Starting phenix.real_space_refine on Mon May 19 16:41:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kfa_37203/05_2025/8kfa_37203.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kfa_37203/05_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_37203/05_2025/8kfa_37203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kfa_37203/05_2025/8kfa_37203.map" model { file = "/net/cci-nas-00/data/ceres_data/8kfa_37203/05_2025/8kfa_37203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kfa_37203/05_2025/8kfa_37203.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP: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, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 17} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP: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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 15} 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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 113 Time building chain proxies: 10.81, per 1000 atoms: 0.58 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: 4.42 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.61 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: 6.45 Time building geometry restraints manager: 5.12 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: 4.630 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: 0.760 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 41.620 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.120 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.001 TRP B 174 HIS 0.004 0.001 HIS E 35 PHE 0.021 0.001 PHE C 650 TYR 0.013 0.001 TYR C 296 ARG 0.004 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.20711 ( 605) hydrogen bonds : angle 8.76171 ( 1581) covalent geometry : bond 0.00222 (19130) covalent geometry : angle 0.48432 (26083) *********************** 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 : 2.016 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: 0.2770 time to fit residues: 107.4641 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 : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 95 optimal weight: 0.0570 chunk 185 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 overall best weight: 2.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.067600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.052613 restraints weight = 71845.234| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.69 r_work: 0.2977 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 19130 Z= 0.300 Angle : 0.598 7.903 26083 Z= 0.319 Chirality : 0.045 0.412 2892 Planarity : 0.004 0.049 3393 Dihedral : 4.354 17.822 2656 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.95 % Allowed : 8.43 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2391 helix: 0.66 (0.27), residues: 330 sheet: -0.64 (0.19), residues: 762 loop : -0.01 (0.19), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 174 HIS 0.006 0.002 HIS A 516 PHE 0.026 0.002 PHE H 29 TYR 0.024 0.002 TYR F 91 ARG 0.004 0.000 ARG C 599 Details of bonding type rmsd hydrogen bonds : bond 0.04554 ( 605) hydrogen bonds : angle 6.59617 ( 1581) covalent geometry : bond 0.00662 (19130) covalent geometry : angle 0.59774 (26083) *********************** 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 244 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 1.914 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 3 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8491 (tp-100) REVERT: H 5 VAL cc_start: 0.8883 (t) cc_final: 0.8516 (m) REVERT: H 60 TYR cc_start: 0.8394 (m-80) cc_final: 0.8092 (m-10) REVERT: H 65 LYS cc_start: 0.8936 (mmmt) cc_final: 0.7956 (mmmt) REVERT: H 90 ASP cc_start: 0.8990 (m-30) cc_final: 0.8781 (m-30) REVERT: H 93 MET cc_start: 0.8230 (tpp) cc_final: 0.7917 (tpp) REVERT: H 119 MET cc_start: 0.8585 (tpp) cc_final: 0.8083 (tpp) REVERT: L 70 GLU cc_start: 0.8197 (tp30) cc_final: 0.7935 (tp30) REVERT: A 265 TYR cc_start: 0.7972 (p90) cc_final: 0.7497 (p90) REVERT: D 65 LYS cc_start: 0.9159 (mmtt) cc_final: 0.8850 (mmpt) REVERT: D 73 ASP cc_start: 0.8509 (t0) cc_final: 0.8153 (t0) REVERT: B 232 MET cc_start: 0.8459 (mpp) cc_final: 0.8184 (mpp) REVERT: B 265 TYR cc_start: 0.7795 (p90) cc_final: 0.7429 (p90) REVERT: B 326 TYR cc_start: 0.2825 (t80) cc_final: 0.2414 (t80) REVERT: B 677 MET cc_start: 0.9301 (mmp) cc_final: 0.8932 (mmp) REVERT: E 46 GLU cc_start: 0.8070 (tp30) cc_final: 0.7788 (tp30) REVERT: E 65 LYS cc_start: 0.9133 (tppt) cc_final: 0.8923 (tppt) REVERT: E 73 ASP cc_start: 0.8441 (t0) cc_final: 0.8053 (t0) REVERT: E 93 MET cc_start: 0.8339 (tpp) cc_final: 0.8045 (tpp) REVERT: G 27 GLN cc_start: 0.8358 (pp30) cc_final: 0.8105 (pp30) REVERT: C 174 TRP cc_start: 0.7404 (t60) cc_final: 0.7196 (t60) REVERT: C 421 MET cc_start: 0.9309 (mpp) cc_final: 0.8215 (mpp) outliers start: 18 outliers final: 16 residues processed: 236 average time/residue: 0.2600 time to fit residues: 98.2983 Evaluate side-chains 223 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 19 VAL 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 69 THR 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 164 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 213 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 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 = 0.3557 r_free = 0.3557 target = 0.069381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.054523 restraints weight = 70326.017| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.70 r_work: 0.3036 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1468 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= 0.147 Angle : 0.503 7.858 26083 Z= 0.267 Chirality : 0.043 0.375 2892 Planarity : 0.003 0.041 3393 Dihedral : 4.081 16.738 2656 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.27 % Allowed : 10.96 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2391 helix: 0.89 (0.28), residues: 330 sheet: -0.58 (0.19), residues: 765 loop : 0.03 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.005 0.001 HIS D 35 PHE 0.021 0.001 PHE D 113 TYR 0.013 0.001 TYR B 213 ARG 0.004 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 605) hydrogen bonds : angle 6.06915 ( 1581) covalent geometry : bond 0.00324 (19130) covalent geometry : angle 0.50293 (26083) *********************** 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 250 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 VAL cc_start: 0.8893 (t) cc_final: 0.8631 (m) REVERT: H 46 GLU cc_start: 0.8077 (tp30) cc_final: 0.7834 (tp30) REVERT: H 53 HIS cc_start: 0.8546 (p-80) cc_final: 0.8243 (p-80) REVERT: H 60 TYR cc_start: 0.8474 (m-80) cc_final: 0.8174 (m-10) REVERT: H 65 LYS cc_start: 0.8913 (mmmt) cc_final: 0.7868 (mmmt) REVERT: H 90 ASP cc_start: 0.9100 (m-30) cc_final: 0.8888 (m-30) REVERT: H 93 MET cc_start: 0.8279 (tpp) cc_final: 0.7892 (mmp) REVERT: H 113 PHE cc_start: 0.7986 (t80) cc_final: 0.7709 (t80) REVERT: H 119 MET cc_start: 0.8701 (tpp) cc_final: 0.8440 (tpp) REVERT: L 70 GLU cc_start: 0.8163 (tp30) cc_final: 0.7963 (tp30) REVERT: A 265 TYR cc_start: 0.7860 (p90) cc_final: 0.7174 (p90) REVERT: A 520 MET cc_start: 0.9029 (mmm) cc_final: 0.8656 (mmm) REVERT: A 587 MET cc_start: 0.6520 (mtm) cc_final: 0.5879 (mtm) REVERT: D 73 ASP cc_start: 0.8584 (t0) cc_final: 0.8227 (t0) REVERT: B 232 MET cc_start: 0.8342 (mpp) cc_final: 0.8093 (mpp) REVERT: B 265 TYR cc_start: 0.7761 (p90) cc_final: 0.7481 (p90) REVERT: B 326 TYR cc_start: 0.2787 (t80) cc_final: 0.2326 (t80) REVERT: B 502 GLU cc_start: 0.8817 (pm20) cc_final: 0.8600 (pm20) REVERT: B 677 MET cc_start: 0.9309 (mmp) cc_final: 0.8943 (mmp) REVERT: E 46 GLU cc_start: 0.8072 (tp30) cc_final: 0.7755 (tp30) REVERT: E 60 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.8846 (m-80) REVERT: E 65 LYS cc_start: 0.9119 (tppt) cc_final: 0.8861 (tppt) REVERT: E 73 ASP cc_start: 0.8500 (t0) cc_final: 0.8098 (t0) REVERT: E 93 MET cc_start: 0.8564 (tpp) cc_final: 0.8261 (tpp) REVERT: E 113 PHE cc_start: 0.7984 (t80) cc_final: 0.7723 (t80) REVERT: E 116 GLN cc_start: 0.9153 (tp40) cc_final: 0.8869 (mm-40) REVERT: E 119 MET cc_start: 0.8332 (tpp) cc_final: 0.7719 (tpp) REVERT: G 27 GLN cc_start: 0.8348 (pp30) cc_final: 0.8109 (pp30) outliers start: 24 outliers final: 17 residues processed: 241 average time/residue: 0.2702 time to fit residues: 103.9787 Evaluate side-chains 228 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 2.073 ------------------------------------------------------------------------------- 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 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 60 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 C residue 288 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.066079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.051068 restraints weight = 72577.055| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.64 r_work: 0.2936 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 