Starting phenix.real_space_refine on Sun Aug 24 09:25:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kfa_37203/08_2025/8kfa_37203.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kfa_37203/08_2025/8kfa_37203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kfa_37203/08_2025/8kfa_37203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kfa_37203/08_2025/8kfa_37203.map" model { file = "/net/cci-nas-00/data/ceres_data/8kfa_37203/08_2025/8kfa_37203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kfa_37203/08_2025/8kfa_37203.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 42 5.16 5 C 11851 2.51 5 N 3211 2.21 5 O 3561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18665 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 946 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 787 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 4474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4474 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 17, 'GLU:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "D" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 946 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 787 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 4498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4498 Classifications: {'peptide': 576} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 15, 'GLU:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 110 Chain: "E" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 781 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 4488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4488 Classifications: {'peptide': 576} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 16, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 113 Time building chain proxies: 5.27, per 1000 atoms: 0.28 Number of scatterers: 18665 At special positions: 0 Unit cell: (152.168, 139.763, 175.324, 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 42 16.00 O 3561 8.00 N 3211 7.00 C 11851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 916.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4518 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 50 sheets defined 18.8% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.763A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 303 through 310 removed outlier: 4.028A pdb=" N GLY A 306 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N HIS A 308 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 309 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 410 through 429 removed outlier: 4.037A pdb=" N GLY A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 546 removed outlier: 4.898A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.605A pdb=" N ILE A 664 " --> pdb=" O ARG A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 698 removed outlier: 4.310A pdb=" N GLY A 698 " --> pdb=" O ILE A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 717 removed outlier: 4.238A pdb=" N ASP A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 714 " --> pdb=" O GLN A 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.749A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.960A pdb=" N GLY B 306 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N HIS B 308 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 410 through 429 removed outlier: 3.923A pdb=" N GLY B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 546 removed outlier: 4.920A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.662A pdb=" N ILE B 664 " --> pdb=" O ARG B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 701 through 717 removed outlier: 4.542A pdb=" N ASP B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU B 714 " --> pdb=" O GLN B 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.868A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.974A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.996A pdb=" N GLY C 306 " --> pdb=" O TYR C 303 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N HIS C 308 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 410 through 429 removed outlier: 3.903A pdb=" N GLY C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 546 removed outlier: 4.899A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 690 through 698 removed outlier: 4.237A pdb=" N GLY C 698 " --> pdb=" O ILE C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 717 removed outlier: 4.346A pdb=" N ASP C 713 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU C 714 " --> pdb=" O GLN C 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.507A pdb=" N VAL H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.711A pdb=" N VAL H 120 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.006A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 98 through 99 removed outlier: 3.978A pdb=" N PHE H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AA7, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.836A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR L 85 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 574 through 576 removed outlier: 3.584A pdb=" N PHE A 113 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 559 through 561 removed outlier: 4.629A pdb=" N THR A 123 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL C 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN A 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 145 through 152 removed outlier: 6.726A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 366 through 372 current: chain 'A' and resid 448 through 457 Processing sheet with id=AB2, first strand: chain 'A' and resid 157 through 175 removed outlier: 8.515A pdb=" N TYR A 164 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS A 166 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG A 189 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 168 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU A 187 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL A 170 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE A 185 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLN A 172 " --> pdb=" O MET A 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 180 through 191 current: chain 'A' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 246 through 248 current: chain 'A' and resid 287 through 288 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 287 through 288 current: chain 'A' and resid 340 through 345 removed outlier: 3.606A pdb=" N VAL A 352 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AB4, first strand: chain 'A' and resid 213 through 214 Processing sheet with id=AB5, first strand: chain 'A' and resid 384 through 388 Processing sheet with id=AB6, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB7, first strand: chain 'A' and resid 638 through 643 removed outlier: 6.834A pdb=" N TYR A 647 