Starting phenix.real_space_refine on Mon Aug 25 01:30:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sla_40576/08_2025/8sla_40576.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sla_40576/08_2025/8sla_40576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sla_40576/08_2025/8sla_40576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sla_40576/08_2025/8sla_40576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sla_40576/08_2025/8sla_40576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sla_40576/08_2025/8sla_40576.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.032 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 80 5.16 5 C 15839 2.51 5 N 4247 2.21 5 O 4325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24491 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 6125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 6125 Classifications: {'peptide': 902} Incomplete info: {'truncation_to_alanine': 319} Link IDs: {'PTRANS': 35, 'TRANS': 866} Chain breaks: 15 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1207 Unresolved non-hydrogen angles: 1521 Unresolved non-hydrogen dihedrals: 985 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'GLU:plan': 38, 'ASN:plan1': 15, 'PHE:plan': 16, 'ARG:plan': 28, 'TRP:plan': 3, 'ASP:plan': 25, 'GLN:plan1': 19, 'HIS:plan': 7, 'TYR:plan': 7} Unresolved non-hydrogen planarities: 694 Chain: "C" Number of atoms: 6116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 6116 Classifications: {'peptide': 901} Incomplete info: {'truncation_to_alanine': 319} Link IDs: {'PTRANS': 35, 'TRANS': 865} Chain breaks: 16 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1207 Unresolved non-hydrogen angles: 1521 Unresolved non-hydrogen dihedrals: 985 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'GLU:plan': 38, 'ASN:plan1': 15, 'PHE:plan': 16, 'ARG:plan': 28, 'TRP:plan': 3, 'ASP:plan': 25, 'GLN:plan1': 19, 'HIS:plan': 7, 'TYR:plan': 7} Unresolved non-hydrogen planarities: 694 Chain: "A" Number of atoms: 6125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 6125 Classifications: {'peptide': 902} Incomplete info: {'truncation_to_alanine': 319} Link IDs: {'PTRANS': 35, 'TRANS': 866} Chain breaks: 15 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1207 Unresolved non-hydrogen angles: 1521 Unresolved non-hydrogen dihedrals: 985 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'GLU:plan': 38, 'ASN:plan1': 15, 'PHE:plan': 16, 'ARG:plan': 28, 'TRP:plan': 3, 'ASP:plan': 25, 'GLN:plan1': 19, 'HIS:plan': 7, 'TYR:plan': 7} Unresolved non-hydrogen planarities: 694 Chain: "B" Number of atoms: 6125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 6125 Classifications: {'peptide': 902} Incomplete info: {'truncation_to_alanine': 319} Link IDs: {'PTRANS': 35, 'TRANS': 866} Chain breaks: 15 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1207 Unresolved non-hydrogen angles: 1521 Unresolved non-hydrogen dihedrals: 985 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'GLU:plan': 38, 'ASN:plan1': 15, 'PHE:plan': 16, 'ARG:plan': 28, 'TRP:plan': 3, 'ASP:plan': 25, 'GLN:plan1': 19, 'HIS:plan': 7, 'TYR:plan': 7} Unresolved non-hydrogen planarities: 694 Time building chain proxies: 5.93, per 1000 atoms: 0.24 Number of scatterers: 24491 At special positions: 0 Unit cell: (137.16, 137.16, 154.44, 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 80 16.00 O 4325 8.00 N 4247 7.00 C 15839 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: 2.29 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6886 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 12 sheets defined 71.2% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 81 through 99 removed outlier: 3.716A pdb=" N GLN D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.645A pdb=" N HIS D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 238 through 248 removed outlier: 3.512A pdb=" N ALA D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 270 removed outlier: 4.063A pdb=" N ALA D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 288 Processing helix chain 'D' and resid 295 through 310 removed outlier: 3.684A pdb=" N ILE D 299 " --> pdb=" O SER D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 314 removed outlier: 6.375A pdb=" N HIS D 314 " --> pdb=" O ALA D 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 311 through 314' Processing helix chain 'D' and resid 330 through 345 removed outlier: 3.727A pdb=" N SER D 345 " --> pdb=" O CYS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 362 Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 380 through 392 removed outlier: 3.829A pdb=" N VAL D 392 " --> pdb=" O THR D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 404 removed outlier: 3.606A pdb=" N VAL D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 424 Processing helix chain 'D' and resid 429 through 446 Processing helix chain 'D' and resid 465 through 477 removed