Starting phenix.real_space_refine on Mon May 19 14:41:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5z_44232/05_2025/9b5z_44232.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5z_44232/05_2025/9b5z_44232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5z_44232/05_2025/9b5z_44232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5z_44232/05_2025/9b5z_44232.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5z_44232/05_2025/9b5z_44232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5z_44232/05_2025/9b5z_44232.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 12136 2.51 5 N 3018 2.21 5 O 3398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18680 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1521 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1524 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3182 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3167 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 408, 3167 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3219 Chain: "B" Number of atoms: 3177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3222 Chain: "A" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3160 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 3180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3215 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS C 435 " occ=0.86 ... (18 atoms not shown) pdb=" NE2BHIS C 435 " occ=0.14 residue: pdb=" N APHE B 623 " occ=0.46 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.54 residue: pdb=" N APHE D 623 " occ=0.62 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.38 Time building chain proxies: 15.92, per 1000 atoms: 0.85 Number of scatterers: 18680 At special positions: 0 Unit cell: (113.98, 109.88, 146.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3398 8.00 N 3018 7.00 C 12136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 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: 4.46 Conformation dependent library (CDL) restraints added in 4.5 seconds 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4422 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 22 sheets defined 60.8% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.558A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 128 removed outlier: 3.954A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 163 removed outlier: 4.017A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP H 163 " --> pdb=" O ALA H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.612A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 128 removed outlier: 3.809A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 161 removed outlier: 3.699A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 6.710A pdb=" N SER F 165 " --> pdb=" O GLY F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 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 461 through 469 removed outlier: 3.521A pdb=" N TYR C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.781A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 630 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.797A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 4.192A pdb=" N LYS C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET C 670 " --> pdb=" O VAL C 666 " (cutoff:3.500A) 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 788 through 791 Processing helix chain 'C' and resid 792 through 825 removed outlier: 3.550A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.938A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.511A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.905A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.578A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.555A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.617A pdb=" N ASP B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 removed outlier: 3.548A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.538A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 825 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.832A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.785A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 630 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.749A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.679A pdb=" N MET A 670 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) 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 825 Processing helix chain 'D' and resid 416 through 419 removed outlier: 4.325A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.660A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.910A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.651A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.599A pdb=" N TYR D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.880A pdb=" N ALA D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 825 removed outlier: 3.505A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 127 removed outlier: 3.944A pdb=" N GLU E 126 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.734A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.526A pdb=" N ILE E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.905A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.599A pdb=" N ALA G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 removed outlier: 3.840A pdb=" N CYS F 67 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.233A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL C 396 " --> pdb=" O ILE C 474 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE C 476 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR C 398 " --> pdb=" O ILE C 476 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA C 477 " --> pdb=" O ASP C 733 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP C 733 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU C 479 " --> pdb=" O GLY C 731 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY C 731 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.233A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL C 396 " --> pdb=" O ILE C 474 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE C 476 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR C 398 " --> pdb=" O ILE C 476 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA C 477 " --> pdb=" O ASP C 733 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP C 733 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU C 479 " --> pdb=" O GLY C 731 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY C 731 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.495A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 439 through 444 Processing sheet with id=AA8, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA9, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AB1, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.002A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.457A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 395 through 399 Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.778A pdb=" N ASP A 454 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A 459 " --> pdb=" O ASP A 454 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AB6, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.798A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.490A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 441 through 444 removed outlier: 5.553A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 476 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ALA D 477 " --> pdb=" O ASP D 733 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 441 through 444 removed outlier: 5.553A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 476 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ALA D 477 " --> pdb=" O ASP D 733 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 removed outlier: 3.601A pdb=" N GLU D 422 " --> pdb=" O MET D 407 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.565A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC4, first strand: chain 'G' and resid 77 through 79 1184 hydrogen bonds defined for protein. 3439 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: 6.45 Time building geometry restraints manager: 5.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5772 1.34 - 1.46: 4951 1.46 - 1.58: 8172 1.58 - 1.70: 1 1.70 - 1.82: 208 Bond restraints: 19104 Sorted by residual: bond pdb=" CB PRO H 164 " pdb=" CG PRO H 164 " ideal model delta sigma weight residual 1.492 1.651 -0.159 5.00e-02 4.00e+02 1.02e+01 bond pdb=" N PRO H 164 " pdb=" CD PRO H 164 " ideal model delta sigma weight residual 1.473 1.498 -0.025 1.40e-02 5.10e+03 3.25e+00 bond pdb=" N PRO H 164 " pdb=" CA PRO H 164 " ideal model delta sigma weight residual 1.469 1.447 0.021 1.28e-02 6.10e+03 2.74e+00 bond pdb=" CB GLU A 637 " pdb=" CG GLU A 637 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" CG GLU A 637 " pdb=" CD GLU A 637 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.12e+00 ... (remaining 19099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 25739 3.31 - 6.63: 84 6.63 - 9.94: 9 9.94 - 13.26: 6 13.26 - 16.57: 1 Bond angle restraints: 25839 Sorted by residual: angle pdb=" CA PRO H 164 " pdb=" N PRO H 164 " pdb=" CD PRO H 164 " ideal model delta sigma weight residual 112.00 95.43 16.57 1.40e+00 5.10e-01 1.40e+02 angle pdb=" N PRO H 164 " pdb=" CD PRO H 164 " pdb=" CG PRO H 164 " ideal model delta sigma weight residual 103.20 96.06 7.14 1.50e+00 4.44e-01 2.27e+01 angle pdb=" CB MET C 408 " pdb=" CG MET C 408 " pdb=" SD MET C 408 " ideal model delta sigma weight residual 112.70 125.70 -13.00 3.00e+00 1.11e-01 1.88e+01 angle pdb=" CB MET B 408 " pdb=" CG MET B 408 " pdb=" SD MET B 408 " ideal model delta sigma weight residual 112.70 124.89 -12.19 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CB MET D 708 " pdb=" CG MET D 708 " pdb=" SD MET D 708 " ideal model delta sigma weight residual 112.70 124.60 -11.90 3.00e+00 1.11e-01 1.57e+01 ... (remaining 25834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 9527 17.67 - 35.33: 1241 35.33 - 53.00: 341 53.00 - 70.67: 60 70.67 - 88.34: 30 Dihedral angle restraints: 11199 sinusoidal: 4271 harmonic: 6928 Sorted by residual: dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 163.98 -70.98 1 1.00e+01 1.00e-02 6.47e+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 93.00 143.90 -50.90 1 1.00e+01 1.00e-02 3.55e+01 dihedral pdb=" CB CYS D 718 " pdb=" SG CYS D 718 " pdb=" SG CYS D 773 " pdb=" CB CYS D 773 " ideal model delta sinusoidal sigma weight residual 93.00 139.44 -46.44 1 1.00e+01 1.00e-02 2.98e+01 ... (remaining 11196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2355 0.048 - 0.096: 456 0.096 - 0.144: 89 0.144 - 0.192: 3 0.192 - 0.240: 2 Chirality restraints: 2905 Sorted by residual: chirality pdb=" CA PRO H 164 " pdb=" N PRO H 164 " pdb=" C PRO H 164 " pdb=" CB PRO H 164 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CG LEU A 811 " pdb=" CB LEU A 811 " pdb=" CD1 LEU A 811 " pdb=" CD2 LEU A 811 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE C 476 " pdb=" N ILE C 476 " pdb=" C ILE C 476 " pdb=" CB ILE C 476 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 2902 not shown) Planarity restraints: 3198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 163 " 0.083 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO H 164 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO H 164 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 164 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 644 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" CD GLU C 644 " 0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU C 644 