19130 Z= 0.369 Angle : 0.640 7.392 26083 Z= 0.340 Chirality : 0.046 0.439 2892 Planarity : 0.004 0.043 3393 Dihedral : 4.599 19.210 2656 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.27 % Allowed : 13.23 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.18), residues: 2391 helix: 0.32 (0.26), residues: 345 sheet: -0.93 (0.19), residues: 774 loop : -0.23 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 174 HIS 0.007 0.002 HIS H 35 PHE 0.027 0.002 PHE H 29 TYR 0.025 0.002 TYR F 91 ARG 0.005 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 605) hydrogen bonds : angle 6.16870 ( 1581) covalent geometry : bond 0.00811 (19130) covalent geometry : angle 0.63981 (26083) *********************** 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 252 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8957 (tp-100) cc_final: 0.8652 (tp-100) REVERT: H 5 VAL cc_start: 0.9147 (t) cc_final: 0.8539 (m) REVERT: H 43 LYS cc_start: 0.8417 (mppt) cc_final: 0.8210 (mppt) REVERT: H 65 LYS cc_start: 0.8900 (mmmt) cc_final: 0.7838 (mmmt) REVERT: H 90 ASP cc_start: 0.9069 (m-30) cc_final: 0.8833 (m-30) REVERT: H 93 MET cc_start: 0.8360 (tpp) cc_final: 0.7951 (tpp) REVERT: H 119 MET cc_start: 0.9058 (tpp) cc_final: 0.8689 (tpp) REVERT: L 70 GLU cc_start: 0.8218 (tp30) cc_final: 0.7965 (tp30) REVERT: L 103 LYS cc_start: 0.9272 (mmmt) cc_final: 0.9030 (mmmt) REVERT: A 265 TYR cc_start: 0.8008 (p90) cc_final: 0.7653 (p90) REVERT: A 520 MET cc_start: 0.9114 (mmm) cc_final: 0.8693 (mmm) REVERT: D 73 ASP cc_start: 0.8560 (t0) cc_final: 0.8230 (t0) REVERT: D 116 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8511 (mm-40) REVERT: B 174 TRP cc_start: 0.7636 (t60) cc_final: 0.7368 (t60) REVERT: B 232 MET cc_start: 0.8607 (mpp) cc_final: 0.8256 (mpp) REVERT: B 265 TYR cc_start: 0.7907 (p90) cc_final: 0.7622 (p90) REVERT: B 677 MET cc_start: 0.9311 (mmp) cc_final: 0.8967 (mmp) REVERT: E 3 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8566 (tm-30) REVERT: E 46 GLU cc_start: 0.8050 (tp30) cc_final: 0.7838 (tp30) REVERT: E 60 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.8914 (m-80) REVERT: E 91 THR cc_start: 0.9086 (m) cc_final: 0.8869 (p) REVERT: E 93 MET cc_start: 0.8617 (tpp) cc_final: 0.8149 (tpt) REVERT: G 24 ARG cc_start: 0.8300 (ttm110) cc_final: 0.8038 (ttm-80) REVERT: G 27 GLN cc_start: 0.8366 (pp30) cc_final: 0.8110 (pp30) REVERT: C 265 TYR cc_start: 0.7875 (p90) cc_final: 0.7270 (p90) REVERT: C 520 MET cc_start: 0.9099 (mmm) cc_final: 0.8766 (mmm) outliers start: 43 outliers final: 34 residues processed: 243 average time/residue: 0.2618 time to fit residues: 102.0019 Evaluate side-chains 237 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 2.008 ------------------------------------------------------------------------------- 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 18 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 D residue 2 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 18 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 170 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 60 TYR Chi-restraints excluded: chain E residue 69 THR 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 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 330 LEU Chi-restraints excluded: chain C residue 363 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 48 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 206 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 710 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 = 0.3506 r_free = 0.3506 target = 0.067215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.052327 restraints weight = 71497.013| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.70 r_work: 0.2970 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19130 Z= 0.217 Angle : 0.545 9.725 26083 Z= 0.289 Chirality : 0.043 0.401 2892 Planarity : 0.004 0.040 3393 Dihedral : 4.347 17.131 2656 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.21 % Allowed : 15.02 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2391 helix: 0.40 (0.26), residues: 345 sheet: -0.89 (0.19), residues: 774 loop : -0.24 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 114 HIS 0.006 0.001 HIS E 35 PHE 0.026 0.001 PHE E 113 TYR 0.015 0.001 TYR F 91 ARG 0.003 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 605) hydrogen bonds : angle 5.95223 ( 1581) covalent geometry : bond 0.00479 (19130) covalent geometry : angle 0.54535 (26083) *********************** 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 254 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 2.137 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8970 (tp-100) cc_final: 0.8649 (tp-100) REVERT: H 5 VAL cc_start: 0.9028 (t) cc_final: 0.8613 (m) REVERT: H 90 ASP cc_start: 0.9116 (m-30) cc_final: 0.8879 (m-30) REVERT: H 93 MET cc_start: 0.8339 (tpp) cc_final: 0.8101 (tpp) REVERT: L 103 LYS cc_start: 0.9230 (mmmt) cc_final: 0.8970 (mmmt) REVERT: A 265 TYR cc_start: 0.7953 (p90) cc_final: 0.6954 (p90) REVERT: A 438 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8585 (mp10) REVERT: A 520 MET cc_start: 0.9103 (mmm) cc_final: 0.8842 (mmm) REVERT: A 587 MET cc_start: 0.6496 (mtm) cc_final: 0.5812 (mtm) REVERT: D 65 LYS cc_start: 0.9235 (tppt) cc_final: 0.8924 (tppt) REVERT: D 73 ASP cc_start: 0.8616 (t0) cc_final: 0.8246 (t0) REVERT: B 174 TRP cc_start: 0.7531 (t60) cc_final: 0.6969 (t60) REVERT: B 232 MET cc_start: 0.8576 (mpp) cc_final: 0.8175 (mpp) REVERT: B 265 TYR cc_start: 0.7909 (p90) cc_final: 0.7569 (p90) REVERT: B 677 MET cc_start: 0.9317 (mmp) cc_final: 0.8977 (mmp) REVERT: E 3 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8636 (tm-30) REVERT: E 60 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.8864 (m-80) REVERT: E 73 ASP cc_start: 0.8507 (t0) cc_final: 0.8115 (t0) REVERT: E 93 MET cc_start: 0.8649 (tpp) cc_final: 0.8346 (tpp) REVERT: G 11 LEU cc_start: 0.8983 (mt) cc_final: 0.8528 (pp) REVERT: G 24 ARG cc_start: 0.8324 (ttm110) cc_final: 0.8040 (ttm-80) REVERT: G 27 GLN cc_start: 0.8416 (pp30) cc_final: 0.8052 (pp30) REVERT: C 265 TYR cc_start: 0.7843 (p90) cc_final: 0.7080 (p90) REVERT: C 371 GLU cc_start: 0.8890 (mp0) cc_final: 0.8634 (mp0) REVERT: C 520 MET cc_start: 0.9050 (mmm) cc_final: 0.8684 (mmm) outliers start: 42 outliers final: 34 residues processed: 241 average time/residue: 0.3130 time to fit residues: 121.2933 Evaluate side-chains 234 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 THR 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 438 GLN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 76 LYS 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 330 LEU 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 Chi-restraints excluded: chain G residue 52 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 110 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 194 optimal weight: 0.0070 chunk 165 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 210 optimal weight: 5.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- 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 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 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 = 0.3524 r_free = 0.3524 target = 0.067951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.053088 restraints weight = 71539.008| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.72 r_work: 0.2991 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19130 Z= 0.162 Angle : 0.523 8.511 26083 Z= 0.276 Chirality : 0.043 0.386 2892 Planarity : 0.003 0.040 3393 Dihedral : 4.180 16.984 2656 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.00 % Allowed : 16.13 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.18), residues: 2391 helix: 0.57 (0.27), residues: 345 sheet: -0.79 (0.19), residues: 762 loop : -0.22 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.005 0.001 HIS E 35 PHE 0.013 0.001 PHE A 650 TYR 0.012 0.001 TYR A 296 ARG 0.003 0.000 ARG H 16 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 605) hydrogen bonds : angle 5.76273 ( 1581) covalent geometry : bond 0.00360 (19130) covalent geometry : angle 0.52347 (26083) *********************** 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 260 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 2.089 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8950 (tp-100) cc_final: 0.8070 (tp-100) REVERT: H 5 VAL cc_start: 0.9155 (t) cc_final: 0.8630 (m) REVERT: H 29 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: H 65 LYS cc_start: 0.9247 (tppt) cc_final: 0.8761 (mmmt) REVERT: H 90 ASP cc_start: 0.9122 (m-30) cc_final: 0.8879 (m-30) REVERT: A 265 TYR cc_start: 0.7863 (p90) cc_final: 0.6880 (p90) REVERT: A 438 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8555 (mp10) REVERT: A 587 MET cc_start: 0.6560 (mtm) cc_final: 0.5979 (mtm) REVERT: D 73 ASP cc_start: 0.8649 (t0) cc_final: 0.8285 (t0) REVERT: F 89 