 GLN cc_start: 0.6906 (mm110) cc_final: 0.6670 (mm110) REVERT: D 651 ASP cc_start: 0.8125 (t0) cc_final: 0.7795 (p0) REVERT: D 682 PHE cc_start: 0.7658 (m-80) cc_final: 0.7422 (m-80) REVERT: E 24 MET cc_start: 0.8255 (tpt) cc_final: 0.7767 (tpt) REVERT: E 40 CYS cc_start: 0.7364 (OUTLIER) cc_final: 0.7026 (m) REVERT: E 131 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.5781 (mmm160) REVERT: F 6 ARG cc_start: 0.6797 (tmt170) cc_final: 0.6475 (ttm-80) REVERT: G 41 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.6050 (ptmm) REVERT: G 65 ARG cc_start: 0.7089 (mtm110) cc_final: 0.6798 (mtm-85) REVERT: G 130 THR cc_start: 0.7703 (OUTLIER) cc_final: 0.7470 (t) REVERT: G 132 HIS cc_start: 0.6875 (OUTLIER) cc_final: 0.6346 (m90) REVERT: H 10 MET cc_start: 0.8295 (tpp) cc_final: 0.8002 (tpp) REVERT: H 65 ARG cc_start: 0.7077 (ptt180) cc_final: 0.6842 (ptt-90) REVERT: H 129 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7757 (mtpp) outliers start: 59 outliers final: 21 residues processed: 364 average time/residue: 0.1327 time to fit residues: 72.0948 Evaluate side-chains 302 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 275 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 686 THR Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 782 GLU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 129 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN D 569 ASN E 133 ASN F 132 HIS F 205 HIS G 132 HIS G 205 HIS ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.098989 restraints weight = 58934.189| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.69 r_work: 0.2725 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18745 Z= 0.126 Angle : 0.538 6.766 25336 Z= 0.284 Chirality : 0.040 0.207 2825 Planarity : 0.004 0.041 3073 Dihedral : 11.906 109.773 2979 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.48 % Allowed : 9.52 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.18), residues: 2290 helix: 2.59 (0.14), residues: 1352 sheet: -1.16 (0.38), residues: 188 loop : -1.96 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 661 TYR 0.013 0.001 TYR B 673 PHE 0.012 0.001 PHE A 546 TRP 0.020 0.001 TRP D 460 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00276 (18733) covalent geometry : angle 0.53739 (25312) SS BOND : bond 0.00514 ( 12) SS BOND : angle 1.19773 ( 24) hydrogen bonds : bond 0.04200 ( 1107) hydrogen bonds : angle 3.73155 ( 3244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 315 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 431 GLU cc_start: 0.7695 (tp30) cc_final: 0.7474 (tp30) REVERT: B 486 GLU cc_start: 0.8391 (tp30) cc_final: 0.7801 (tp30) REVERT: B 816 TYR cc_start: 0.7749 (t80) cc_final: 0.7405 (t80) REVERT: C 505 LYS cc_start: 0.7255 (tptp) cc_final: 0.6873 (mtpp) REVERT: D 674 MET cc_start: 0.7419 (mtp) cc_final: 0.7104 (mtp) REVERT: D 766 TRP cc_start: 0.7653 (m100) cc_final: 0.7086 (m100) REVERT: E 24 MET cc_start: 0.8802 (tpt) cc_final: 0.8477 (tpt) REVERT: E 77 CYS cc_start: 0.6156 (OUTLIER) cc_final: 0.5633 (m) REVERT: E 78 LYS cc_start: 0.8622 (ptmt) cc_final: 0.8329 (ptmm) REVERT: E 95 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7633 (pt0) REVERT: E 131 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6545 (mmm160) REVERT: F 6 ARG cc_start: 0.7740 (tmt170) cc_final: 0.7344 (ttm-80) REVERT: F 65 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7520 (mtm110) REVERT: F 74 LYS cc_start: 0.7481 (mttp) cc_final: 0.7262 (mmtm) REVERT: F 99 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.7600 (mtp180) REVERT: G 65 ARG cc_start: 0.7533 (mtm110) cc_final: 0.7232 (mtm-85) REVERT: H 65 ARG cc_start: 0.7536 (ptt180) cc_final: 0.7292 (ptt-90) outliers start: 27 outliers final: 14 residues processed: 329 average time/residue: 0.1195 time to fit residues: 59.1990 Evaluate side-chains 