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 644 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 204 " -0.130 9.50e-02 1.11e+02 5.83e-02 2.45e+00 pdb=" NE ARG G 204 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG G 204 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG G 204 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG G 204 " -0.001 2.00e-02 2.50e+03 ... (remaining 3195 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3396 2.76 - 3.30: 17983 3.30 - 3.83: 32653 3.83 - 4.37: 36848 4.37 - 4.90: 63727 Nonbonded interactions: 154607 Sorted by model distance: nonbonded pdb=" O SER H 105 " pdb=" OG SER H 105 " model vdw 2.227 3.040 nonbonded pdb=" N GLU C 637 " pdb=" OE1 GLU C 637 " model vdw 2.258 3.120 nonbonded pdb=" N GLU A 644 " pdb=" OE1 GLU A 644 " model vdw 2.259 3.120 nonbonded pdb=" NH2 ARG A 420 " pdb=" OH TYR A 421 " model vdw 2.305 3.120 nonbonded pdb=" OD2 ASP D 454 " pdb=" OG1 THR D 457 " model vdw 2.306 3.040 ... (remaining 154602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 575 or (resid 576 and (name N or name CA or name C or name \ O or name CB )) or resid 577 through 622 or resid 624 through 626 or (resid 627 \ and (name N or name CA or name C or name O or name CB )) or resid 628 through 7 \ 63 or resid 765 through 812 or (resid 813 and (name N or name CA or name C or na \ me O or name CB )) or resid 814 through 818 or (resid 819 through 820 and (name \ N or name CA or name C or name O or name CB )) or resid 821 through 825)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 508 or (resid 509 and (name N or name CA or name C or name \ O or name CB )) or resid 510 or (resid 511 and (name N or name CA or name C or \ name O or name CB )) or resid 512 through 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 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 763 or resid 765 through 773 or (resid 784 an \ d (name N or name CA or name C or name O or name CB )) or resid 785 through 825) \ ) selection = (chain 'C' and (resid 393 through 434 or resid 436 through 593 or (resid 594 and \ (name N or name CA or name C or name O or name CB )) or resid 595 through 622 o \ r resid 624 through 626 or (resid 627 and (name N or name CA or name C or name O \ or name CB )) or resid 628 through 666 or (resid 667 and (name N or name CA or \ name C or name O or name CB )) or resid 668 through 763 or resid 765 through 812 \ or (resid 813 and (name N or name CA or name C or name O or name CB )) or resid \ 814 through 818 or (resid 819 through 820 and (name N or name CA or name C or n \ ame O or name CB )) or resid 821 through 825)) selection = (chain 'D' and (resid 393 through 434 or resid 436 through 508 or (resid 509 and \ (name N or name CA or name C or name O or name CB )) or resid 510 or (resid 511 \ and (name N or name CA or name C or name O or name CB )) or resid 512 through 5 \ 75 or (resid 576 and (name N or name CA or name C or name O or name CB )) or res \ id 577 through 593 or (resid 594 and (name N or name CA or name C or name O or n \ ame CB )) or resid 595 through 622 or resid 624 through 666 or (resid 667 and (n \ ame N or name CA or name C or name O or name CB )) or resid 668 through 763 or r \ esid 765 through 773 or (resid 784 and (name N or name CA or name C or name O or \ name CB )) or resid 785 through 825)) } ncs_group { reference = (chain 'E' and resid 5 through 214) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 162 or resid 173 through \ 214)) selection = (chain 'G' and resid 5 through 214) selection = (chain 'H' and (resid 5 through 41 or resid 55 through 162 or resid 173 through \ 214)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.12 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 50.900 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.100 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:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.159 19116 Z= 0.128 Angle : 0.561 16.575 25863 Z= 0.292 Chirality : 0.038 0.240 2905 Planarity : 0.004 0.113 3198 Dihedral : 17.446 88.337 6741 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.33 % Rotamer: Outliers : 2.18 % Allowed : 32.15 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.17), residues: 2373 helix: 2.53 (0.14), residues: 1375 sheet: -0.83 (0.35), residues: 200 loop : -0.62 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 671 HIS 0.010 0.001 HIS H 60 PHE 0.019 0.001 PHE E 127 TYR 0.022 0.001 TYR A 673 ARG 0.012 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.19297 ( 1179) hydrogen bonds : angle 5.69712 ( 3439) SS BOND : bond 0.00216 ( 12) SS BOND : angle 0.95009 ( 24) covalent geometry : bond 0.00301 (19104) covalent geometry : angle 0.56045 (25839) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 273 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6743 (mptt) REVERT: C 642 GLN cc_start: 0.7759 (pp30) cc_final: 0.7423 (pp30) REVERT: C 715 ARG cc_start: 0.7516 (mmp80) cc_final: 0.7281 (mpt180) REVERT: A 420 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.6878 (mpp-170) REVERT: A 756 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8055 (mp10) REVERT: E 10 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8183 (mmm) REVERT: G 99 ARG cc_start: 0.6918 (mtt180) cc_final: 0.6592 (ptp-110) outliers start: 43 outliers final: 34 residues processed: 309 average time/residue: 1.2338 time to fit residues: 431.5205 Evaluate side-chains 305 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 818 SER Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 155 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.6980 chunk 177 optimal weight: 0.0870 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS F 149 ASN F 160 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS G 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.171483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.119403 