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLN A 658 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR A 649 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 665 through 667 removed outlier: 4.025A pdb=" N THR A 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR B 123 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.536A pdb=" N VAL D 120 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 50 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN D 59 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 98 through 99 removed outlier: 3.996A pdb=" N PHE D 113 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 11 Processing sheet with id=AC5, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.531A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR F 49 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR F 85 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 574 through 576 removed outlier: 3.505A pdb=" N PHE B 113 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.653A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 366 through 372 current: chain 'B' and resid 448 through 457 Processing sheet with id=AC8, first strand: chain 'B' and resid 157 through 166 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 190 through 191 current: chain 'B' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 287 through 288 current: chain 'B' and resid 340 through 346 Processing sheet with id=AC9, first strand: chain 'B' and resid 180 through 187 removed outlier: 5.369A pdb=" N GLN B 172 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE B 185 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 170 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AD2, first strand: chain 'B' and resid 210 through 215 removed outlier: 3.552A pdb=" N ALA B 222 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 383 through 388 Processing sheet with id=AD4, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AD5, first strand: chain 'B' and resid 638 through 643 removed outlier: 4.214A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 665 through 667 removed outlier: 3.967A pdb=" N THR B 665 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR C 123 " --> pdb=" O VAL C 570 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.854A pdb=" N GLN E 59 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL E 120 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 98 through 99 removed outlier: 3.927A pdb=" N PHE E 113 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'G' and resid 10 through 11 Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 54 removed outlier: 6.426A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR G 49 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR G 85 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 574 through 576 removed outlier: 3.516A pdb=" N PHE C 113 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AE6, first strand: chain 'C' and resid 145 through 152 removed outlier: 6.780A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 366 through 372 current: chain 'C' and resid 449 through 457 Processing sheet with id=AE7, first strand: chain 'C' and resid 157 through 166 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 190 through 191 current: chain 'C' and resid 246 through 248 Processing sheet with id=AE8, first strand: chain 'C' and resid 180 through 187 removed outlier: 5.309A pdb=" N GLN C 172 " --> pdb=" O MET C 183 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE C 185 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL C 170 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE C 262 " --> pdb=" O PHE C 175 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AF1, first strand: chain 'C' and resid 213 through 215 Processing sheet with id=AF2, first strand: chain 'C' and resid 321 through 325 removed outlier: 5.074A pdb=" N ASP C 323 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG C 342 " --> pdb=" O ASP C 323 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 383 through 388 Processing sheet with id=AF4, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AF5, first strand: chain 'C' and resid 638 through 643 removed outlier: 3.526A pdb=" N TYR C 649 " --> pdb=" O HIS C 657 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 605 hydrogen bonds defined for protein. 1581 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: 4.22 Time building geometry restraints manager: 2.36 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: 6157 1.34 - 1.46: 4725 1.46 - 1.58: 8165 1.58 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 19130 Sorted by residual: bond pdb=" CB ASN B 620 " pdb=" CG ASN B 620 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.43e-01 bond pdb=" CB PRO F 8 " pdb=" CG PRO F 8 " ideal model delta sigma weight residual 1.506 1.473 0.033 3.90e-02 6.57e+02 7.35e-01 bond pdb=" CA ILE A 501 " pdb=" C ILE A 501 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.12e-02 7.97e+03 7.08e-01 bond pdb=" C ILE C 719 " pdb=" N ASP C 720 " ideal model delta sigma weight residual 1.332 1.321 0.011 1.40e-02 5.10e+03 6.64e-01 bond pdb=" CB PRO G 8 " pdb=" CG PRO G 8 " ideal model delta sigma weight residual 1.506 1.474 0.032 3.90e-02 6.57e+02 6.58e-01 ... (remaining 19125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 25802 2.01 - 4.02: 255 4.02 - 6.04: 22 6.04 - 8.05: 2 8.05 - 10.06: 2 Bond angle restraints: 26083 Sorted by residual: angle pdb=" CB MET C 421 " pdb=" CG MET C 421 " pdb=" SD MET C 421 " ideal model delta sigma weight residual 112.70 122.76 -10.06 3.00e+00 1.11e-01 1.12e+01 angle pdb=" N ILE A 501 " pdb=" CA ILE A 501 " pdb=" C ILE A 501 " ideal model delta sigma weight residual 111.91 108.95 2.96 8.90e-01 1.26e+00 1.11e+01 angle pdb=" C ALA L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 126.60 -5.06 1.91e+00 2.74e-01 7.03e+00 angle pdb=" C ALA G 50 " pdb=" N ALA G 51 " pdb=" CA ALA G 51 " ideal model delta sigma weight residual 121.54 126.57 -5.03 1.91e+00 2.74e-01 6.93e+00 angle pdb=" C ALA F 50 " pdb=" N ALA F 51 " pdb=" CA ALA F 51 " ideal model delta sigma weight residual 121.54 126.28 -4.74 1.91e+00 2.74e-01 6.15e+00 ... (remaining 26078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 10138 17.33 - 34.67: 878 34.67 - 52.00: 109 52.00 - 69.33: 25 69.33 - 86.67: 32 Dihedral angle restraints: 11182 sinusoidal: 4133 harmonic: 7049 Sorted by residual: dihedral pdb=" CA ARG A 428 " pdb=" C ARG A 428 " pdb=" N TYR A 429 " pdb=" CA TYR A 429 " ideal model delta harmonic sigma weight residual -180.00 -163.11 -16.89 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASP C 389 " pdb=" CB ASP C 389 " pdb=" CG ASP C 389 " pdb=" OD1 ASP C 389 " ideal model delta sinusoidal sigma weight residual -30.00 -86.57 56.57 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ALA D 110 " pdb=" C