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8869 (tm-30) REVERT: B 174 TRP cc_start: 0.7425 (t60) cc_final: 0.6920 (t60) REVERT: B 232 MET cc_start: 0.8524 (mpp) cc_final: 0.8140 (mpp) REVERT: B 265 TYR cc_start: 0.7875 (p90) cc_final: 0.7359 (p90) REVERT: E 3 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8657 (tm-30) REVERT: E 73 ASP cc_start: 0.8496 (t0) cc_final: 0.8097 (t0) REVERT: E 93 MET cc_start: 0.8670 (tpp) cc_final: 0.8274 (tpt) REVERT: G 11 LEU cc_start: 0.8984 (mt) cc_final: 0.8587 (pp) REVERT: G 24 ARG cc_start: 0.8326 (ttm110) cc_final: 0.8096 (ttm-80) REVERT: G 27 GLN cc_start: 0.8472 (pp30) cc_final: 0.8092 (pp30) REVERT: C 265 TYR cc_start: 0.7810 (p90) cc_final: 0.7521 (p90) REVERT: C 371 GLU cc_start: 0.8859 (mp0) cc_final: 0.8590 (mp0) REVERT: C 520 MET cc_start: 0.9024 (mmm) cc_final: 0.8703 (mmm) outliers start: 38 outliers final: 34 residues processed: 248 average time/residue: 0.2698 time to fit residues: 107.3118 Evaluate side-chains 245 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 2.166 ------------------------------------------------------------------------------- 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 438 GLN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 76 LYS 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 492 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 G residue 52 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 4 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 227 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 233 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 229 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.067499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.052648 restraints weight = 70799.832| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.68 r_work: 0.2980 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 19130 Z= 0.210 Angle : 0.550 11.394 26083 Z= 0.288 Chirality : 0.043 0.368 2892 Planarity : 0.003 0.039 3393 Dihedral : 4.224 16.858 2656 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.53 % Allowed : 16.66 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2391 helix: 0.55 (0.27), residues: 345 sheet: -0.83 (0.19), residues: 762 loop : -0.23 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.005 0.001 HIS E 35 PHE 0.012 0.001 PHE E 113 TYR 0.014 0.001 TYR F 91 ARG 0.003 0.000 ARG H 16 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 605) hydrogen bonds : angle 5.73116 ( 1581) covalent geometry : bond 0.00467 (19130) covalent geometry : angle 0.55000 (26083) *********************** 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 264 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 VAL cc_start: 0.9135 (t) cc_final: 0.8593 (m) REVERT: H 46 GLU cc_start: 0.8098 (tp30) cc_final: 0.7848 (tp30) REVERT: H 90 ASP cc_start: 0.9127 (m-30) cc_final: 0.8903 (m-30) REVERT: H 113 PHE cc_start: 0.8005 (t80) cc_final: 0.7580 (t80) REVERT: A 265 TYR cc_start: 0.7889 (p90) cc_final: 0.6982 (p90) REVERT: A 438 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8573 (mp10) REVERT: D 73 ASP cc_start: 0.8646 (t0) cc_final: 0.8280 (t0) REVERT: F 89 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8816 (tm-30) REVERT: B 174 TRP cc_start: 0.7475 (t60) cc_final: 0.6989 (t60) REVERT: B 232 MET cc_start: 0.8558 (mpp) cc_final: 0.8163 (mpp) REVERT: B 265 TYR cc_start: 0.7866 (p90) cc_final: 0.7379 (p90) REVERT: B 677 MET cc_start: 0.9274 (mmp) cc_final: 0.9019 (mmp) REVERT: E 3 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8744 (tm-30) REVERT: E 53 HIS cc_start: 0.8747 (p-80) cc_final: 0.8381 (p90) REVERT: E 73 ASP cc_start: 0.8478 (t0) cc_final: 0.8086 (t0) REVERT: E 93 MET cc_start: 0.8666 (tpp) cc_final: 0.8299 (tpt) REVERT: G 11 LEU cc_start: 0.8999 (mt) cc_final: 0.8622 (pp) REVERT: G 24 ARG cc_start: 0.8330 (ttm110) cc_final: 0.8091 (ttm-80) REVERT: G 27 GLN cc_start: 0.8495 (pp30) cc_final: 0.8091 (pp30) REVERT: G 89 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8891 (tm-30) REVERT: C 265 TYR cc_start: 0.7801 (p90) cc_final: 0.7116 (p90) REVERT: C 371 GLU cc_start: 0.8862 (mp0) cc_final: 0.8653 (mp0) REVERT: C 421 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.8546 (mpp) REVERT: C 520 MET cc_start: 0.9052 (mmm) cc_final: 0.8761 (mmm) outliers start: 48 outliers final: 41 residues processed: 250 average time/residue: 0.2753 time to fit residues: 110.0847 Evaluate side-chains 249 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 