outlier: 4.320A pdb=" N VAL D 469 " --> pdb=" O SER D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 527 removed outlier: 3.736A pdb=" N ASP D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN D 527 " --> pdb=" O TRP D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 545 through 559 Processing helix chain 'D' and resid 563 through 572 removed outlier: 3.513A pdb=" N GLU D 572 " --> pdb=" O ARG D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 589 removed outlier: 3.872A pdb=" N ASN D 589 " --> pdb=" O GLU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 599 removed outlier: 4.060A pdb=" N VAL D 599 " --> pdb=" O PHE D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 617 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 625 through 638 removed outlier: 3.569A pdb=" N GLY D 638 " --> pdb=" O LYS D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 652 Processing helix chain 'D' and resid 656 through 664 Processing helix chain 'D' and resid 719 through 727 Processing helix chain 'D' and resid 729 through 754 Processing helix chain 'D' and resid 764 through 787 removed outlier: 4.344A pdb=" N VAL D 768 " --> pdb=" O SER D 764 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR D 769 " --> pdb=" O GLY D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 803 Processing helix chain 'D' and resid 805 through 824 Processing helix chain 'D' and resid 825 through 828 removed outlier: 6.252A pdb=" N SER D 828 " --> pdb=" O MET D 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 825 through 828' Processing helix chain 'D' and resid 829 through 848 removed outlier: 3.855A pdb=" N MET D 842 " --> pdb=" O ALA D 838 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 848 " --> pdb=" O PHE D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 853 Processing helix chain 'D' and resid 858 through 895 removed outlier: 3.966A pdb=" N ILE D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE D 863 " --> pdb=" O GLY D 859 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS D 870 " --> pdb=" O GLU D 866 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP D 871 " --> pdb=" O ARG D 867 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE D 874 " --> pdb=" O LYS D 870 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS D 895 " --> pdb=" O GLN D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 915 Proline residue: D 912 - end of helix Processing helix chain 'D' and resid 921 through 926 Processing helix chain 'D' and resid 950 through 985 removed outlier: 4.204A pdb=" N VAL D 964 " --> pdb=" O THR D 960 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR D 965 " --> pdb=" O PHE D 961 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN D 966 " --> pdb=" O LEU D 962 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN D 982 " --> pdb=" O SER D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 1006 Processing helix chain 'D' and resid 1013 through 1027 Processing helix chain 'D' and resid 1044 through 1071 Processing helix chain 'D' and resid 1072 through 1094 Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 81 through 99 removed outlier: 3.717A pdb=" N GLN C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.645A pdb=" N HIS C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.512A pdb=" N ALA C 246 " --> pdb=" O ARG C 242 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 270 removed outlier: 4.063A pdb=" N ALA C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 288 Processing helix chain 'C' and resid 295 through 310 removed outlier: 3.684A pdb=" N ILE C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 314 removed outlier: 6.375A pdb=" N HIS C 314 " --> pdb=" O ALA C 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 311 through 314' Processing helix chain 'C' and resid 330 through 345 removed outlier: 3.728A pdb=" N SER C 345 " --> pdb=" O CYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 362 Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 380 through 392 removed outlier: 3.829A pdb=" N VAL C 392 " --> pdb=" O THR C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 404 removed outlier: 3.606A pdb=" N VAL C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 424 Processing helix chain 'C' and resid 429 through 446 Processing helix chain 'C' and resid 465 through 477 removed outlier: 4.320A pdb=" N VAL C 469 " --> pdb=" O SER C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 527 removed outlier: 3.736A pdb=" N ASP C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN C 527 " --> pdb=" O TRP C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 538 Processing helix chain 'C' and resid 545 through 559 Processing helix chain 'C' and resid 563 through 572 removed outlier: 3.513A pdb=" N GLU C 572 " --> pdb=" O ARG C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 589 removed outlier: 3.871A pdb=" N ASN C 589 " --> pdb=" O GLU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 