ALA D 110 " pdb=" N PHE D 111 " pdb=" CA PHE D 111 " ideal model delta harmonic sigma weight residual -180.00 -163.67 -16.33 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 11179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2411 0.053 - 0.105: 405 0.105 - 0.158: 75 0.158 - 0.210: 0 0.210 - 0.263: 1 Chirality restraints: 2892 Sorted by residual: chirality pdb=" CB ILE D 107 " pdb=" CA ILE D 107 " pdb=" CG1 ILE D 107 " pdb=" CG2 ILE D 107 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CG LEU B 711 " pdb=" CB LEU B 711 " pdb=" CD1 LEU B 711 " pdb=" CD2 LEU B 711 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE A 185 " pdb=" N ILE A 185 " pdb=" C ILE A 185 " pdb=" CB ILE A 185 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 2889 not shown) Planarity restraints: 3393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 13 " 0.031 5.00e-02 4.00e+02 4.79e-02 3.68e+00 pdb=" N PRO D 14 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 599 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO B 600 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 600 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 600 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 599 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 600 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 600 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 600 " -0.022 5.00e-02 4.00e+02 ... (remaining 3390 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2818 2.76 - 3.30: 18503 3.30 - 3.83: 32202 3.83 - 4.37: 36807 4.37 - 4.90: 64749 Nonbonded interactions: 155079 Sorted by model distance: nonbonded pdb=" O THR B 143 " pdb=" OH TYR B 452 " model vdw 2.226 3.040 nonbonded pdb=" O THR A 143 " pdb=" OH TYR A 452 " model vdw 2.232 3.040 nonbonded pdb=" O GLU A 152 " pdb=" OH TYR B 689 " model vdw 2.240 3.040 nonbonded pdb=" O GLY B 447 " pdb=" OG1 THR B 497 " model vdw 2.245 3.040 nonbonded pdb=" O GLU B 152 " pdb=" OH TYR C 689 " model vdw 2.250 3.040 ... (remaining 155074 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 111 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 193 or (resid 194 and (name N \ or name CA or name C or name O or name CB )) or resid 195 through 312 or (resid \ 313 and (name N or name CA or name C or name O or name CB )) or resid 314 throug \ h 319 or (resid 320 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD )) or resid 321 through 427 or (resid 428 and (name N or name CA \ or name C or name O or name CB )) or resid 429 through 519 or (resid 520 and (n \ ame N or name CA or name C or name O or name CB or name CG or name SD )) or resi \ d 521 through 552 or (resid 553 and (name N or name CA or name C or name O or na \ me CB )) or resid 554 through 559 or (resid 560 through 561 and (name N or name \ CA or name C or name O )) or resid 562 through 586 or (resid 587 and (name N or \ name CA or name C or name O or name CB )) or resid 588 through 596 or (resid 597 \ and (name N or name CA or name C or name O or name CB )) or resid 598 through 6 \ 60 or (resid 661 through 662 and (name N or name CA or name C or name O or name \ CB )) or resid 663 through 686 or (resid 687 and (name N or name CA or name C or \ name O or name CB )) or resid 688 through 707 or (resid 708 and (name N or name \ CA or name C or name O or name CB )) or resid 709 through 725)) selection = (chain 'B' and (resid 111 through 128 or (resid 129 and (name N or name CA or na \ me C or name O or name CB )) or resid 130 through 177 or (resid 178 and (name N \ or name CA or name C or name O or name CB )) or resid 179 through 193 or (resid \ 194 and (name N or name CA or name C or name O or name CB )) or resid 195 throug \ h 214 or (resid 215 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name NE or name CZ )) or resid 216 through 319 or (resid 320 \ and (name N or name CA or name C or name O or name CB or name CG or name CD )) o \ r resid 321 through 361 or (resid 362 and (name N or name CA or name C or name O \ or name CB )) or resid 363 through 373 or (resid 374 and (name N or name CA or \ name C or name O or name CB )) or resid 375 through 400 or (resid 401 and (name \ N or name CA or name C or name O or name CB )) or resid 402 through 500 or (resi \ d 501 and (name N or name CA or name C or name O or name CB )) or resid 502 thro \ ugh 552 or (resid 553 and (name N or name CA or name C or name O or name CB )) o \ r resid 554 through 559 or (resid 560 through 561 and (name N or name CA or name \ C or name O )) or resid 562 through 571 or (resid 572 through 574 and (name N o \ r name CA or name C or name O or name CB )) or resid 575 through 586 or (resid 5 \ 87 and (name N or name CA or name C or name O or name CB )) or resid 588 through \ 596 or (resid 597 and (name N or name CA or name C or name O or name CB )) or r \ esid 598 through 604 or (resid 605 and (name N or name CA or name C or name O or \ name CB )) or resid 606 through 660 or (resid 661 through 662 and (name N or na \ me CA or name C or name O or name CB )) or resid 663 through 681 or (resid 682 a \ nd (name N or name CA or name C or name O or name CB )) or resid 683 through 686 \ or (resid 687 and (name N or name CA or name C or name O or name CB )) or resid \ 688 through 690 or (resid 691 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name NE or name CZ )) or resid 692 through 707 or \ (resid 708 and (name N or name CA or name C or name O or name CB )) or resid 709 \ through 712 or (resid 713 and (name N or name CA or name C or name O or name CB \ )) or resid 714 through 725)) selection = (chain 'C' and (resid 111 through 128 or (resid 129 and (name N or name CA or na \ me C or name O or name CB )) or resid 130 through 137 or (resid 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 throug \ h 177 or (resid 178 and (name N or name CA or name C or name O or name CB )) or \ resid 179 through 214 or (resid 215 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name NE or name CZ )) or resid 216 through 31 \ 2 or (resid 313 and (name N or name CA or name C or name O or name CB )) or resi \ d 314 through 361 or (resid 362 and (name N or name CA or name C or name O or na \ me CB )) or resid 363 through 373 or (resid 374 and (name N or name CA or name C \ or name O or name CB )) or resid 375 through 379 or (resid 380 and (name N or n \ ame CA or name C or name O or name CB )) or resid 381 through 384 or (resid 385 \ and (name N or name CA or name C or name O or name CB )) or resid 386 through 40 \ 0 or (resid 401 and (name N or name CA or name C or name O or name CB )) or resi \ d 402 through 427 or (resid 428 and (name N or name CA or name C or name O or na \ me CB )) or resid 429 through 519 or (resid 520 and (name N or name CA or name C \ or name O or name CB or name CG or name SD )) or resid 521 through 560 or (resi \ d 561 and (name N or name