2.086 ------------------------------------------------------------------------------- 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 18 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 438 GLN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 76 LYS 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 170 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 492 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 20 THR Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 52 TYR 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 330 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 222 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 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 = 0.3518 r_free = 0.3518 target = 0.067679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.052834 restraints weight = 71402.129| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.67 r_work: 0.2987 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19130 Z= 0.193 Angle : 0.554 10.034 26083 Z= 0.290 Chirality : 0.043 0.345 2892 Planarity : 0.003 0.039 3393 Dihedral : 4.203 16.867 2656 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.74 % Allowed : 17.13 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2391 helix: 0.56 (0.27), residues: 345 sheet: -0.81 (0.19), residues: 762 loop : -0.23 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 174 HIS 0.005 0.001 HIS E 35 PHE 0.014 0.001 PHE A 650 TYR 0.014 0.001 TYR B 284 ARG 0.003 0.000 ARG H 16 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 605) hydrogen bonds : angle 5.70374 ( 1581) covalent geometry : bond 0.00431 (19130) covalent geometry : angle 0.55429 (26083) *********************** 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 268 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 216 time to evaluate : 2.100 Fit side-chains revert: symmetry clash REVERT: H 5 VAL cc_start: 0.9003 (t) cc_final: 0.8801 (p) REVERT: H 46 GLU cc_start: 0.8092 (tp30) cc_final: 0.7843 (tp30) REVERT: H 65 LYS cc_start: 0.9247 (tppt) cc_final: 0.8388 (mmmt) REVERT: H 93 MET cc_start: 0.7840 (tpp) cc_final: 0.7391 (tpp) REVERT: H 113 PHE cc_start: 0.7997 (t80) cc_final: 0.7704 (t80) REVERT: A 174 TRP cc_start: 0.7611 (t60) cc_final: 0.7289 (t60) REVERT: A 265 TYR cc_start: 0.7872 (p90) cc_final: 0.7052 (p90) REVERT: A 438 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8564 (mp10) REVERT: A 587 MET cc_start: 0.6494 (mtm) cc_final: 0.5791 (mtm) REVERT: D 73 ASP cc_start: 0.8635 (t0) cc_final: 0.8271 (t0) REVERT: F 89 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8831 (tm-30) REVERT: B 174 TRP cc_start: 0.7423 (t60) cc_final: 0.7035 (t60) REVERT: B 232 MET cc_start: 0.8523 (mpp) cc_final: 0.8106 (mpp) REVERT: B 265 TYR cc_start: 0.7860 (p90) cc_final: 0.7411 (p90) REVERT: B 534 HIS cc_start: 0.8698 (OUTLIER) cc_final: 0.8094 (t-90) REVERT: B 677 MET cc_start: 0.9287 (mmp) cc_final: 0.9026 (mmp) REVERT: E 3 GLN cc_start: 0.8998 (tp-100) cc_final: 0.8714 (tm-30) REVERT: E 46 GLU cc_start: 0.7976 (tp30) cc_final: 0.7753 (tp30) REVERT: E 73 ASP cc_start: 0.8491 (t0) cc_final: 0.8108 (t0) REVERT: E 93 MET cc_start: 0.8709 (tpp) cc_final: 0.8384 (tpt) REVERT: G 11 LEU cc_start: 0.9001 (mt) cc_final: 0.8616 (pp) REVERT: G 24 ARG cc_start: 0.8314 (ttm110) cc_final: 0.8076 (ttm-80) REVERT: G 27 GLN cc_start: 0.8516 (pp30) cc_final: 0.8041 (pp30) REVERT: G 89 GLN cc_start: 0.9135 (tm-30) cc_final: 0.8876 (tm-30) REVERT: C 265 TYR cc_start: 0.7764 (p90) cc_final: 0.6885 (p90) REVERT: C 371 GLU cc_start: 0.8844 (mp0) cc_final: 0.8632 (mp0) REVERT: C 404 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8666 (tt) REVERT: C 421 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.8545 (mpp) REVERT: C 520 MET cc_start: 0.9045 (mmm) cc_final: 0.8751 (mmm) outliers start: 52 outliers final: 42 residues processed: 253 average time/residue: 0.2669 time to fit residues: 108.5931 Evaluate side-chains 254 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 LEU 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 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 438 GLN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 THR 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 170 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 534 HIS 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 20 THR Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 52 TYR 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 