599 removed outlier: 4.059A pdb=" N VAL C 599 " --> pdb=" O PHE C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 617 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 638 removed outlier: 3.569A pdb=" N GLY C 638 " --> pdb=" O LYS C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 652 Processing helix chain 'C' and resid 656 through 664 Processing helix chain 'C' and resid 719 through 727 Processing helix chain 'C' and resid 729 through 754 Processing helix chain 'C' and resid 764 through 787 removed outlier: 4.344A pdb=" N VAL C 768 " --> pdb=" O SER C 764 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 803 Processing helix chain 'C' and resid 805 through 824 Processing helix chain 'C' and resid 825 through 828 removed outlier: 6.252A pdb=" N SER C 828 " --> pdb=" O MET C 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 825 through 828' Processing helix chain 'C' and resid 829 through 848 removed outlier: 3.855A pdb=" N MET C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 848 " --> pdb=" O PHE C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 853 Processing helix chain 'C' and resid 858 through 895 removed outlier: 3.966A pdb=" N ILE C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE C 863 " --> pdb=" O GLY C 859 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS C 870 " --> pdb=" O GLU C 866 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP C 871 " --> pdb=" O ARG C 867 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 874 " --> pdb=" O LYS C 870 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS C 895 " --> pdb=" O GLN C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 915 Proline residue: C 912 - end of helix Processing helix chain 'C' and resid 921 through 926 Processing helix chain 'C' and resid 950 through 985 removed outlier: 4.204A pdb=" N VAL C 964 " --> pdb=" O THR C 960 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR C 965 " --> pdb=" O PHE C 961 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN C 982 " --> pdb=" O SER C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 1006 Processing helix chain 'C' and resid 1013 through 1027 Processing helix chain 'C' and resid 1044 through 1071 Processing helix chain 'C' and resid 1072 through 1094 Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 81 through 99 removed outlier: 3.715A pdb=" N GLN A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.645A pdb=" N HIS A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.512A pdb=" N ALA A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 removed outlier: 4.063A pdb=" N ALA A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.684A pdb=" N ILE A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 314 removed outlier: 6.375A pdb=" N HIS A 314 " --> pdb=" O ALA A 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 311 through 314' Processing helix chain 'A' and resid 330 through 345 removed outlier: 3.728A pdb=" N SER A 345 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 362 Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 380 through 392 removed outlier: 3.829A pdb=" N VAL A 392 " --> pdb=" O THR A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 404 removed outlier: 3.607A pdb=" N VAL A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 424 Processing helix chain 'A' and resid 429 through 446 Processing helix chain 'A' and resid 465 through 477 removed outlier: 4.319A pdb=" N VAL A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.736A pdb=" N ASP A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN A 527 " --> pdb=" O TRP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 538 Processing helix chain 'A' and resid 545 through 559 Processing helix chain 'A' and resid 563 through 572 removed outlier: 3.513A pdb=" N GLU A 572 " --> pdb=" O ARG A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 589 removed outlier: 3.872A pdb=" N ASN A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 599 removed outlier: 4.060A pdb=" N VAL A 599 " --> pdb=" O PHE A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 638 removed outlier: 3.568A pdb=" N GLY A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 729 through 754 Processing helix chain 'A' and resid 764 through 787 removed outlier: 4.343A pdb=" N VAL A 768 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 803 Processing helix chain 'A' and resid 805 through 824 Processing helix chain 'A' and resid 825 through 828 removed outlier: 6.252A pdb=" N SER A 828 " --> pdb=" O MET A 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 825 through 828' Processing helix chain 'A' and resid 829 through 848 removed outlier: 3.854A pdb=" N MET A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 848 " --> pdb=" O PHE A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 853 Processing helix chain 'A' and resid 858 through 895 removed outlier: 3.966A pdb=" N