restraints weight = 54293.661| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.40 r_work: 0.3337 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19116 Z= 0.118 Angle : 0.514 10.133 25863 Z= 0.270 Chirality : 0.039 0.188 2905 Planarity : 0.003 0.035 3198 Dihedral : 5.171 58.369 2652 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.33 % Favored : 97.63 % Rotamer: Outliers : 3.96 % Allowed : 28.80 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.17), residues: 2373 helix: 2.84 (0.14), residues: 1397 sheet: -0.84 (0.38), residues: 156 loop : -0.62 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 766 HIS 0.012 0.001 HIS H 60 PHE 0.013 0.001 PHE B 438 TYR 0.018 0.001 TYR A 673 ARG 0.008 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 1179) hydrogen bonds : angle 4.03260 ( 3439) SS BOND : bond 0.00206 ( 12) SS BOND : angle 1.47624 ( 24) covalent geometry : bond 0.00257 (19104) covalent geometry : angle 0.51247 (25839) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 319 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7472 (tp) REVERT: H 37 ARG cc_start: 0.8598 (mtt-85) cc_final: 0.8385 (mtt-85) REVERT: H 78 LYS cc_start: 0.8164 (tmmt) cc_final: 0.7452 (ttmt) REVERT: F 31 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: F 65 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.6905 (ppt-90) REVERT: F 86 ASP cc_start: 0.5468 (OUTLIER) cc_final: 0.4834 (m-30) REVERT: F 167 SER cc_start: 0.6752 (OUTLIER) cc_final: 0.6441 (m) REVERT: C 463 MET cc_start: 0.8200 (mmm) cc_final: 0.7988 (mpp) REVERT: C 642 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7238 (pp30) REVERT: C 671 TRP cc_start: 0.7843 (t-100) cc_final: 0.7530 (t-100) REVERT: B 506 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8404 (ttmm) REVERT: A 439 LYS cc_start: 0.7918 (pmtt) cc_final: 0.7553 (pptt) REVERT: D 407 MET cc_start: 0.8183 (ptt) cc_final: 0.7930 (mtm) REVERT: D 458 LYS cc_start: 0.7878 (tppt) cc_final: 0.7371 (tppp) REVERT: D 818 SER cc_start: 0.8172 (t) cc_final: 0.7912 (p) REVERT: E 68 CYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7698 (m) REVERT: G 102 ARG cc_start: 0.7282 (tpt90) cc_final: 0.7078 (tmt170) outliers start: 78 outliers final: 30 residues processed: 375 average time/residue: 1.1983 time to fit residues: 507.9449 Evaluate side-chains 316 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 278 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 642 GLN Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 175 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 43 optimal weight: 0.0370 chunk 90 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 50 optimal weight: 0.0370 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN F 205 HIS A 726 ASN E 207 GLN G 132 HIS G 160 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.171571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.120915 restraints weight = 59852.191| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.54 r_work: 0.3344 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19116 Z= 0.110 Angle : 0.504 11.044 25863 Z= 0.262 Chirality : 0.039 0.197 2905 Planarity : 0.003 0.036 3198 Dihedral : 3.798 42.441 2610 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.41 % Favored : 97.54 % Rotamer: Outliers : 3.91 % Allowed : 28.95 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.17), residues: 2373 helix: 2.94 (0.14), residues: 1401 sheet: -0.73 (0.40), residues: 144 loop : -0.64 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 178 HIS 0.010 0.001 HIS H 60 PHE 0.010 0.001 PHE A 584 TYR 0.011 0.001 TYR C 673 ARG 0.005 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 1179) hydrogen bonds : angle 3.84394 ( 3439) SS BOND : bond 0.00470 ( 12) SS BOND : angle 2.00008 ( 24) covalent geometry : bond 0.00237 (19104) covalent geometry : angle 0.50027 (25839) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 312 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 HIS cc_start: 0.7329 (p-80) cc_final: 0.7058 (p90) REVERT: H 65 ARG cc_start: 0.6800 (ptp90) cc_final: 0.6565 (ptp90) REVERT: F 149 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8085 (t160) REVERT: F 167 SER cc_start: 0.6766 (OUTLIER) cc_final: 0.6458 (m) REVERT: C 463 MET cc_start: 0.8249 (mmm) cc_final: 0.7830 (mpp) REVERT: C 642 GLN cc_start: 0.7608 (pp30) cc_final: 0.7396 (pp30) REVERT: A 413 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6641 (mm-30) REVERT: A 439 LYS cc_start: 0.7927 (pmtt) cc_final: 0.7714 (ttpt) REVERT: A 674 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8159 (mtm) REVERT: A 756 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8021 (mp10) REVERT: D 407 MET cc_start: 0.8178 (ptt) cc_final: 0.7893 (mtm) REVERT: D 458 LYS cc_start: 0.7875 (tppt) cc_final: 0.7370 (tppp) REVERT: E 97 PHE cc_start: 0.7696 (t80) cc_final: 0.7322 (t80) outliers start: 77 outliers final: 31 residues processed: 363 average time/residue: 1.2013 time to fit residues: 495.0354 Evaluate side-chains 317 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 281 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 214 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 87 optimal weight: 0.1980 chunk 140 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 96 optimal weight: 0.0170 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS F 160 ASN B 412 HIS G 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.168079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.115541 restraints weight = 63769.603| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.97 r_work: 0.3210 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19116 Z= 0.106 Angle : 0.489 11.537 25863 Z= 0.254 Chirality : 0.038 0.183 2905 Planarity : 0.003 0.057 3198 Dihedral : 3.675 43.439 2608 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.38 % Rotamer: Outliers : 4.42 % Allowed : 28.09 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.18), residues: 2373 helix: 2.98 (0.14), residues: 1405 sheet: -0.88 (0.39), residues: 158 loop : -0.52 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 178 HIS 0.008 0.001 HIS H 60 PHE 0.014 0.001 PHE D 546 TYR 0.011 0.001 TYR F 174 ARG 0.008 0.000 ARG G 204 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 1179) hydrogen bonds : angle 3.73982 ( 3439) SS BOND : bond 0.00481 ( 12) SS BOND : angle 1.83173 ( 24) covalent geometry : bond 0.00229 (19104) covalent geometry : angle 0.48651 (25839) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 310 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 HIS cc_start: 0.7070 (p-80) cc_final: 0.6802 (p90) REVERT: H 166 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6612 (mptt) REVERT: H 207 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7865 (mt0) REVERT: F 65 ARG cc_start: 0.7540 (ppt-90) cc_final: 0.7218 (ppt-90) REVERT: F 86 ASP cc_start: 0.5686 (OUTLIER) cc_final: 0.5026 (m-30) REVERT: F 149 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8060 (t0) REVERT: F 167 SER cc_start: 0.6646 (OUTLIER) cc_final: 0.6392 (m) REVERT: C 463 MET cc_start: 0.8275 (mmm) cc_final: 0.7113 (mpp) REVERT: B 439 LYS cc_start: 0.8830 (mmtp) cc_final: 0.8471 (mppt) REVERT: A 439 LYS cc_start: 0.7919 (pmtt) cc_final: 0.7569 (pptt) REVERT: A 637 GLU cc_start: 0.7344 (tp30) cc_final: 0.6829 (tp30) REVERT: A 674 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8211 (mtm) REVERT: D 407 MET cc_start: 0.8185 (ptt) cc_final: 0.7893 (mtm) REVERT: D 458 LYS cc_start: 0.7807 (tppt) cc_final: 0.7293 (tppp) REVERT: D 503 MET cc_start: 0.8728 (ptm) cc_final: 0.8424 (ttp) REVERT: E 10 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8297 (mmm) REVERT: E 37 ARG cc_start: 0.7767 (mmm160) cc_final: 0.7487 (mmt90) REVERT: E 97 PHE cc_start: 0.7595 (t80) cc_final: 0.7314 (t80) REVERT: G 209 ARG cc_start: 0.7100 (tpp80) cc_final: 0.6799 (mtm-85) outliers start: 87 outliers final: 32 residues processed: 371 average time/residue: 1.1368 time to fit residues: 480.2503 Evaluate side-chains 331 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 293 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain G residue 10 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 175 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 199 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 GLN H 205 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS G 160 ASN G 205 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.166016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112935 restraints weight = 58943.116| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.83 r_work: 0.3170 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19116 Z= 0.130 Angle : 0.522 11.786 25863 Z= 0.270 Chirality : 0.039 0.203 2905 Planarity : 0.003 0.041 3198 Dihedral : 3.562 31.267 2604 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 4.27 % Allowed : 27.83 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.17), residues: 2373 helix: 2.92 (0.14), residues: 1397 sheet: -0.81 (0.36), residues: 178 loop : -0.61 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 671 HIS 0.009 0.001 HIS H 60 PHE 0.011 0.001 PHE C 584 TYR 0.013 0.001 TYR A 523 ARG 0.007 0.000 ARG E 204 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 1179) hydrogen bonds : angle 3.81691 ( 3439) SS BOND : bond 0.00185 ( 12) SS BOND : angle 2.04155 ( 24) covalent geometry : bond 0.00301 (19104) covalent geometry : angle 0.51897 (25839) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 299 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 HIS cc_start: 0.7301 (p-80) cc_final: 0.7058 (p90) REVERT: H 99 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.7918 (mtt90) REVERT: H 166 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6565 (mptt) REVERT: H 207 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7866 (mt0) REVERT: F 30 THR cc_start: 0.8641 (m) cc_final: 0.8087 (p) REVERT: F 65 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7118 (ppt-90) REVERT: F 86 ASP cc_start: 0.5587 (OUTLIER) cc_final: 0.4917 (m-30) REVERT: F 149 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8119 (t160) REVERT: F 167 SER cc_start: 0.6661 (OUTLIER) cc_final: 0.6446 (m) REVERT: C 419 GLU cc_start: 0.8409 (mp0) cc_final: 0.8126 (mp0) REVERT: C 463 MET cc_start: 0.8310 (mmm) cc_final: 0.7173 (mpp) REVERT: B 439 LYS cc_start: 0.8832 (mmtp) cc_final: 0.8501 (mppt) REVERT: B 506 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8390 (ttmm) REVERT: A 413 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6740 (mm-30) REVERT: A 439 LYS cc_start: 0.7874 (pmtt) cc_final: 0.7668 (ttpt) REVERT: A 637 GLU cc_start: 0.7348 (tp30) cc_final: 0.7010 (tp30) REVERT: D 407 MET cc_start: 0.8269 (ptt) cc_final: 0.8029 (mtm) REVERT: D 458 LYS cc_start: 0.7852 (tppt) cc_final: 0.7346 (tppp) REVERT: E 37 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7534 (mtp85) REVERT: E 97 PHE cc_start: 0.7440 (t80) cc_final: 0.7221 (t80) REVERT: G 209 ARG cc_start: 0.6945 (tpp80) cc_final: 0.6693 (ttm-80) outliers start: 84 outliers final: 37 residues processed: 361 average time/residue: 1.1904 time to fit residues: 486.0146 Evaluate side-chains 328 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 205 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 127 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 GLN H 205 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN B 756 GLN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 GLN G 132 HIS G 160 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.165652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112211 restraints weight = 57744.340| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.43 r_work: 