CA or name C or name O )) or resid 562 through 571 or \ (resid 572 through 574 and (name N or name CA or name C or name O or name CB )) \ or resid 575 through 604 or (resid 605 and (name N or name CA or name C or name \ O or name CB )) or resid 606 through 681 or (resid 682 and (name N or name CA or \ name C or name O or name CB )) or resid 683 through 712 or (resid 713 and (name \ N or name CA or name C or name O or name CB )) or resid 714 through 725)) } ncs_group { reference = (chain 'D' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 56 or (resid 57 and (name N or name \ CA or name C or name O or name CB or name CG1 or name CG2)) or resid 58 or (res \ id 59 and (name N or name CA or name C or name O or name CB )) or resid 60 throu \ gh 85 or (resid 86 and (name N or name CA or name C or name O or name CB )) or r \ esid 87 through 108 or (resid 109 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) \ or resid 110 through 124)) selection = (chain 'E' and (resid 1 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 15 or (resid 16 and (name N or name \ CA or name C or name O or name CB )) or resid 17 through 26 or (resid 27 and (n \ ame N or name CA or name C or name O or name CB )) or resid 28 through 56 or (re \ sid 57 and (name N or name CA or name C or name O or name CB or name CG1 or name \ CG2)) or resid 58 or (resid 59 and (name N or name CA or name C or name O or na \ me CB )) or resid 60 through 85 or (resid 86 and (name N or name CA or name C or \ name O or name CB )) or resid 87 through 108 or (resid 109 and (name N or name \ CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 \ or name CE2 or name CZ )) or resid 110 through 124)) selection = (chain 'H' and (resid 1 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 15 or (resid 16 and (name N or name \ CA or name C or name O or name CB )) or resid 17 through 82 or (resid 83 and (n \ ame N or name CA or name C or name O or name CB )) or resid 84 through 124)) } ncs_group { reference = (chain 'F' and (resid 1 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 107)) selection = chain 'G' selection = (chain 'L' and (resid 1 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 107)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.230 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.400 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.002 0.033 19130 Z= 0.101 Angle : 0.484 10.061 26083 Z= 0.253 Chirality : 0.041 0.263 2892 Planarity : 0.003 0.048 3393 Dihedral : 13.594 86.665 6664 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.18), residues: 2391 helix: 0.93 (0.28), residues: 330 sheet: -0.61 (0.19), residues: 822 loop : 0.07 (0.19), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.013 0.001 TYR C 296 PHE 0.021 0.001 PHE C 650 TRP 0.023 0.001 TRP B 174 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00222 (19130) covalent geometry : angle 0.48432 (26083) hydrogen bonds : bond 0.20711 ( 605) hydrogen bonds : angle 8.76171 ( 1581) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.754 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 5 VAL cc_start: 0.8461 (t) cc_final: 0.8204 (t) REVERT: H 53 HIS cc_start: 0.8297 (p-80) cc_final: 0.8036 (p-80) REVERT: H 113 PHE cc_start: 0.7511 (t80) cc_final: 0.7128 (t80) REVERT: L 62 LEU cc_start: 0.9003 (mt) cc_final: 0.8795 (mt) REVERT: A 265 TYR cc_start: 0.6924 (p90) cc_final: 0.6202 (p90) REVERT: A 326 TYR cc_start: 0.2576 (t80) cc_final: 0.2244 (t80) REVERT: D 62 ASP cc_start: 0.8919 (t0) cc_final: 0.8668 (t0) REVERT: D 73 ASP cc_start: 0.8334 (t0) cc_final: 0.8047 (t0) REVERT: D 113 PHE cc_start: 0.7542 (t80) cc_final: 0.7237 (t80) REVERT: B 174 TRP cc_start: 0.6700 (t60) cc_final: 0.6334 (t60) REVERT: B 232 MET cc_start: 0.7516 (mpp) cc_final: 0.7260 (mpp) REVERT: B 265 TYR cc_start: 0.6885 (p90) cc_final: 0.6304 (p90) REVERT: B 326 TYR cc_start: 0.2466 (t80) cc_final: 0.2215 (t80) REVERT: B 502 GLU cc_start: 0.8188 (pm20) cc_final: 0.7925 (pm20) REVERT: B 677 MET cc_start: 0.8901 (mmp) cc_final: 0.8563 (mmm) REVERT: E 53 HIS cc_start: 0.8506 (p-80) cc_final: 0.8204 (p-80) REVERT: E 65 LYS cc_start: 0.9156 (tppt) cc_final: 0.8911 (tppt) REVERT: E 73 ASP cc_start: 0.8148 (t0) cc_final: 0.7881 (t0) REVERT: C 265 TYR cc_start: 0.6781 (p90) cc_final: 0.6063 (p90) REVERT: C 421 MET cc_start: 0.9177 (mpp) cc_final: 0.8134 (mpp) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1354 time to fit residues: 52.3449 Evaluate side-chains 214 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.0980 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN D 3 GLN C 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.070885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.056085 restraints weight = 70328.231| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.75 r_work: 0.3075 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19130 Z= 0.117 Angle : 0.500 6.601 26083 Z= 0.265 Chirality : 0.042 0.323 2892 Planarity : 0.003 0.046 3393 Dihedral : 3.887 16.050 2656 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.63 % Allowed : 6.75 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.18), residues: 2391 helix: 0.93 (0.28), residues: 330 sheet: -0.50 (0.19), residues: 804 loop : 0.08 (0.19), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 72 TYR 0.012 0.001 TYR B 179 PHE 0.025 0.001 PHE B 650 TRP 0.015 0.001 TRP B 174 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00258 (19130) covalent geometry : angle 0.49954 (26083) hydrogen bonds : bond 0.03819 ( 605) hydrogen bonds : angle 6.48815 ( 1581) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 246 time to evaluate : 1.067 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: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8365 (tp-100) REVERT: H 5 VAL cc_start: 0.8783 (t) cc_final: 0.8446 (m) REVERT: H 53 HIS cc_start: 0.8516 (p-80) cc_final: 0.8175 (p-80) REVERT: H 60 TYR cc_start: 0.8354 (m-80) cc_final: 0.8015 (m-10) REVERT: H 65 LYS cc_start: 0.8924 (mmmt) cc_final: 0.7836 (mmmt) REVERT: H 93 MET cc_start: 0.8069 (tpp) cc_final: 0.7762 (tpp) REVERT: H 119 MET cc_start: 0.8342 (tpp) cc_final: 0.7781 (tpp) REVERT: L 70 GLU cc_start: 0.8191 (tp30) cc_final: 0.7966 (tp30) REVERT: A 520 MET cc_start: 0.9029 (mmm) cc_final: 0.8683 (mmm) REVERT: A 587 MET cc_start: 0.6602 (mtm) cc_final: 0.6016 (mtm) REVERT: D 5 VAL cc_start: 0.9148 (t) cc_final: 0.8543 (p) REVERT: D 73 ASP cc_start: 0.8599 (t0) cc_final: 0.8255 (t0) REVERT: D 113 PHE cc_start: 0.7695 (t80) cc_final: 0.7411 (t80) REVERT: F 45 GLU cc_start: 0.7236 (pm20) cc_final: 0.7029 (pm20) REVERT: B 265 TYR cc_start: 0.7725 (p90) cc_final: 0.7401 (p90) REVERT: B 326 TYR cc_start: 0.2782 (t80) cc_final: 0.2423 (t80) REVERT: B 502 GLU cc_start: 0.8771 (pm20) cc_final: 0.8443 (pm20) REVERT: B 677 MET cc_start: 0.9299 (mmp) cc_final: 0.8832 (mmm) REVERT: B 702 