ILE A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 863 " --> pdb=" O GLY A 859 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 870 " --> pdb=" O GLU A 866 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP A 871 " --> pdb=" O ARG A 867 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 895 " --> pdb=" O GLN A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 915 Proline residue: A 912 - end of helix Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'A' and resid 950 through 985 removed outlier: 4.204A pdb=" N VAL A 964 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 982 " --> pdb=" O SER A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1006 Processing helix chain 'A' and resid 1013 through 1027 Processing helix chain 'A' and resid 1044 through 1071 Processing helix chain 'A' and resid 1072 through 1094 Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 81 through 99 removed outlier: 3.716A pdb=" N GLN B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.645A pdb=" N HIS B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.511A pdb=" N ALA B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 270 removed outlier: 4.062A pdb=" N ALA B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 288 Processing helix chain 'B' and resid 295 through 310 removed outlier: 3.684A pdb=" N ILE B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 314 removed outlier: 6.375A pdb=" N HIS B 314 " --> pdb=" O ALA B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 311 through 314' Processing helix chain 'B' and resid 330 through 345 removed outlier: 3.727A pdb=" N SER B 345 " --> pdb=" O CYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 362 Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'B' and resid 380 through 392 removed outlier: 3.829A pdb=" N VAL B 392 " --> pdb=" O THR B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 404 removed outlier: 3.606A pdb=" N VAL B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 424 Processing helix chain 'B' and resid 429 through 446 Processing helix chain 'B' and resid 465 through 477 removed outlier: 4.320A pdb=" N VAL B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 527 removed outlier: 3.737A pdb=" N ASP B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN B 527 " --> pdb=" O TRP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 538 Processing helix chain 'B' and resid 545 through 559 Processing helix chain 'B' and resid 563 through 572 removed outlier: 3.513A pdb=" N GLU B 572 " --> pdb=" O ARG B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 589 removed outlier: 3.872A pdb=" N ASN B 589 " --> pdb=" O GLU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 599 removed outlier: 4.060A pdb=" N VAL B 599 " --> pdb=" O PHE B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 638 removed outlier: 3.569A pdb=" N GLY B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 656 through 664 Processing helix chain 'B' and resid 719 through 727 Processing helix chain 'B' and resid 729 through 754 Processing helix chain 'B' and resid 764 through 787 removed outlier: 4.343A pdb=" N VAL B 768 " --> pdb=" O SER B 764 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR B 769 " --> pdb=" O GLY B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 803 Processing helix chain 'B' and resid 805 through 824 Processing helix chain 'B' and resid 825 through 828 removed outlier: 6.252A pdb=" N SER B 828 " --> pdb=" O MET B 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 825 through 828' Processing helix chain 'B' and resid 829 through 848 removed outlier: 3.855A pdb=" N MET B 842 " --> pdb=" O ALA B 838 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 848 " --> pdb=" O PHE B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 853 Processing helix chain 'B' and resid 858 through 895 removed outlier: 3.966A pdb=" N ILE B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE B 863 " --> pdb=" O GLY B 859 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS B 870 " --> pdb=" O GLU B 866 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP B 871 " --> pdb=" O ARG B 867 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 874 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS B 895 " --> pdb=" O GLN B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 915 Proline residue: B 912 - end of helix Processing helix chain 'B' and resid 921 through 926 Processing helix chain 'B' and resid 950 through 985 removed outlier: 4.203A pdb=" N VAL B 964 " --> pdb=" O THR B 960 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 965 " --> pdb=" O PHE B 961 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 982 " --> pdb=" O SER B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 1006 Processing helix chain 'B' and resid 1013 through 1027 Processing helix chain 'B' and resid 1044 through 1071 Processing helix chain 'B' and resid 1072 through 