330 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 68 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 209 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.067325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.052406 restraints weight = 71715.089| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.69 r_work: 0.2973 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19130 Z= 0.226 Angle : 0.581 10.965 26083 Z= 0.304 Chirality : 0.043 0.345 2892 Planarity : 0.004 0.039 3393 Dihedral : 4.304 17.088 2656 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.69 % Allowed : 17.45 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2391 helix: 0.50 (0.27), residues: 345 sheet: -0.94 (0.19), residues: 792 loop : -0.21 (0.19), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.014 0.001 HIS C 534 PHE 0.014 0.001 PHE A 650 TYR 0.027 0.001 TYR B 689 ARG 0.004 0.000 ARG H 16 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 605) hydrogen bonds : angle 5.74413 ( 1581) covalent geometry : bond 0.00504 (19130) covalent geometry : angle 0.58088 (26083) *********************** 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 262 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 211 time to evaluate : 2.035 Fit side-chains revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8107 (tp30) cc_final: 0.7860 (tp30) REVERT: H 65 LYS cc_start: 0.9244 (tppt) cc_final: 0.8367 (mmmt) REVERT: H 93 MET cc_start: 0.7742 (tpp) cc_final: 0.7353 (tpp) REVERT: H 113 PHE cc_start: 0.8090 (t80) cc_final: 0.7770 (t80) REVERT: H 119 MET cc_start: 0.8508 (tpp) cc_final: 0.7147 (ptt) REVERT: A 265 TYR cc_start: 0.7892 (p90) cc_final: 0.7090 (p90) REVERT: A 438 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8582 (mp10) REVERT: A 587 MET cc_start: 0.6589 (mtm) cc_final: 0.5906 (mtm) REVERT: D 65 LYS cc_start: 0.9091 (tppt) cc_final: 0.8208 (mmmt) REVERT: D 73 ASP cc_start: 0.8602 (t0) cc_final: 0.8223 (t0) REVERT: B 174 TRP cc_start: 0.7475 (t60) cc_final: 0.7061 (t60) REVERT: B 232 MET cc_start: 0.8562 (mpp) cc_final: 0.8137 (mpp) REVERT: B 265 TYR cc_start: 0.7924 (p90) cc_final: 0.7578 (p90) REVERT: B 534 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.8141 (t-90) REVERT: B 677 MET cc_start: 0.9298 (mmp) cc_final: 0.9032 (mmp) REVERT: E 46 GLU cc_start: 0.8034 (tp30) cc_final: 0.7765 (tp30) REVERT: E 73 ASP cc_start: 0.8479 (t0) cc_final: 0.8078 (t0) REVERT: E 93 MET cc_start: 0.8743 (tpp) cc_final: 0.8398 (tpt) REVERT: G 11 LEU cc_start: 0.8994 (mt) cc_final: 0.8618 (pp) REVERT: G 24 ARG cc_start: 0.8335 (ttm110) cc_final: 0.8084 (ttm-80) REVERT: G 27 GLN cc_start: 0.8521 (pp30) cc_final: 0.8101 (pp30) REVERT: G 89 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8851 (tm-30) REVERT: C 265 TYR cc_start: 0.7830 (p90) cc_final: 0.7150 (p90) REVERT: C 371 GLU cc_start: 0.8901 (mp0) cc_final: 0.8686 (mp0) REVERT: C 421 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.8545 (mpp) REVERT: C 520 MET cc_start: 0.9058 (mmm) cc_final: 0.8781 (mmm) outliers start: 51 outliers final: 45 residues processed: 248 average time/residue: 0.2610 time to fit residues: 103.4362 Evaluate side-chains 248 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 LEU 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 18 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 438 GLN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 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 170 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 534 HIS 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 20 THR Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 52 TYR 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 330 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 203 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 175 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 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 = 0.3547 r_free = 0.3547 target = 0.068874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054116 restraints weight = 70801.049| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.67 r_work: 0.3024 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19130 Z= 0.132 Angle : 0.552 11.047 26083 Z= 0.286 Chirality : 0.042 0.301 2892 Planarity : 0.003 0.039 3393 Dihedral : 4.118 22.199 2656 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.32 % Allowed : 18.03 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2391 helix: 0.69 (0.28), residues: 