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.6235 (m-10) REVERT: E 46 GLU cc_start: 0.8003 (tp30) cc_final: 0.7716 (tp30) REVERT: E 73 ASP cc_start: 0.8566 (t0) cc_final: 0.8175 (t0) REVERT: E 93 MET cc_start: 0.8280 (tpp) cc_final: 0.7981 (tpp) REVERT: E 119 MET cc_start: 0.8518 (tpt) cc_final: 0.8075 (tpp) REVERT: G 27 GLN cc_start: 0.8357 (pp30) cc_final: 0.8067 (pp30) REVERT: C 265 TYR cc_start: 0.7766 (p90) cc_final: 0.7560 (p90) outliers start: 12 outliers final: 10 residues processed: 253 average time/residue: 0.1163 time to fit residues: 47.5232 Evaluate side-chains 232 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 221 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 88 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 34 optimal weight: 0.0870 chunk 4 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 156 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 202 optimal weight: 0.7980 chunk 219 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.069723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.054773 restraints weight = 71321.032| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.75 r_work: 0.3038 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19130 Z= 0.172 Angle : 0.514 8.336 26083 Z= 0.271 Chirality : 0.043 0.302 2892 Planarity : 0.003 0.042 3393 Dihedral : 3.975 15.878 2656 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.95 % Allowed : 9.96 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.18), residues: 2391 helix: 0.93 (0.27), residues: 330 sheet: -0.57 (0.19), residues: 798 loop : 0.05 (0.19), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 72 TYR 0.016 0.001 TYR F 91 PHE 0.019 0.001 PHE B 650 TRP 0.017 0.001 TRP B 174 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00381 (19130) covalent geometry : angle 0.51358 (26083) hydrogen bonds : bond 0.03755 ( 605) hydrogen bonds : angle 6.00408 ( 1581) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 VAL cc_start: 0.8865 (t) cc_final: 0.8475 (m) REVERT: H 53 HIS cc_start: 0.8534 (p-80) cc_final: 0.8209 (p-80) REVERT: H 113 PHE cc_start: 0.7991 (t80) cc_final: 0.7667 (t80) REVERT: H 119 MET cc_start: 0.8542 (tpp) cc_final: 0.8086 (tpt) REVERT: L 70 GLU cc_start: 0.8186 (tp30) cc_final: 0.7928 (tp30) REVERT: A 520 MET cc_start: 0.9089 (mmm) cc_final: 0.8822 (mmm) REVERT: A 587 MET cc_start: 0.6639 (mtm) cc_final: 0.6200 (mtm) REVERT: D 65 LYS cc_start: 0.9243 (tppt) cc_final: 0.8908 (tppt) REVERT: D 73 ASP cc_start: 0.8576 (t0) cc_final: 0.8242 (t0) REVERT: F 45 GLU cc_start: 0.7305 (pm20) cc_final: 0.7087 (pm20) REVERT: B 265 TYR cc_start: 0.7853 (p90) cc_final: 0.7453 (p90) REVERT: B 326 TYR cc_start: 0.2838 (t80) cc_final: 0.2404 (t80) REVERT: B 677 MET cc_start: 0.9297 (mmp) cc_final: 0.8721 (mmm) REVERT: E 46 GLU cc_start: 0.8109 (tp30) cc_final: 0.7815 (tp30) REVERT: E 60 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8827 (m-80) REVERT: E 65 LYS cc_start: 0.9073 (tppt) cc_final: 0.8820 (tppt) REVERT: E 73 ASP cc_start: 0.8486 (t0) cc_final: 0.8075 (t0) REVERT: E 116 GLN cc_start: 0.9176 (tp40) cc_final: 0.8860 (mm-40) REVERT: G 27 GLN cc_start: 0.8343 (pp30) cc_final: 0.8126 (pp30) REVERT: C 265 TYR cc_start: 0.7761 (p90) cc_final: 0.7523 (p90) outliers start: 18 outliers final: 15 residues processed: 235 average time/residue: 0.1054 time to fit residues: 40.0294 Evaluate side-chains 224 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 209 optimal weight: 0.0470 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 217 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 HIS D 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.069786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.054741 restraints weight = 71106.078| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.83 r_work: 0.3036 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19130 Z= 0.155 Angle : 0.510 11.707 26083 Z= 0.267 Chirality : 0.043 0.331 2892 Planarity : 0.003 0.041 3393 Dihedral : 3.967 16.718 2656 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.16 % Allowed : 11.65 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.18), residues: 2391 helix: 0.93 (0.27), residues: 330 sheet: -0.61 (0.19), residues: 801 loop : 0.05 (0.19), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.014 0.001 TYR F 91 PHE 0.021 0.001 PHE B 650 TRP 0.012 0.001 TRP B 174 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00346 (19130) covalent geometry : angle 0.51004 (26083) hydrogen bonds : bond 0.03553 ( 605) hydrogen bonds : angle 5.81692 ( 1581) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8178 (tp-100) REVERT: H 5 VAL cc_start: 0.8995 (t) cc_final: 0.8488 (m) REVERT: H 53 HIS cc_start: 0.8555 (p-80) cc_final: 0.8251 (p-80) REVERT: H 60 TYR cc_start: 0.8436 (m-80) cc_final: 0.8167 (m-10) REVERT: H 65 LYS cc_start: 0.9050 (mmmt) cc_final: 0.7994 (mmmt) REVERT: H 93 MET cc_start: 0.7912 (mmp) cc_final: 0.6959 (tpp) REVERT: H 113 PHE cc_start: 0.8017 (t80) cc_final: 0.7547 (t80) REVERT: H 119 MET cc_start: 0.8603 (tpp) cc_final: 0.7342 (ptt) REVERT: L 70 GLU cc_start: 0.8163 (tp30) cc_final: 0.7922 (tp30) REVERT: A 265 TYR cc_start: 0.7890 (p90) cc_final: 0.7577 (p90) REVERT: A 520 MET cc_start: 0.9076 (mmm) cc_final: 0.8779 (mmm) REVERT: A 587 MET cc_start: 0.6809 (mtm) cc_final: 0.6426 (mtm) REVERT: D 65 LYS cc_start: 0.9274 (tppt) cc_final: 0.8841 (tppt) REVERT: D 73 ASP cc_start: 0.8608 (t0) cc_final: 0.8264 (t0) REVERT: D 116 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8178 (pm20) REVERT: F 45 GLU cc_start: 0.7373 (pm20) cc_final: 0.7146 (pm20) REVERT: B 265 TYR cc_start: 0.7884 (p90) cc_final: 0.7541 (p90) REVERT: B 326 TYR cc_start: 0.2775 (t80) cc_final: 0.2291 (t80) REVERT: B 677 MET cc_start: 0.9301 (mmp) cc_final: 0.8988 (mmp) REVERT: E 3 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8494 (tm-30) REVERT: E 46 GLU cc_start: 0.8105 (tp30) cc_final: 0.7901 (tp30) REVERT: E 73 ASP cc_start: 0.8444 (t0) cc_final: 0.8039 (t0) REVERT: E 93 MET cc_start: 0.8651 (tpp) cc_final: 0.8376 (tpp) REVERT: E 116 GLN cc_start: 0.9161 (tp40) cc_final: 0.8843 (mm-40) REVERT: E 119 MET cc_start: 0.8325 (tpp) cc_final: 0.7635 (tpp) REVERT: G 24 ARG cc_start: 0.8341 (ttm110) cc_final: 0.8066 (ttm-80) REVERT: G 27 GLN cc_start: 0.8373 (pp30) cc_final: 0.8124 (pp30) REVERT: C 265 TYR cc_start: 0.7786 (p90) cc_final: 0.7504 (p90) REVERT: C 520 MET cc_start: 0.9083 (mmm) cc_final: 0.8749 (mmm) outliers start: 22 outliers final: 17 residues processed: 244 average time/residue: 0.1114 time to fit residues: 43.6838 Evaluate side-chains 235 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 144 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.070009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.055118 restraints weight = 70640.116| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.73 