0.3192 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19116 Z= 0.129 Angle : 0.526 12.213 25863 Z= 0.271 Chirality : 0.039 0.221 2905 Planarity : 0.003 0.044 3198 Dihedral : 3.611 34.800 2604 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.01 % Allowed : 28.03 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.17), residues: 2373 helix: 2.91 (0.14), residues: 1393 sheet: -0.75 (0.37), residues: 178 loop : -0.61 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 551 HIS 0.011 0.001 HIS G 205 PHE 0.011 0.001 PHE A 584 TYR 0.013 0.001 TYR A 523 ARG 0.013 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 1179) hydrogen bonds : angle 3.79940 ( 3439) SS BOND : bond 0.00370 ( 12) SS BOND : angle 2.08623 ( 24) covalent geometry : bond 0.00298 (19104) covalent geometry : angle 0.52233 (25839) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 296 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 HIS cc_start: 0.7381 (p-80) cc_final: 0.7164 (p90) REVERT: H 65 ARG cc_start: 0.6914 (ptp-170) cc_final: 0.6449 (pmm-80) REVERT: H 99 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7899 (mtt90) REVERT: H 166 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6614 (mptt) REVERT: H 207 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7864 (mt0) REVERT: F 30 THR cc_start: 0.8596 (m) cc_final: 0.8089 (p) REVERT: F 65 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7184 (ppt-90) REVERT: F 86 ASP cc_start: 0.5522 (OUTLIER) cc_final: 0.4824 (m-30) REVERT: F 149 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.8123 (t160) REVERT: F 167 SER cc_start: 0.6692 (OUTLIER) cc_final: 0.6457 (m) REVERT: C 419 GLU cc_start: 0.8362 (mp0) cc_final: 0.8100 (mp0) REVERT: C 463 MET cc_start: 0.8258 (mmm) cc_final: 0.6947 (mpp) REVERT: C 466 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7389 (tt0) REVERT: C 642 GLN cc_start: 0.7571 (pp30) cc_final: 0.7355 (pp30) REVERT: B 439 LYS cc_start: 0.8820 (mmtp) cc_final: 0.8537 (mppt) REVERT: B 506 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8397 (ttmm) REVERT: A 413 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6743 (mm-30) REVERT: A 634 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7909 (tm-30) REVERT: A 637 GLU cc_start: 0.7322 (tp30) cc_final: 0.6956 (tp30) REVERT: A 641 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7713 (mtmt) REVERT: D 407 MET cc_start: 0.8237 (ptt) cc_final: 0.7989 (mtm) REVERT: D 431 GLU cc_start: 0.8114 (mp0) cc_final: 0.7679 (mp0) REVERT: D 458 LYS cc_start: 0.7867 (tppt) cc_final: 0.7345 (tppp) REVERT: D 714 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7953 (mm110) REVERT: E 37 ARG cc_start: 0.7707 (mmm160) cc_final: 0.7495 (mtp85) REVERT: E 97 PHE cc_start: 0.7471 (t80) cc_final: 0.7268 (t80) REVERT: G 58 MET cc_start: 0.7505 (tpt) cc_final: 0.7178 (mmp) REVERT: G 209 ARG cc_start: 0.6944 (tpp80) cc_final: 0.6725 (ttm-80) outliers start: 79 outliers final: 39 residues processed: 354 average time/residue: 1.1968 time to fit residues: 478.5857 Evaluate side-chains 327 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 175 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 32 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 182 optimal weight: 0.6980 chunk 232 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN E 207 GLN G 132 HIS G 160 ASN G 205 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.166055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112930 restraints weight = 61264.233| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.92 r_work: 0.3175 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19116 Z= 0.118 Angle : 0.520 12.652 25863 Z= 0.267 Chirality : 0.039 0.232 2905 Planarity : 0.003 0.059 3198 Dihedral : 3.560 36.804 2603 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.61 % Allowed : 28.54 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.18), residues: 2373 helix: 2.91 (0.14), residues: 1399 sheet: -0.66 (0.38), residues: 168 loop : -0.55 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 551 HIS 0.007 0.001 HIS H 60 PHE 0.010 0.001 PHE A 584 TYR 0.015 0.001 TYR A 523 ARG 0.011 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 1179) hydrogen bonds : angle 3.76056 ( 3439) SS BOND : bond 0.00506 ( 12) SS BOND : angle 2.11273 ( 24) covalent geometry : bond 0.00269 (19104) covalent geometry : angle 0.51629 (25839) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 303 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 HIS cc_start: 0.7407 (p-80) cc_final: 0.7159 (p90) REVERT: H 99 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7898 (mtt90) REVERT: H 166 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6833 (mtmt) REVERT: H 207 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7850 (mt0) REVERT: F 30 THR cc_start: 0.8575 (m) cc_final: 0.8085 (p) REVERT: F 65 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7203 (ppt-90) REVERT: F 86 ASP cc_start: 0.5693 (OUTLIER) cc_final: 0.4993 (m-30) REVERT: F 149 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.8105 (t160) REVERT: F 167 SER cc_start: 0.6538 (OUTLIER) cc_final: 0.6326 (m) REVERT: C 419 GLU cc_start: 0.8394 (mp0) cc_final: 0.8121 (mp0) REVERT: C 463 MET cc_start: 0.8275 (mmm) cc_final: 0.6958 (mpp) REVERT: C 466 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7400 (tt0) REVERT: C 674 MET cc_start: 0.8343 (mpp) cc_final: 0.8103 (mtm) REVERT: B 439 LYS cc_start: 0.8835 (mmtp) cc_final: 0.8507 (mppt) REVERT: B 506 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8397 (ttmm) REVERT: A 413 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6859 (mm-30) REVERT: A 634 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: D 407 MET cc_start: 0.8272 (ptt) cc_final: 0.8031 (mtm) REVERT: D 431 GLU cc_start: 0.8119 (mp0) cc_final: 0.7625 (mp0) REVERT: D 458 LYS cc_start: 0.7858 (tppt) cc_final: 0.7344 (tppp) REVERT: E 37 ARG cc_start: 0.7712 (mmm160) cc_final: 0.7498 (mtp85) REVERT: E 59 THR cc_start: 0.7567 (p) cc_final: 0.6879 (t) outliers start: 71 outliers final: 40 residues processed: 357 average time/residue: 1.2137 time to fit residues: 490.3278 Evaluate side-chains 334 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 286 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 175 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 8 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 190 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 223 optimal weight: 0.0070 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS G 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.166478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112169 restraints weight = 46690.379| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.16 r_work: 0.3215 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19116 Z= 0.114 Angle : 0.534 13.051 25863 Z= 0.274 Chirality : 0.039 0.232 2905 Planarity : 0.003 0.049 3198 Dihedral : 3.529 37.632 2603 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.35 % Allowed : 28.90 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.18), residues: 2373 helix: 2.94 (0.14), residues: 1399 sheet: -0.64 (0.38), residues: 168 loop : -0.53 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 551 HIS 0.007 0.001 HIS H 60 PHE 0.010 0.001 PHE B 438 TYR 0.015 0.001 TYR A 523 ARG 0.011 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 1179) hydrogen bonds : angle 3.72891 ( 3439) SS BOND : bond 0.00571 ( 12) SS BOND : angle 2.08944 ( 24) covalent geometry : bond 0.00259 (19104) covalent geometry : angle 0.53077 (25839) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 304 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.8586 (mtt-85) cc_final: 0.8304 (mtt-85) REVERT: H 60 HIS cc_start: 0.7296 (p-80) cc_final: 0.7096 (p90) REVERT: H 65 ARG cc_start: 0.6896 (ptp-170) cc_final: 0.6469 (pmm-80) REVERT: H 99 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7876 (mtt90) REVERT: H 166 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6871 (mtmt) REVERT: H 207 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7887 (mt0) REVERT: F 30 THR cc_start: 0.8568 (m) cc_final: 0.8093 (p) REVERT: F 65 ARG cc_start: 0.7575 (ppt-90) cc_final: 0.7210 (ppt-90) REVERT: F 86 ASP cc_start: 0.5559 (OUTLIER) cc_final: 0.4877 (m-30) REVERT: F 149 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8062 (t0) REVERT: C 419 GLU cc_start: 0.8370 (mp0) cc_final: 0.8106 (mp0) REVERT: C 463 MET cc_start: 0.8266 (mmm) cc_final: 0.6970 (mpp) REVERT: C 466 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7388 (tt0) REVERT: B 403 SER cc_start: 0.9220 (m) cc_final: 0.8714 (t) REVERT: B 439 LYS cc_start: 0.8815 (mmtp) cc_final: 0.8531 (mppt) REVERT: B 506 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8381 (ttmm) REVERT: A 407 MET cc_start: 0.7757 (mtm) cc_final: 0.7241 (mtm) REVERT: A 413 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6888 (mm-30) REVERT: A 634 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: D 407 MET cc_start: 0.8249 (ptt) cc_final: 0.7989 (mtm) REVERT: D 431 GLU cc_start: 0.8075 (mp0) cc_final: 0.7560 (mp0) REVERT: E 59 THR cc_start: 0.7419 (p) cc_final: 0.6771 (t) REVERT: E 65 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6571 (ptm160) REVERT: E 97 PHE cc_start: 0.7605 (t80) cc_final: 0.7289 (t80) REVERT: G 99 ARG cc_start: 0.7367 (mtt180) cc_final: 0.7103 (mmt90) outliers start: 66 outliers final: 42 residues processed: 351 average time/residue: 1.2569 time to fit residues: 497.1818 Evaluate side-chains 342 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 293 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 175 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 170 optimal weight: 0.0470 chunk 1 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 229 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN B 756 GLN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.165809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113771 restraints weight = 63770.328| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 4.01 r_work: 0.3176 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19116 Z= 0.124 Angle : 0.554 13.348 25863 Z= 0.282 Chirality : 0.039 0.223 2905 Planarity : 0.003 0.044 3198 Dihedral : 3.572 39.869 2603 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.89 % Allowed : 29.81 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.17), residues: 2373 helix: 2.88 (0.14), residues: 1399 sheet: -0.77 (0.38), residues: 158 loop : -0.51 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 551 HIS 0.007 0.001 HIS H 60 PHE 0.011 0.001 PHE B 438 TYR 0.029 0.001 TYR A 673 ARG 0.010 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 1179) hydrogen bonds : angle 3.74650 ( 3439) SS BOND : bond 0.00452 ( 12) SS BOND : angle 2.07054 ( 24) covalent geometry : bond 0.00287 (19104) covalent geometry : angle 0.55112 (25839) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 302 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.8590 (mtt-85) cc_final: 0.8296 (mtt-85) REVERT: H 60 HIS cc_start: 0.7402 (p-80) cc_final: 0.7149 (p90) REVERT: H 99 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7916 (mtt90) REVERT: H 166 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6910 (mtmt) REVERT: H 207 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7890 (mt0) REVERT: F 30 THR cc_start: 0.8587 (m) cc_final: 0.8130 (p) REVERT: F 65 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7285 (ppt-90) REVERT: F 86 ASP cc_start: 0.5693 (OUTLIER) cc_final: 0.5043 (m-30) REVERT: F 149 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8134 (t160) REVERT: C 419 GLU cc_start: 0.8446 (mp0) cc_final: 0.8165 (mp0) REVERT: C 463 MET cc_start: 