345 sheet: -0.79 (0.19), residues: 780 loop : -0.17 (0.19), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 174 HIS 0.005 0.001 HIS E 35 PHE 0.011 0.001 PHE A 650 TYR 0.037 0.001 TYR C 179 ARG 0.004 0.000 ARG H 16 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 605) hydrogen bonds : angle 5.59410 ( 1581) covalent geometry : bond 0.00299 (19130) covalent geometry : angle 0.55157 (26083) ********************** 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 264 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 2.080 Fit side-chains revert: symmetry clash REVERT: H 53 HIS cc_start: 0.8518 (p-80) cc_final: 0.8259 (p-80) REVERT: H 60 TYR cc_start: 0.8372 (m-80) cc_final: 0.8047 (m-10) REVERT: H 65 LYS cc_start: 0.9234 (tppt) cc_final: 0.8395 (mmmt) REVERT: H 93 MET cc_start: 0.7737 (tpp) cc_final: 0.7166 (tpp) REVERT: H 113 PHE cc_start: 0.7973 (t80) cc_final: 0.7720 (t80) REVERT: H 119 MET cc_start: 0.8430 (tpp) cc_final: 0.7105 (ptt) REVERT: A 174 TRP cc_start: 0.7501 (t60) cc_final: 0.7173 (t60) REVERT: A 265 TYR cc_start: 0.7783 (p90) cc_final: 0.7046 (p90) REVERT: A 438 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8512 (mp10) REVERT: A 587 MET cc_start: 0.6610 (mtm) cc_final: 0.5955 (mtm) REVERT: D 73 ASP cc_start: 0.8656 (t0) cc_final: 0.8295 (t0) REVERT: F 45 GLU cc_start: 0.7732 (pm20) cc_final: 0.7354 (pm20) REVERT: B 174 TRP cc_start: 0.7372 (t60) cc_final: 0.7011 (t60) REVERT: B 232 MET cc_start: 0.8452 (mpp) cc_final: 0.8031 (mpp) REVERT: B 265 TYR cc_start: 0.7841 (p90) cc_final: 0.7518 (p90) REVERT: B 326 TYR cc_start: 0.2293 (t80) cc_final: 0.1892 (t80) REVERT: B 438 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8374 (mp10) REVERT: B 534 HIS cc_start: 0.8611 (OUTLIER) cc_final: 0.7970 (t-90) REVERT: B 677 MET cc_start: 0.9267 (mmp) cc_final: 0.9009 (mmp) REVERT: E 46 GLU cc_start: 0.8009 (tp30) cc_final: 0.7693 (tp30) REVERT: E 73 ASP cc_start: 0.8491 (t0) cc_final: 0.8094 (t0) REVERT: E 93 MET cc_start: 0.8714 (tpp) cc_final: 0.8379 (tpt) REVERT: G 11 LEU cc_start: 0.8974 (mt) cc_final: 0.8659 (pp) REVERT: G 24 ARG cc_start: 0.8310 (ttm110) cc_final: 0.8082 (ttm-80) REVERT: G 27 GLN cc_start: 0.8588 (pp30) cc_final: 0.8089 (pp30) REVERT: G 89 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8925 (tm-30) REVERT: C 265 TYR cc_start: 0.7763 (p90) cc_final: 0.6861 (p90) REVERT: C 371 GLU cc_start: 0.8803 (mp0) cc_final: 0.8521 (mp0) REVERT: C 421 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8535 (mpp) REVERT: C 520 MET cc_start: 0.9019 (mmm) cc_final: 0.8713 (mmm) outliers start: 44 outliers final: 36 residues processed: 252 average time/residue: 0.2855 time to fit residues: 116.0473 Evaluate side-chains 251 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 LEU 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 438 GLN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 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 170 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 534 HIS 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 G residue 52 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 14 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 226 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 194 optimal weight: 0.4980 chunk 178 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 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 = 0.3528 r_free = 0.3528 target = 0.068116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.053251 restraints weight = 71365.825| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.69 r_work: 0.2998 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19130 Z= 0.182 Angle : 0.572 11.460 26083 Z= 0.297 Chirality : 0.043 0.296 2892 Planarity : 0.003 0.039 3393 Dihedral : 4.163 22.711 2656 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.32 % Allowed : 18.19 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2391 helix: 0.64 (0.27), residues: 345 sheet: -0.79 (0.19), residues: 780 loop : -0.17 (0.19), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 174 HIS 0.005 0.001 HIS E 35 PHE 0.014 0.001 PHE D 113 TYR 0.013 0.001 TYR C 296 ARG 0.005 0.000 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 605) hydrogen bonds : angle 5.58806 ( 1581) covalent geometry : bond 0.00409 (19130) covalent geometry : angle 0.57207 (26083) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9332.84 seconds wall clock time: 162 minutes 24.78 seconds (9744.78 seconds total)