295 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 279 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain H residue 68 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 96 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN C 764 ASN E 199 HIS G 205 HIS ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.146182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.091352 restraints weight = 55306.670| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.28 r_work: 0.2747 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18745 Z= 0.178 Angle : 0.550 9.131 25336 Z= 0.290 Chirality : 0.041 0.265 2825 Planarity : 0.004 0.042 3073 Dihedral : 11.119 106.413 2940 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.19 % Allowed : 10.89 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.18), residues: 2290 helix: 2.47 (0.14), residues: 1356 sheet: -1.23 (0.40), residues: 164 loop : -1.76 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 661 TYR 0.017 0.001 TYR C 673 PHE 0.011 0.001 PHE A 495 TRP 0.017 0.001 TRP D 460 HIS 0.005 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00428 (18733) covalent geometry : angle 0.54648 (25312) SS BOND : bond 0.00716 ( 12) SS BOND : angle 2.00050 ( 24) hydrogen bonds : bond 0.04609 ( 1107) hydrogen bonds : angle 3.69845 ( 3244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 292 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 756 GLN cc_start: 0.8540 (mm110) cc_final: 0.8049 (mm-40) REVERT: B 431 GLU cc_start: 0.7660 (tp30) cc_final: 0.7413 (tp30) REVERT: B 486 GLU cc_start: 0.8392 (tp30) cc_final: 0.7752 (tp30) REVERT: B 675 ARG cc_start: 0.7726 (ptm160) cc_final: 0.7513 (ptm160) REVERT: B 816 TYR cc_start: 0.7780 (t80) cc_final: 0.7405 (t80) REVERT: C 421 TYR cc_start: 0.7908 (m-80) cc_final: 0.7678 (m-10) REVERT: C 642 GLN cc_start: 0.7119 (pp30) cc_final: 0.6860 (pp30) REVERT: D 569 ASN cc_start: 0.6693 (m-40) cc_final: 0.6473 (m-40) REVERT: D 629 MET cc_start: 0.7520 (mmm) cc_final: 0.7316 (mtt) REVERT: D 674 MET cc_start: 0.7338 (mtp) cc_final: 0.6996 (mtp) REVERT: D 766 TRP cc_start: 0.7699 (m100) cc_final: 0.7368 (m100) REVERT: E 24 MET cc_start: 0.8818 (tpt) cc_final: 0.8469 (tpt) REVERT: E 77 CYS cc_start: 0.5895 (OUTLIER) cc_final: 0.5475 (m) REVERT: E 78 LYS cc_start: 0.8696 (ptmt) cc_final: 0.8426 (ptmm) REVERT: E 131 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6442 (mmm160) REVERT: F 6 ARG cc_start: 0.7753 (tmt170) cc_final: 0.7282 (ttm-80) REVERT: F 41 LYS cc_start: 0.5825 (tptp) cc_final: 0.5508 (tptp) REVERT: F 65 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7432 (mtm110) REVERT: F 74 LYS cc_start: 0.7501 (mttp) cc_final: 0.7176 (mmtm) REVERT: F 99 ARG cc_start: 0.7948 (mmm-85) cc_final: 0.7517 (mtp180) REVERT: G 65 ARG cc_start: 0.7586 (mtm110) cc_final: 0.7174 (mtm-85) outliers start: 40 outliers final: 27 residues processed: 317 average time/residue: 0.1300 time to fit residues: 62.2455 Evaluate side-chains 304 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 275 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 163 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 218 optimal weight: 0.0970 chunk 186 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 747 ASN C 764 ASN G 205 HIS H 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.150660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101099 restraints weight = 67355.584| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.31 r_work: 0.2723 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18745 Z= 0.099 Angle : 0.468 7.645 25336 Z= 0.247 Chirality : 0.038 0.224 2825 Planarity : 0.003 0.041 3073 Dihedral : 10.074 106.363 2939 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.08 % Allowed : 11.98 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.18), residues: 2290 