1094 Processing sheet with id=AA1, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.600A pdb=" N LYS D 39 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU D 187 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL D 41 " --> pdb=" O LEU D 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 68 through 71 removed outlier: 7.584A pdb=" N LEU D 254 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS D 230 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU D 256 " --> pdb=" O CYS D 230 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU D 232 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 317 " --> pdb=" O TRP D 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 102 through 103 Processing sheet with id=AA4, first strand: chain 'C' and resid 39 through 42 removed outlier: 6.600A pdb=" N LYS C 39 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU C 187 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL C 41 " --> pdb=" O LEU C 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 68 through 71 removed outlier: 7.584A pdb=" N LEU C 254 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS C 230 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU C 256 " --> pdb=" O CYS C 230 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU C 232 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 317 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 42 removed outlier: 6.600A pdb=" N LYS A 39 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU A 187 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL A 41 " --> pdb=" O LEU A 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 68 through 71 removed outlier: 7.583A pdb=" N LEU A 254 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N CYS A 230 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU A 256 " --> pdb=" O CYS A 230 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU A 232 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 317 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AB1, first strand: chain 'B' and resid 39 through 42 removed outlier: 6.599A pdb=" N LYS B 39 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU B 187 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL B 41 " --> pdb=" O LEU B 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 68 through 71 removed outlier: 7.584A pdb=" N LEU B 254 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N CYS B 230 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU B 256 " --> pdb=" O CYS B 230 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU B 232 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 317 " --> pdb=" O TRP B 253 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 102 through 103 1736 hydrogen bonds defined for protein. 5184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.19 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8019 1.34 - 1.46: 5541 1.46 - 1.58: 11342 1.58 - 1.69: 0 1.69 - 1.81: 124 Bond restraints: 25026 Sorted by residual: bond pdb=" CA ILE D 226 " pdb=" C ILE D 226 " ideal model delta sigma weight residual 1.522 1.553 -0.030 8.30e-03 1.45e+04 1.34e+01 bond pdb=" CA ILE A 226 " pdb=" C ILE A 226 " ideal model delta sigma weight residual 1.522 1.553 -0.030 8.30e-03 1.45e+04 1.34e+01 bond pdb=" CA ILE B 226 " pdb=" C ILE B 226 " ideal model delta sigma weight residual 1.522 1.553 -0.030 8.30e-03 1.45e+04 1.34e+01 bond pdb=" CA ILE C 226 " pdb=" C ILE C 226 " ideal model delta sigma weight residual 1.522 1.552 -0.030 8.30e-03 1.45e+04 1.29e+01 bond pdb=" CA GLN D 225 " pdb=" C GLN D 225 " ideal model delta sigma weight residual 1.521 1.560 -0.039 1.21e-02 6.83e+03 1.03e+01 ... (remaining 25021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 33592 1.85 - 3.70: 637 3.70 - 5.55: 96 5.55 - 7.40: 16 7.40 - 9.25: 12 Bond angle restraints: 34353 Sorted by residual: angle pdb=" N ILE C 226 " pdb=" CA ILE C 226 " pdb=" C ILE C 226 " ideal model delta sigma weight residual 108.45 115.72 -7.27 1.20e+00 6.94e-01 3.67e+01 angle pdb=" N ILE B 226 " pdb=" CA ILE B 226 " pdb=" C ILE B 226 " ideal model delta sigma weight residual 108.45 115.71 -7.26 1.20e+00 6.94e-01 3.66e+01 angle pdb=" N ILE A 226 " pdb=" CA ILE A 226 " pdb=" C ILE A 226 " ideal model delta sigma weight residual 108.45 115.71 -7.26 1.20e+00 6.94e-01 3.66e+01 angle pdb=" N ILE D 226 " pdb=" CA ILE D 226 " pdb=" C ILE D 226 " ideal model delta sigma weight residual 108.45 115.69 -7.24 1.20e+00 6.94e-01 3.64e+01 angle pdb=" C ILE D 226 " pdb=" N PRO D 227 " pdb=" CA PRO D 227 " ideal model delta sigma weight residual 119.84 126.53 -6.69 1.25e+00 6.40e-01 2.86e+01 ... (remaining 34348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 13414 17.79 - 35.58: 792 35.58 - 53.37: 143 53.37 - 71.16: 4 71.16 - 88.94: 4 Dihedral angle restraints: 14357 sinusoidal: 3869 harmonic: 10488 Sorted by residual: dihedral pdb=" CA MET C 640 " pdb=" C MET C 640 " pdb=" N ALA C 641 " pdb=" CA ALA C 641 " ideal model delta harmonic sigma weight residual -180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA MET B 640 " pdb=" C MET B 640 " pdb=" N ALA B 641 " pdb=" CA ALA B 641 " ideal model delta harmonic sigma weight residual -180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA MET A 640 " pdb=" C MET A 640 " pdb=" N ALA A 641 " pdb=" CA ALA A 641 " ideal model delta harmonic sigma weight residual -180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 14354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2864 0.037 - 0.074: 1047 0.074 - 0.110: 235 0.110 - 0.147: 41 0.147 - 0.184: 8 Chirality restraints: 4195 Sorted by residual: chirality pdb=" CB VAL C 265 " pdb=" CA VAL C 265 " pdb=" CG1 VAL C 265 " pdb=" CG2 VAL C 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CB VAL B 265 " pdb=" CA VAL B 265 " pdb=" CG1 VAL B 265 " pdb=" CG2 VAL B 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CB VAL D 265 " pdb=" CA VAL D 265 " pdb=" CG1 VAL D 265 " pdb=" CG2 VAL D 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.25e-01 ... (remaining 4192 not shown) Planarity restraints: 4377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 226 " 0.052 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO B 227 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 227 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 227 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 226 " 0.052 5.00e-02 4.00e+02 8.04e-02 1.04e+01 pdb=" N PRO C 227 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 227 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 227 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 226 " -0.052 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO A 227 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 227 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 227 " -0.041 5.00e-02 4.00e+02 ... (remaining 4374 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 410 2.69 - 3.24: 26045 3.24 - 3.80: 37970 3.80 - 4.35: 44923 4.35 - 4.90: 73621 Nonbonded interactions: 182969 Sorted by model distance: nonbonded pdb=" O ASP A 479 " pdb=" OG SER A 606 " model vdw 2.139 3.040 nonbonded pdb=" O ASP C 479 " pdb=" OG SER C 606 " model vdw 2.139 3.040 nonbonded pdb=" O ASP B 479 " pdb=" OG SER B 606 " model vdw 2.139 3.040 nonbonded pdb=" O ASP D 479 " pdb=" OG SER D 606 " model vdw 2.139 3.040 nonbonded pdb=" OE2 GLU B 384 " pdb=" NH2 ARG B 417 " model vdw 2.149 3.120 ... (remaining 182964 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 24 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 1094)) selection = (chain 'B' and (resid 24 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 1094)) selection = chain 'C' selection = (chain 'D' and (resid 24 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 1094)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.320 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5762 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 : 0.004 0.039 25026 Z= 0.198 Angle : 0.658 9.250 34353 Z= 0.375 Chirality : 0.039 0.184 4195 Planarity : 0.005 0.081 4377 Dihedral : 12.247 88.945 7471 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.12), residues: 3477 helix: -1.40 (0.09), residues: 2480 sheet: -1.77 (0.32), residues: 181 loop : -3.86 (0.16), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 417 TYR 0.018 0.001 TYR A 535 PHE 0.022 0.002 PHE B 878 TRP 0.018 0.002 TRP A 636 HIS 0.007 0.001 HIS C1004 Details of bonding type rmsd covalent geometry : bond 0.00387 (25026) covalent geometry : angle 0.65757 (34353) hydrogen bonds : bond 0.11918 ( 1736) hydrogen bonds : angle 5.54073 ( 5184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 723 TRP cc_start: 0.6464 (t60) cc_final: 0.6163 (t60) REVERT: D 1073 GLU cc_start: 0.6563 (mm-30) cc_final: 0.6177 (mm-30) REVERT: C 723 TRP cc_start: 0.6829 (t60) cc_final: 0.6378 (t60) REVERT: C 786 PHE cc_start: 0.6489 (m-10) cc_final: 0.6253 (m-10) REVERT: C 825 MET cc_start: 0.6264 (mmm) cc_final: 0.5840 (mpp) REVERT: A 602 ASN cc_start: 0.7779 (m-40) cc_final: 0.7513 (m110) REVERT: A 723 TRP cc_start: 0.6725 (t60) cc_final: 0.6344 (t60) REVERT: B 602 ASN cc_start: 0.7774 (m-40) cc_final: 0.7497 (m110) REVERT: B 973 LEU cc_start: 0.7755 (tp) cc_final: 0.7491 (tp) REVERT: B 1073 GLU cc_start: 0.6534 (mm-30) cc_final: 0.6331 (mm-30) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.1476 time to fit residues: 86.2870 Evaluate side-chains 291 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 210 HIS D 737 ASN D1057 GLN C 210 HIS C 314 HIS C 344 HIS C 349 GLN C 737 ASN C1057 GLN A 210 HIS A 314 HIS A 349 GLN A 602 ASN A 737 ASN A1057 GLN B 210 HIS B 314 HIS B 349 GLN B 602 ASN B 737 ASN B1057 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.223323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.210383 restraints weight = 34408.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.207071 restraints weight = 46598.