r_work: 0.3047 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19130 Z= 0.135 Angle : 0.504 14.020 26083 Z= 0.263 Chirality : 0.042 0.295 2892 Planarity : 0.003 0.039 3393 Dihedral : 3.902 17.935 2656 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.32 % Allowed : 12.55 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.18), residues: 2391 helix: 0.70 (0.27), residues: 348 sheet: -0.60 (0.19), residues: 798 loop : -0.03 (0.19), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 16 TYR 0.027 0.001 TYR B 689 PHE 0.016 0.001 PHE A 650 TRP 0.016 0.001 TRP B 174 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00304 (19130) covalent geometry : angle 0.50384 (26083) hydrogen bonds : bond 0.03412 ( 605) hydrogen bonds : angle 5.68894 ( 1581) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8360 (tp-100) cc_final: 0.8008 (tp-100) REVERT: H 5 VAL cc_start: 0.8854 (t) cc_final: 0.8355 (m) REVERT: H 43 LYS cc_start: 0.8371 (mtmm) cc_final: 0.8165 (mtmm) REVERT: H 53 HIS cc_start: 0.8537 (p-80) cc_final: 0.8220 (p-80) REVERT: H 65 LYS cc_start: 0.9025 (mmmt) cc_final: 0.7963 (mmmt) REVERT: H 93 MET cc_start: 0.7912 (mmp) cc_final: 0.7639 (tpp) REVERT: H 119 MET cc_start: 0.8624 (tpp) cc_final: 0.8262 (tpp) REVERT: L 24 ARG cc_start: 0.8248 (tpp80) cc_final: 0.8004 (tpp80) REVERT: L 70 GLU cc_start: 0.8146 (tp30) cc_final: 0.7845 (tp30) REVERT: D 65 LYS cc_start: 0.9296 (tppt) cc_final: 0.8946 (tppt) REVERT: D 73 ASP cc_start: 0.8622 (t0) cc_final: 0.8283 (t0) REVERT: F 89 GLN cc_start: 0.9188 (tm-30) cc_final: 0.8922 (tm-30) REVERT: B 265 TYR cc_start: 0.7863 (p90) cc_final: 0.7458 (p90) REVERT: B 326 TYR cc_start: 0.2754 (t80) cc_final: 0.2262 (t80) REVERT: B 677 MET cc_start: 0.9288 (mmp) cc_final: 0.8973 (mmp) REVERT: E 3 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8448 (tm-30) REVERT: E 73 ASP cc_start: 0.8473 (t0) cc_final: 0.8075 (t0) REVERT: E 93 MET cc_start: 0.8612 (tpp) cc_final: 0.8144 (tpt) REVERT: E 116 GLN cc_start: 0.9146 (tp40) cc_final: 0.8818 (mm-40) REVERT: G 11 LEU cc_start: 0.8973 (mt) cc_final: 0.8498 (pp) REVERT: G 24 ARG cc_start: 0.8304 (ttm110) cc_final: 0.8020 (ttm-80) REVERT: G 27 GLN cc_start: 0.8393 (pp30) cc_final: 0.8090 (pp30) REVERT: G 89 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8911 (tm-30) REVERT: C 232 MET cc_start: 0.8397 (mtm) cc_final: 0.7745 (mtm) REVERT: C 265 TYR cc_start: 0.7744 (p90) cc_final: 0.7439 (p90) REVERT: C 371 GLU cc_start: 0.8744 (mp0) cc_final: 0.8527 (mp0) REVERT: C 520 MET cc_start: 0.9048 (mmm) cc_final: 0.8709 (mmm) outliers start: 25 outliers final: 20 residues processed: 247 average time/residue: 0.1185 time to fit residues: 46.6294 Evaluate side-chains 240 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain C residue 288 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 132 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN D 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.068369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.053473 restraints weight = 70524.078| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.68 r_work: 0.3006 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19130 Z= 0.205 Angle : 0.543 15.728 26083 Z= 0.283 Chirality : 0.043 0.307 2892 Planarity : 0.003 0.040 3393 Dihedral : 4.068 16.773 2656 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.63 % Allowed : 13.39 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.18), residues: 2391 helix: 0.65 (0.27), residues: 348 sheet: -0.64 (0.19), residues: 765 loop : -0.06 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 16 TYR 0.020 0.001 TYR B 689 PHE 0.021 0.001 PHE E 113 TRP 0.013 0.001 TRP E 114 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00457 (19130) covalent geometry : angle 0.54276 (26083) hydrogen bonds : bond 0.03672 ( 605) hydrogen bonds : angle 5.66079 ( 1581) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8455 (tp-100) cc_final: 0.8159 (tp-100) REVERT: H 5 VAL cc_start: 0.8921 (t) cc_final: 0.8523 (m) REVERT: H 43 LYS cc_start: 0.8423 (mtmm) cc_final: 0.8214 (mtmm) REVERT: H 93 MET cc_start: 0.8033 (mmp) cc_final: 0.7414 (mmp) REVERT: H 119 MET cc_start: 0.8670 (tpp) cc_final: 0.7606 (ptt) REVERT: L 70 GLU cc_start: 0.8137 (tp30) cc_final: 0.7897 (tp30) REVERT: A 534 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.8495 (t-90) REVERT: D 73 ASP cc_start: 0.8602 (t0) cc_final: 0.8263 (t0) REVERT: F 89 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8850 (tm-30) REVERT: B 187 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8228 (tm-30) REVERT: B 265 TYR cc_start: 0.7845 (p90) cc_final: 0.7342 (p90) REVERT: B 677 MET cc_start: 0.9282 (mmp) cc_final: 0.9019 (mmp) REVERT: E 3 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8471 (tm-30) REVERT: E 73 ASP cc_start: 0.8461 (t0) cc_final: 0.8087 (t0) REVERT: E 91 THR cc_start: 0.9079 (m) cc_final: 0.8875 (p) REVERT: E 93 MET cc_start: 0.8596 (tpp) cc_final: 0.8277 (tpp) REVERT: E 119 MET cc_start: 0.8423 (tpp) cc_final: 0.6851 (ptm) REVERT: G 11 LEU cc_start: 0.8976 (mt) cc_final: 0.8604 (pp) REVERT: G 89 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8855 (tm-30) REVERT: C 265 TYR cc_start: 0.7789 (p90) cc_final: 0.7504 (p90) REVERT: C 371 GLU cc_start: 0.8801 (mp0) cc_final: 0.8533 (mp0) REVERT: C 520 MET cc_start: 0.9075 (mmm) cc_final: 0.8771 (mmm) outliers start: 31 outliers final: 27 residues processed: 246 average time/residue: 0.1259 time to fit residues: 49.6227 Evaluate side-chains 240 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 363 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 133 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 0.0870 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.069183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.054286 restraints weight = 70573.592| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.74 r_work: 0.3027 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 0.053 19130 Z= 0.147 Angle : 0.523 15.815 26083 Z= 0.271 Chirality : 0.042 0.289 2892 Planarity : 0.003 0.038 3393 Dihedral : 3.967 16.814 2656 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.58 % Allowed : 14.07 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.18), residues: 2391 helix: 0.70 (0.27), residues: 348 sheet: -0.62 (0.19), residues: 765 loop : -0.05 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 24 TYR 0.019 0.001 TYR B 689 PHE 0.026 0.001 PHE B 650 TRP 0.020 0.001 TRP B 174 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00329 (19130) covalent geometry : angle 0.52305 (26083) hydrogen bonds : bond 0.03460 ( 605) hydrogen bonds : angle 5.54244 ( 1581) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.513 Fit side-chains REVERT: H 3 GLN cc_start: 0.8376 (tp-100) cc_final: 0.8084 (tp-100) REVERT: H 5 VAL cc_start: 0.8925 (t) cc_final: 0.8494 (m) REVERT: H 43 