helix: 2.80 (0.14), residues: 1357 sheet: -1.23 (0.38), residues: 186 loop : -1.64 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 661 TYR 0.019 0.001 TYR C 673 PHE 0.009 0.001 PHE C 584 TRP 0.017 0.001 TRP D 460 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00213 (18733) covalent geometry : angle 0.46406 (25312) SS BOND : bond 0.00203 ( 12) SS BOND : angle 2.02499 ( 24) hydrogen bonds : bond 0.03490 ( 1107) hydrogen bonds : angle 3.42367 ( 3244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 311 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 592 SER cc_start: 0.9173 (OUTLIER) cc_final: 0.8939 (m) REVERT: B 486 GLU cc_start: 0.8428 (tp30) cc_final: 0.8187 (tp30) REVERT: B 816 TYR cc_start: 0.7828 (t80) cc_final: 0.7511 (t80) REVERT: C 421 TYR cc_start: 0.7816 (m-80) cc_final: 0.7557 (m-10) REVERT: C 431 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8246 (tm-30) REVERT: C 642 GLN cc_start: 0.7235 (pp30) cc_final: 0.6384 (pp30) REVERT: C 770 LYS cc_start: 0.8575 (mptt) cc_final: 0.8153 (mptt) REVERT: C 816 TYR cc_start: 0.7397 (t80) cc_final: 0.7173 (t80) REVERT: D 405 TYR cc_start: 0.8016 (m-80) cc_final: 0.7575 (m-80) REVERT: D 674 MET cc_start: 0.7165 (mtp) cc_final: 0.6943 (mtp) REVERT: D 714 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: D 766 TRP cc_start: 0.7670 (m100) cc_final: 0.7412 (m100) REVERT: E 77 CYS cc_start: 0.6100 (OUTLIER) cc_final: 0.5683 (m) REVERT: E 78 LYS cc_start: 0.8765 (ptmt) cc_final: 0.8469 (ptmm) REVERT: E 95 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7642 (pt0) REVERT: F 6 ARG cc_start: 0.7774 (tmt170) cc_final: 0.7400 (ttm-80) REVERT: F 10 MET cc_start: 0.8453 (tpp) cc_final: 0.7874 (mmm) REVERT: F 41 LYS cc_start: 0.5731 (tptp) cc_final: 0.5430 (tptp) REVERT: F 65 ARG cc_start: 0.7645 (mtm-85) cc_final: 0.7080 (mtm-85) REVERT: F 74 LYS cc_start: 0.7571 (mttp) cc_final: 0.7226 (mmtm) REVERT: F 99 ARG cc_start: 0.8036 (mmm-85) cc_final: 0.7614 (mtp180) REVERT: G 65 ARG cc_start: 0.7604 (mtm110) cc_final: 0.7346 (mtm-85) REVERT: H 37 ARG cc_start: 0.7549 (mtp85) cc_final: 0.7319 (mtp-110) outliers start: 38 outliers final: 25 residues processed: 332 average time/residue: 0.1218 time to fit residues: 61.3582 Evaluate side-chains 319 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 291 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 160 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 190 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 36 optimal weight: 0.0170 chunk 197 optimal weight: 0.4980 chunk 58 optimal weight: 0.0570 chunk 154 optimal weight: 3.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 569 ASN G 205 HIS ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.150908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105044 restraints weight = 74872.001| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.24 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18745 Z= 0.098 Angle : 0.467 8.928 25336 Z= 0.245 Chirality : 0.038 0.282 2825 Planarity : 0.003 0.044 3073 Dihedral : 9.580 102.947 2934 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.91 % Allowed : 13.02 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.18), residues: 2290 helix: 2.89 (0.14), residues: 1358 sheet: -1.17 (0.36), residues: 198 loop : -1.57 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 661 TYR 0.020 0.001 TYR C 673 PHE 0.009 0.001 PHE H 201 TRP 0.024 0.001 TRP D 460 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00210 (18733) covalent geometry : angle 0.46202 (25312) SS BOND : bond 0.00340 ( 12) SS BOND : angle 2.20200 ( 24) hydrogen bonds : bond 0.03424 ( 1107) hydrogen bonds : angle 3.35826 ( 3244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 306 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 642 GLN cc_start: 0.7790 (pp30) cc_final: 