0.8267 (mmm) cc_final: 0.6790 (mpp) REVERT: C 466 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7399 (tt0) REVERT: B 403 SER cc_start: 0.9229 (m) cc_final: 0.8742 (t) REVERT: B 439 LYS cc_start: 0.8799 (mmtp) cc_final: 0.8513 (mppt) REVERT: B 506 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8395 (ttmm) REVERT: A 413 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: A 634 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: A 661 ARG cc_start: 0.8154 (ptp90) cc_final: 0.7894 (mtm-85) REVERT: D 407 MET cc_start: 0.8280 (ptt) cc_final: 0.8032 (mtm) REVERT: D 431 GLU cc_start: 0.8114 (mp0) cc_final: 0.7584 (mp0) REVERT: E 59 THR cc_start: 0.7367 (p) cc_final: 0.6692 (t) REVERT: E 65 ARG cc_start: 0.6999 (ptm160) cc_final: 0.6678 (ptm160) REVERT: E 97 PHE cc_start: 0.7638 (t80) cc_final: 0.7373 (t80) outliers start: 57 outliers final: 40 residues processed: 343 average time/residue: 1.2376 time to fit residues: 478.0284 Evaluate side-chains 338 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 291 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 128 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 209 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 205 optimal weight: 0.2980 chunk 203 optimal weight: 0.4980 chunk 173 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS B 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.165872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.113062 restraints weight = 67286.176| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 4.17 r_work: 0.3164 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19116 Z= 0.123 Angle : 0.557 13.482 25863 Z= 0.284 Chirality : 0.040 0.216 2905 Planarity : 0.003 0.057 3198 Dihedral : 3.613 40.635 2603 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.84 % Allowed : 30.12 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.18), residues: 2373 helix: 2.88 (0.14), residues: 1399 sheet: -0.76 (0.38), residues: 158 loop : -0.52 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 551 HIS 0.007 0.001 HIS H 60 PHE 0.011 0.001 PHE B 438 TYR 0.015 0.001 TYR A 523 ARG 0.012 0.000 ARG E 204 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 1179) hydrogen bonds : angle 3.75560 ( 3439) SS BOND : bond 0.00422 ( 12) SS BOND : angle 2.09285 ( 24) covalent geometry : bond 0.00287 (19104) covalent geometry : angle 0.55379 (25839) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.8606 (mtt-85) cc_final: 0.8311 (mtt-85) REVERT: H 60 HIS cc_start: 0.7406 (p-80) cc_final: 0.7181 (p90) REVERT: H 99 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7893 (mtt90) REVERT: H 166 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6851 (mtmt) REVERT: H 207 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7885 (mt0) REVERT: F 30 THR cc_start: 0.8589 (m) cc_final: 0.8123 (p) REVERT: F 60 HIS cc_start: 0.7764 (p-80) cc_final: 0.7461 (p90) REVERT: F 65 ARG cc_start: 0.7616 (ppt-90) cc_final: 0.7272 (ppt-90) REVERT: F 86 ASP cc_start: 0.5738 (OUTLIER) cc_final: 0.5095 (m-30) REVERT: F 149 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8124 (t160) REVERT: C 419 GLU cc_start: 0.8466 (mp0) cc_final: 0.8177 (mp0) REVERT: C 463 MET cc_start: 0.8269 (mmm) cc_final: 0.6776 (mpp) REVERT: C 466 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7395 (tt0) REVERT: B 403 SER cc_start: 0.9231 (m) cc_final: 0.8750 (t) REVERT: B 439 LYS cc_start: 0.8798 (mmtp) cc_final: 0.8500 (mppt) REVERT: B 506 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8399 (ttmm) REVERT: A 407 MET cc_start: 0.7789 (mtm) cc_final: 0.7274 (mtm) REVERT: A 413 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7016 (mm-30) REVERT: A 420 ARG cc_start: 0.7867 (mpp-170) cc_final: 0.7368 (mpp80) REVERT: A 634 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: D 407 MET cc_start: 0.8236 (ptt) cc_final: 0.7929 (mtm) REVERT: D 431 GLU cc_start: 0.8125 (mp0) cc_final: 0.7593 (mp0) REVERT: E 59 THR cc_start: 0.7291 (p) cc_final: 0.6612 (t) REVERT: E 97 PHE cc_start: 0.7682 (t80) cc_final: 0.7409 (t80) REVERT: E 200 MET cc_start: 0.8432 (mtp) cc_final: 0.8125 (mtt) REVERT: G 204 ARG cc_start: 0.8022 (ttp-110) cc_final: 0.7698 (ptp-110) outliers start: 56 outliers final: 44 residues processed: 337 average time/residue: 1.2814 time to fit residues: 488.8057 Evaluate side-chains 336 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 286 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 175 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 107 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 114 optimal weight: 0.0770 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS B 756 GLN E 82 HIS E 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.166382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.113695 restraints weight = 54374.958| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.27 r_work: 0.3206 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19116 Z= 0.118 Angle : 0.555 13.449 25863 Z= 0.282 Chirality : 0.039 0.209 2905 Planarity : 0.003 0.056 3198 Dihedral : 3.600 41.102 2603 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.05 % Allowed : 29.71 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.18), residues: 2373 helix: 2.91 (0.14), residues: 1399 sheet: -0.77 (0.39), residues: 158 loop : -0.50 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 551 HIS 0.007 0.001 HIS H 60 PHE 0.022 0.001 PHE D 438 TYR 0.022 0.001 TYR D 673 ARG 0.011 0.000 ARG E 204 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 1179) hydrogen bonds : angle 3.74410 ( 3439) SS BOND : bond 0.00397 ( 12) SS BOND : angle 2.00918 ( 24) covalent geometry : bond 0.00270 (19104) covalent geometry : angle 0.55198 (25839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16586.28 seconds wall clock time: 285 minutes 3.43 seconds (17103.43 seconds total)