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8229 (mtmm) REVERT: H 53 HIS cc_start: 0.8536 (p-80) cc_final: 0.8233 (p-80) REVERT: H 65 LYS cc_start: 0.9250 (tppt) cc_final: 0.8695 (mmmt) REVERT: H 93 MET cc_start: 0.8090 (mmp) cc_final: 0.7500 (mmp) REVERT: H 119 MET cc_start: 0.8635 (tpp) cc_final: 0.7560 (ptt) REVERT: L 24 ARG cc_start: 0.8271 (tpp80) cc_final: 0.8005 (tpp80) REVERT: L 70 GLU cc_start: 0.8117 (tp30) cc_final: 0.7797 (tp30) REVERT: A 534 HIS cc_start: 0.8713 (OUTLIER) cc_final: 0.8479 (t-90) REVERT: D 65 LYS cc_start: 0.9265 (tppt) cc_final: 0.8959 (tppt) REVERT: D 73 ASP cc_start: 0.8612 (t0) cc_final: 0.8266 (t0) REVERT: F 89 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8912 (tm-30) REVERT: B 265 TYR cc_start: 0.7817 (p90) cc_final: 0.7325 (p90) REVERT: B 326 TYR cc_start: 0.2417 (t80) cc_final: 0.1995 (t80) REVERT: B 502 GLU cc_start: 0.8875 (pm20) cc_final: 0.8654 (pm20) REVERT: B 677 MET cc_start: 0.9292 (mmp) cc_final: 0.9049 (mmp) REVERT: E 3 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8523 (tm-30) REVERT: E 73 ASP cc_start: 0.8448 (t0) cc_final: 0.8048 (t0) REVERT: E 93 MET cc_start: 0.8577 (tpp) cc_final: 0.8300 (tpp) REVERT: E 116 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8598 (mm-40) REVERT: E 119 MET cc_start: 0.8554 (tpp) cc_final: 0.8152 (tpp) REVERT: G 11 LEU cc_start: 0.8968 (mt) cc_final: 0.8595 (pp) REVERT: G 24 ARG cc_start: 0.8327 (ttm110) cc_final: 0.8014 (ttm-80) REVERT: G 89 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8884 (tm-30) REVERT: C 265 TYR cc_start: 0.7733 (p90) cc_final: 0.7431 (p90) REVERT: C 371 GLU cc_start: 0.8765 (mp0) cc_final: 0.8496 (mp0) REVERT: C 520 MET cc_start: 0.9050 (mmm) cc_final: 0.8696 (mmm) outliers start: 30 outliers final: 27 residues processed: 248 average time/residue: 0.1208 time to fit residues: 47.3827 Evaluate side-chains 246 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 206 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 214 optimal weight: 0.0970 chunk 5 optimal weight: 5.9990 chunk 148 optimal weight: 0.0870 chunk 118 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.069636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.054834 restraints weight = 70151.076| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.69 r_work: 0.3044 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19130 Z= 0.131 Angle : 0.525 15.942 26083 Z= 0.272 Chirality : 0.042 0.271 2892 Planarity : 0.003 0.038 3393 Dihedral : 3.942 17.596 2656 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.79 % Allowed : 14.50 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.18), residues: 2391 helix: 0.56 (0.27), residues: 366 sheet: -0.64 (0.19), residues: 798 loop : -0.01 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 24 TYR 0.024 0.001 TYR B 689 PHE 0.022 0.001 PHE B 650 TRP 0.014 0.001 TRP A 174 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00295 (19130) covalent geometry : angle 0.52452 (26083) hydrogen bonds : bond 0.03397 ( 605) hydrogen bonds : angle 5.48154 ( 1581) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8357 (tp-100) cc_final: 0.8056 (tp-100) REVERT: H 5 VAL cc_start: 0.8953 (t) cc_final: 0.8524 (m) REVERT: H 53 HIS cc_start: 0.8521 (p-80) cc_final: 0.8214 (p-80) REVERT: H 93 MET cc_start: 0.8122 (mmp) cc_final: 0.7849 (mmp) REVERT: H 119 MET cc_start: 0.8616 (tpp) cc_final: 0.8361 (tpp) REVERT: L 24 ARG cc_start: 0.8278 (tpp80) cc_final: 0.8035 (tpp80) REVERT: L 70 GLU cc_start: 0.8130 (tp30) cc_final: 0.7838 (tp30) REVERT: A 265 TYR cc_start: 0.7834 (p90) cc_final: 0.7619 (p90) REVERT: A 534 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.8388 (t-90) REVERT: D 65 LYS cc_start: 0.9255 (tppt) cc_final: 0.8943 (tppt) REVERT: D 73 ASP cc_start: 0.8642 (t0) cc_final: 0.8312 (t0) REVERT: D 93 MET cc_start: 0.8070 (tpp) cc_final: 0.7710 (tpp) REVERT: F 24 ARG cc_start: 0.8294 (tpp80) cc_final: 0.8058 (tpp80) REVERT: F 45 GLU cc_start: 0.7882 (pm20) cc_final: 0.7516 (pm20) REVERT: F 89 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8927 (tm-30) REVERT: B 187 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8233 (tm-30) REVERT: B 265 TYR cc_start: 0.7827 (p90) cc_final: 0.7388 (p90) REVERT: B 326 TYR cc_start: 0.2398 (t80) cc_final: 0.1974 (t80) REVERT: B 502 GLU cc_start: 0.8835 (pm20) cc_final: 0.8587 (pm20) REVERT: B 534 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.7924 (t-90) REVERT: B 677 MET cc_start: 0.9287 (mmp) cc_final: 0.9070 (mmp) REVERT: E 3 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8479 (tm-30) REVERT: E 46 GLU cc_start: 0.7969 (tp30) cc_final: 0.7702 (tp30) REVERT: E 65 LYS cc_start: 0.9239 (tppt) cc_final: 0.8551 (mmmt) REVERT: E 73 ASP cc_start: 0.8448 (t0) cc_final: 0.8049 (t0) REVERT: E 93 MET cc_start: 0.8571 (tpp) cc_final: 0.8150 (tpt) REVERT: E 116 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8553 (mm-40) REVERT: G 11 LEU cc_start: 0.8978 (mt) cc_final: 0.8612 (pp) REVERT: G 24 ARG cc_start: 0.8308 (ttm110) cc_final: 0.8003 (ttm-80) REVERT: G 89 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8894 (tm-30) REVERT: C 265 TYR cc_start: 0.7728 (p90) cc_final: 0.7424 (p90) REVERT: C 371 GLU cc_start: 0.8749 (mp0) cc_final: 0.8533 (mp0) REVERT: C 520 MET cc_start: 0.9037 (mmm) cc_final: 0.8689 (mmm) REVERT: C 534 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.8495 (t70) outliers start: 34 outliers final: 28 residues processed: 253 average time/residue: 0.1206 time to fit residues: 48.4129 Evaluate side-chains 254 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 534 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 154 optimal weight: 0.0070 chunk 35 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 229 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.069604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.054783 restraints weight = 70406.211| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.71 r_work: 0.3039 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19130 Z= 0.143 Angle : 0.540 16.278 26083 Z= 0.278 Chirality : 0.042 0.265 2892 Planarity : 0.003 0.038 3393 Dihedral : 3.951 19.566 2656 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.95 % Allowed : 14.39 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.18), residues: 2391 helix: 0.55 (0.27), residues: 366 sheet: -0.59 (0.19), residues: 765 loop : -0.03 (0.19), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 24 TYR 0.020 0.001 TYR B 689 PHE 0.025 0.001 PHE E 113 TRP 0.020 0.001 TRP B 174 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00324 (19130) covalent geometry : angle 0.54014 (26083) hydrogen bonds : bond 0.03385 ( 605) hydrogen bonds : angle 5.46002 ( 1581) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8387 (tp-100) cc_final: 0.8102 (tp-100) REVERT: H 5 VAL cc_start: 0.8947 (t) cc_final: 0.8507 (m) REVERT: H 29 