0.6979 (pp30) REVERT: D 405 TYR cc_start: 0.7685 (m-80) cc_final: 0.7324 (m-80) REVERT: E 77 CYS cc_start: 0.4721 (m) cc_final: 0.4410 (m) REVERT: E 131 ARG cc_start: 0.7333 (mmm-85) cc_final: 0.6588 (mmm160) REVERT: F 41 LYS cc_start: 0.5745 (tptp) cc_final: 0.5364 (tptp) REVERT: F 65 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7143 (mtm-85) REVERT: F 99 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7586 (mtp180) REVERT: G 11 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8226 (tt) outliers start: 35 outliers final: 29 residues processed: 326 average time/residue: 0.1293 time to fit residues: 64.7096 Evaluate side-chains 314 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 284 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 126 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 569 ASN G 205 HIS ** H 160 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 = 0.3763 r_free = 0.3763 target = 0.146551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.093999 restraints weight = 58730.960| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.70 r_work: 0.2715 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18745 Z= 0.186 Angle : 0.553 11.734 25336 Z= 0.289 Chirality : 0.041 0.251 2825 Planarity : 0.004 0.043 3073 Dihedral : 10.214 100.248 2933 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.79 % Allowed : 13.29 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.18), residues: 2290 helix: 2.59 (0.14), residues: 1358 sheet: -1.14 (0.39), residues: 184 loop : -1.59 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 661 TYR 0.015 0.001 TYR C 673 PHE 0.013 0.002 PHE H 201 TRP 0.016 0.001 TRP D 460 HIS 0.005 0.001 HIS G 205 Details of bonding type rmsd covalent geometry : bond 0.00447 (18733) covalent geometry : angle 0.54846 (25312) SS BOND : bond 0.00773 ( 12) SS BOND : angle 2.31305 ( 24) hydrogen bonds : bond 0.04491 ( 1107) hydrogen bonds : angle 3.60375 ( 3244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 768 TYR cc_start: 0.8166 (m-10) cc_final: 0.7835 (m-10) REVERT: C 570 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8143 (tp30) REVERT: D 766 TRP cc_start: 0.7668 (m100) cc_final: 0.7039 (m100) REVERT: E 77 CYS cc_start: 0.5995 (OUTLIER) cc_final: 0.5579 (m) REVERT: E 131 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6395 (mmm160) REVERT: F 6 ARG cc_start: 0.7152 (ttm-80) cc_final: 0.6886 (ttm-80) REVERT: F 74 LYS cc_start: 0.7736 (mmtp) cc_final: 0.7489 (mmtp) REVERT: F 99 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7590 (mtp180) REVERT: F 208 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7854 (tp) REVERT: G 11 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8275 (tp) outliers start: 51 outliers final: 36 residues processed: 308 average time/residue: 0.1454 time to fit residues: 68.2167 Evaluate side-chains 312 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 126 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 137 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 191 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 0.0030 chunk 162 optimal weight: 0.9990 chunk 219 optimal weight: 0.6980 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 764 ASN G 60 HIS G 205 HIS H 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.094648 restraints weight = 53429.782| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.25 r_work: 0.2795 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18745 Z= 0.114 Angle : 0.499 11.940 25336 Z= 0.260 Chirality : 0.039 0.180 2825 Planarity : 0.003 0.049 3073 Dihedral : 9.638 100.434 2933 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.41 % Allowed : 13.62 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.18), residues: 2290 helix: 2.75 (0.14), residues: 1358 sheet: -1.16 (0.37), residues: 198 loop : -1.59 