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.206664 restraints weight = 54024.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.205817 restraints weight = 46054.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.205165 restraints weight = 55136.763| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25026 Z= 0.203 Angle : 0.646 10.871 34353 Z= 0.332 Chirality : 0.041 0.145 4195 Planarity : 0.005 0.061 4377 Dihedral : 4.707 19.593 3694 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.87 % Allowed : 15.18 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.14), residues: 3477 helix: 0.27 (0.10), residues: 2417 sheet: -1.13 (0.34), residues: 184 loop : -3.18 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 242 TYR 0.021 0.002 TYR B 535 PHE 0.017 0.002 PHE C 402 TRP 0.022 0.002 TRP C 636 HIS 0.007 0.001 HIS C 344 Details of bonding type rmsd covalent geometry : bond 0.00470 (25026) covalent geometry : angle 0.64624 (34353) hydrogen bonds : bond 0.04442 ( 1736) hydrogen bonds : angle 4.41558 ( 5184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 314 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: D 723 TRP cc_start: 0.6400 (t60) cc_final: 0.6167 (t60) REVERT: D 825 MET cc_start: 0.6354 (mpp) cc_final: 0.6053 (mpp) REVERT: D 1073 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6369 (mm-30) REVERT: C 242 ARG cc_start: 0.5834 (tpt170) cc_final: 0.5611 (tpm170) REVERT: C 723 TRP cc_start: 0.6627 (t60) cc_final: 0.6254 (t60) REVERT: C 825 MET cc_start: 0.6353 (mmm) cc_final: 0.5952 (mpp) REVERT: A 242 ARG cc_start: 0.6045 (tpt170) cc_final: 0.5810 (tpm170) REVERT: A 723 TRP cc_start: 0.6627 (t60) cc_final: 0.6274 (t60) REVERT: B 242 ARG cc_start: 0.6177 (tpt170) cc_final: 0.5943 (tpm170) REVERT: B 1073 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6163 (mm-30) outliers start: 35 outliers final: 21 residues processed: 343 average time/residue: 0.1449 time to fit residues: 80.5638 Evaluate side-chains 315 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 294 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 968 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 301 optimal weight: 7.9990 chunk 255 optimal weight: 40.0000 chunk 296 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 chunk 292 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 324 optimal weight: 0.8980 chunk 271 optimal weight: 30.0000 chunk 64 optimal weight: 7.9990 chunk 240 optimal weight: 0.3980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.224844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.213006 restraints weight = 35031.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.209745 restraints weight = 45998.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.209399 restraints weight = 56446.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.209181 restraints weight = 49289.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.209001 restraints weight = 48601.535| |-----------------------------------------------------------------------------| r_work (final): 0.4483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25026 Z= 0.147 Angle : 0.578 10.569 34353 Z= 0.292 Chirality : 0.039 0.138 4195 Planarity : 0.005 0.053 4377 Dihedral : 4.336 18.336 3694 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.26 % Allowed : 16.89 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.14), residues: 3477 helix: 1.13 (0.11), residues: 2418 sheet: -0.53 (0.41), residues: 152 loop : -2.89 (0.18), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.021 0.002 TYR D 535 PHE 0.016 0.001 PHE C 875 TRP 0.019 0.001 TRP D 636 HIS 0.007 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00333 (25026) covalent geometry : angle 0.57750 (34353) hydrogen bonds : bond 0.03829 ( 1736) hydrogen bonds : angle 3.91791 ( 5184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 312 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: D 361 TRP cc_start: 0.5694 (OUTLIER) cc_final: 0.5481 (m-10) REVERT: D 825 MET cc_start: 0.6526 (mpp) cc_final: 0.6218 (mpp) REVERT: C 361 TRP cc_start: 0.5812 (OUTLIER) cc_final: 0.5531 (m-10) REVERT: C 723 TRP cc_start: 0.6511 (t60) cc_final: 0.6213 (t60) REVERT: C 825 MET cc_start: 0.6477 (mmm) cc_final: 0.6015 (mpp) REVERT: A 242 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.5255 (tpt170) REVERT: A 723 TRP cc_start: 0.6486 (t60) cc_final: 0.6201 (t60) REVERT: B 242 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.5430 (tpm170) REVERT: B 361 TRP cc_start: 0.5806 (OUTLIER) cc_final: 0.5505 (m-10) REVERT: B 1073 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6447 (mm-30) outliers start: 61 outliers final: 30 residues processed: 356 average time/residue: 0.1500 time to fit residues: 87.1273 Evaluate side-chains 326 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 291 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 361 