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: H 53 HIS cc_start: 0.8495 (p-80) cc_final: 0.8179 (p-80) REVERT: H 65 LYS cc_start: 0.9178 (tppt) cc_final: 0.8330 (mmmt) REVERT: H 93 MET cc_start: 0.8102 (mmp) cc_final: 0.7471 (mmp) REVERT: H 119 MET cc_start: 0.8594 (tpp) cc_final: 0.7452 (tmm) REVERT: L 24 ARG cc_start: 0.8296 (tpp80) cc_final: 0.8052 (tpp80) REVERT: L 70 GLU cc_start: 0.8158 (tp30) cc_final: 0.7866 (tp30) REVERT: A 534 HIS cc_start: 0.8630 (OUTLIER) cc_final: 0.8377 (t-90) REVERT: D 65 LYS cc_start: 0.9238 (tppt) cc_final: 0.8896 (tppt) REVERT: D 73 ASP cc_start: 0.8642 (t0) cc_final: 0.8311 (t0) REVERT: D 93 MET cc_start: 0.8089 (tpp) cc_final: 0.7720 (tpp) REVERT: F 24 ARG cc_start: 0.8317 (tpp80) cc_final: 0.8082 (tpp80) REVERT: F 45 GLU cc_start: 0.7874 (pm20) cc_final: 0.7534 (pm20) REVERT: F 89 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8928 (tm-30) REVERT: B 187 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8237 (tm-30) REVERT: B 265 TYR cc_start: 0.7834 (p90) cc_final: 0.7506 (p90) REVERT: B 326 TYR cc_start: 0.2358 (t80) cc_final: 0.1932 (t80) REVERT: B 534 HIS cc_start: 0.8608 (OUTLIER) cc_final: 0.7944 (t-90) REVERT: B 677 MET cc_start: 0.9279 (mmp) cc_final: 0.9063 (mmp) REVERT: E 3 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8481 (tm-30) REVERT: E 46 GLU cc_start: 0.8012 (tp30) cc_final: 0.7718 (tp30) REVERT: E 65 LYS cc_start: 0.9219 (tppt) cc_final: 0.8863 (tppt) REVERT: E 73 ASP cc_start: 0.8453 (t0) cc_final: 0.8053 (t0) REVERT: E 93 MET cc_start: 0.8593 (tpp) cc_final: 0.8090 (tpt) REVERT: E 116 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8569 (mm-40) REVERT: E 119 MET cc_start: 0.8483 (tpp) cc_final: 0.6680 (ptm) REVERT: G 11 LEU cc_start: 0.8994 (mt) cc_final: 0.8626 (pp) REVERT: G 24 ARG cc_start: 0.8328 (ttm110) cc_final: 0.8014 (ttm-80) REVERT: G 89 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8875 (tm-30) REVERT: C 265 TYR cc_start: 0.7728 (p90) cc_final: 0.7086 (p90) REVERT: C 371 GLU cc_start: 0.8764 (mp0) cc_final: 0.8549 (mp0) REVERT: C 520 MET cc_start: 0.9046 (mmm) cc_final: 0.8720 (mmm) outliers start: 37 outliers final: 31 residues processed: 251 average time/residue: 0.1106 time to fit residues: 44.1314 Evaluate side-chains 255 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 86 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.068467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.053496 restraints weight = 70538.012| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.77 r_work: 0.3005 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19130 Z= 0.197 Angle : 0.575 17.295 26083 Z= 0.297 Chirality : 0.043 0.284 2892 Planarity : 0.003 0.038 3393 Dihedral : 4.099 19.066 2656 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.90 % Allowed : 14.87 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.18), residues: 2391 helix: 0.59 (0.27), residues: 348 sheet: -0.66 (0.19), residues: 762 loop : -0.14 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 16 TYR 0.021 0.001 TYR B 689 PHE 0.017 0.001 PHE A 650 TRP 0.015 0.001 TRP A 174 HIS 0.013 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00440 (19130) covalent geometry : angle 0.57461 (26083) hydrogen bonds : bond 0.03650 ( 605) hydrogen bonds : angle 5.55050 ( 1581) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8446 (tp-100) cc_final: 0.8182 (tp-100) REVERT: H 5 VAL cc_start: 0.8984 (t) cc_final: 0.8532 (m) REVERT: H 29 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7500 (m-80) REVERT: H 65 LYS cc_start: 0.9220 (tppt) cc_final: 0.8399 (mmmt) REVERT: H 93 MET cc_start: 0.8157 (mmp) cc_final: 0.7497 (mmp) REVERT: H 119 MET cc_start: 0.8665 (tpp) cc_final: 0.7541 (tmm) REVERT: A 265 TYR cc_start: 0.7857 (p90) cc_final: 0.7648 (p90) REVERT: A 534 HIS cc_start: 0.8765 (OUTLIER) cc_final: 0.8510 (t-90) REVERT: D 65 LYS cc_start: 0.9233 (tppt) cc_final: 0.8881 (tppt) REVERT: D 73 ASP cc_start: 0.8606 (t0) cc_final: 0.8290 (t0) REVERT: F 24 ARG cc_start: 0.8309 (tpp80) cc_final: 0.8042 (tpp80) REVERT: F 45 GLU cc_start: 0.7875 (pm20) cc_final: 0.7520 (pm20) REVERT: F 89 GLN cc_start: 0.9159 (tm-30) cc_final: 0.8878 (tm-30) REVERT: B 187 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8248 (tm-30) REVERT: B 265 TYR cc_start: 0.7876 (p90) cc_final: 0.7626 (p90) REVERT: B 326 TYR cc_start: 0.2431 (t80) cc_final: 0.1972 (t80) REVERT: B 534 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.8057 (t-90) REVERT: B 677 MET cc_start: 0.9265 (mmp) cc_final: 0.9042 (mmp) REVERT: E 3 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8542 (tm-30) REVERT: E 46 GLU cc_start: 0.8024 (tp30) cc_final: 0.7795 (tp30) REVERT: E 73 ASP cc_start: 0.8451 (t0) cc_final: 0.8046 (t0) REVERT: E 90 ASP cc_start: 0.9194 (m-30) cc_final: 0.8955 (m-30) REVERT: E 93 MET cc_start: 0.8620 (tpp) cc_final: 0.8304 (tpp) REVERT: E 116 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8585 (mm-40) REVERT: G 11 LEU cc_start: 0.9015 (mt) cc_final: 0.8641 (pp) REVERT: G 24 ARG cc_start: 0.8332 (ttm110) cc_final: 0.8001 (ttm-80) REVERT: G 89 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8846 (tm-30) REVERT: C 265 TYR cc_start: 0.7763 (p90) cc_final: 0.7156 (p90) REVERT: C 371 GLU cc_start: 0.8792 (mp0) cc_final: 0.8523 (mp0) REVERT: C 520 MET cc_start: 0.9069 (mmm) cc_final: 0.8766 (mmm) outliers start: 36 outliers final: 32 residues processed: 251 average time/residue: 0.1260 time to fit residues: 50.1711 Evaluate side-chains 252 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 233 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 207 optimal weight: 4.9990 chunk 39 optimal weight: 0.1980 chunk 183 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 148 optimal weight: 0.0670 chunk 166 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.070210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.055420 restraints weight = 70210.344| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.70 r_work: 0.3059 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19130 Z= 0.119 Angle : 0.545 15.895 26083 Z= 0.280 Chirality : 0.042 0.261 2892 Planarity : 0.003 0.037 3393 Dihedral : 3.909 17.286 2656 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.63 % Allowed : 15.39 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.18), residues: 2391 helix: 0.57 (0.27), residues: 366 sheet: -0.63 (0.19), residues: 801 loop : -0.04 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 16 TYR 0.023 0.001 TYR B 689 PHE 0.030 0.001 PHE E 113 TRP 0.020 0.001 TRP B 174 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00274 (19130) covalent geometry : angle 0.54547 (26083) hydrogen bonds : bond 0.03265 ( 605) hydrogen bonds : angle 5.44250 ( 1581) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4375.21 seconds wall clock time: 75 minutes 40.23 seconds (4540.23 seconds total)