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 661 TYR 0.018 0.001 TYR C 673 PHE 0.009 0.001 PHE B 584 TRP 0.024 0.001 TRP D 460 HIS 0.004 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00259 (18733) covalent geometry : angle 0.49718 (25312) SS BOND : bond 0.00398 ( 12) SS BOND : angle 1.50175 ( 24) hydrogen bonds : bond 0.03737 ( 1107) hydrogen bonds : angle 3.45369 ( 3244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8143 (mt0) REVERT: C 642 GLN cc_start: 0.7358 (pp30) cc_final: 0.7111 (pp30) REVERT: E 77 CYS cc_start: 0.5718 (OUTLIER) cc_final: 0.5401 (m) REVERT: E 131 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6387 (mmm160) REVERT: F 74 LYS cc_start: 0.7680 (mmtp) cc_final: 0.7442 (mmtp) REVERT: F 99 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.7546 (mtp180) REVERT: F 208 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7803 (tp) REVERT: G 11 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8273 (tp) outliers start: 44 outliers final: 33 residues processed: 303 average time/residue: 0.1455 time to fit residues: 67.2324 Evaluate side-chains 309 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 272 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 126 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.0446 > 50: distance: 47 - 68: 10.601 distance: 51 - 77: 10.042 distance: 57 - 89: 30.078 distance: 63 - 68: 11.343 distance: 64 - 97: 14.097 distance: 68 - 69: 9.185 distance: 69 - 70: 3.600 distance: 69 - 72: 8.442 distance: 70 - 71: 6.947 distance: 70 - 77: 5.289 distance: 71 - 106: 17.375 distance: 72 - 73: 8.556 distance: 73 - 74: 11.943 distance: 74 - 75: 8.550 distance: 74 - 76: 15.774 distance: 77 - 78: 3.717 distance: 78 - 79: 11.245 distance: 78 - 81: 12.346 distance: 79 - 80: 25.323 distance: 79 - 89: 36.216 distance: 81 - 82: 13.795 distance: 82 - 83: 5.538 distance: 82 - 84: 8.752 distance: 83 - 85: 9.268 distance: 84 - 86: 4.969 distance: 85 - 87: 3.379 distance: 86 - 87: 3.954 distance: 87 - 88: 3.375 distance: 89 - 90: 5.899 distance: 90 - 91: 26.011 distance: 90 - 93: 32.849 distance: 91 - 92: 31.368 distance: 91 - 97: 24.533 distance: 93 - 94: 5.358 distance: 93 - 95: 33.351 distance: 94 - 96: 33.832 distance: 97 - 98: 16.317 distance: 98 - 99: 10.094 distance: 98 - 101: 5.346 distance: 99 - 100: 20.827 distance: 99 - 106: 12.975 distance: 101 - 102: 11.261 distance: 102 - 103: 8.298 distance: 103 - 104: 9.682 distance: 103 - 105: 5.723 distance: 106 - 107: 12.510 distance: 107 - 108: 6.465 distance: 107 - 110: 4.133 distance: 108 - 109: 15.315 distance: 108 - 115: 11.007 distance: 110 - 111: 13.220 distance: 111 - 112: 3.084 distance: 112 - 113: 8.132 distance: 112 - 114: 5.652 distance: 115 - 116: 7.788 distance: 116 - 117: 6.994 distance: 116 - 119: 7.435 distance: 117 - 118: 16.534 distance: 117 - 126: 11.377 distance: 119 - 120: 15.298 distance: 120 - 121: 13.003 distance: 121 - 122: 5.871 distance: 122 - 123: 16.034 distance: 123 - 124: 15.440 distance: 123 - 125: 3.838 distance: 126 - 127: 4.353 distance: 127 - 128: 22.145 distance: 127 - 130: 7.538 distance: 128 - 129: 44.401 distance: 128 - 135: 21.373 distance: 130 - 131: 26.179 distance: 131 - 132: 25.844 distance: 132 - 133: 18.929 distance: 133 - 134: 39.633 distance: 135 - 136: 16.482 distance: 135 - 141: 16.877 distance: 136 - 137: 21.640 distance: 136 - 139: 17.134 distance: 137 - 138: 34.899 distance: 137 - 142: 8.844 distance: 139 - 140: 13.092 distance: 142 - 143: 5.639 distance: 143 - 144: 20.789 distance: 143 - 146: 25.560 distance: 144 - 145: 18.564 distance: 144 - 148: 17.954 distance: 146 - 147: 18.117 distance: 147 - 212: 3.843 distance: 148 - 149: 14.687 distance: 149 - 150: 16.168 distance: 150 - 151: 13.450 distance: 150 - 156: 11.827 distance: 152 - 153: 8.600 distance: 153 - 154: 8.936 distance: 153 - 155: 8.742