TRP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 882 TRP Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 361 TRP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 361 TRP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 878 PHE Chi-restraints excluded: chain B residue 882 TRP Chi-restraints excluded: chain B residue 968 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 54 optimal weight: 0.4980 chunk 205 optimal weight: 10.0000 chunk 234 optimal weight: 0.0670 chunk 130 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 189 optimal weight: 50.0000 chunk 51 optimal weight: 0.6980 chunk 310 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 21 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.227167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.215486 restraints weight = 36202.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.212681 restraints weight = 48457.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.211966 restraints weight = 51550.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.211190 restraints weight = 47890.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.210598 restraints weight = 51316.046| |-----------------------------------------------------------------------------| r_work (final): 0.4499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25026 Z= 0.110 Angle : 0.544 11.339 34353 Z= 0.268 Chirality : 0.037 0.132 4195 Planarity : 0.005 0.055 4377 Dihedral : 3.951 16.567 3694 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.62 % Allowed : 18.39 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.15), residues: 3477 helix: 1.73 (0.11), residues: 2422 sheet: -0.21 (0.42), residues: 153 loop : -2.77 (0.18), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B1078 TYR 0.018 0.001 TYR B 801 PHE 0.017 0.001 PHE D 402 TRP 0.018 0.001 TRP C 636 HIS 0.008 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00234 (25026) covalent geometry : angle 0.54404 (34353) hydrogen bonds : bond 0.03240 ( 1736) hydrogen bonds : angle 3.52802 ( 5184) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 322 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: C 242 ARG cc_start: 0.5522 (tpm170) cc_final: 0.3344 (ttm110) REVERT: C 361 TRP cc_start: 0.5729 (OUTLIER) cc_final: 0.5433 (m-10) REVERT: C 723 TRP cc_start: 0.6456 (t60) cc_final: 0.6145 (t60) REVERT: C 825 MET cc_start: 0.6443 (mmm) cc_final: 0.5969 (mpp) REVERT: A 242 ARG cc_start: 0.5728 (OUTLIER) cc_final: 0.5100 (tpt170) REVERT: A 723 TRP cc_start: 0.6428 (t60) cc_final: 0.6146 (t60) REVERT: B 361 TRP cc_start: 0.5734 (OUTLIER) cc_final: 0.5274 (m-10) REVERT: B 792 THR cc_start: 0.4755 (OUTLIER) cc_final: 0.4509 (m) REVERT: B 1073 GLU cc_start: 0.6671 (mm-30) cc_final: 0.6439 (mm-30) outliers start: 49 outliers final: 29 residues processed: 353 average time/residue: 0.1502 time to fit residues: 85.1810 Evaluate side-chains 327 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 294 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 253 TRP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 642 THR Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 878 PHE Chi-restraints excluded: chain D residue 882 TRP Chi-restraints excluded: chain C residue 253 TRP Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 361 TRP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 878 PHE Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 882 TRP Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 361 TRP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 878 PHE Chi-restraints excluded: chain B residue 882 TRP Chi-restraints excluded: chain B residue 968 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 250 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 296 optimal weight: 6.9990 chunk 225 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 63 optimal weight: 0.0770 chunk 226 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.221919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.209593 restraints weight = 34829.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.206937 restraints weight = 47694.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.205118 restraints weight = 50205.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.204486 restraints weight = 58361.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.203710 restraints weight = 52742.410| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 25026 Z= 0.265 Angle : 0.682 10.837 34353 Z= 0.346 Chirality : 0.043 0.172 4195 Planarity : 0.005 0.056 4377 Dihedral : 4.375 21.785 3694 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.44 % Allowed : 18.33 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.15), residues: 3477 helix: 1.28 (0.11), residues: 2446 sheet: -0.13 (0.43), residues: 153 loop : -2.88 (0.18), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 363 TYR 0.018 0.002 TYR D 535 PHE 0.018 0.002 PHE B 734 TRP 0.022 0.002 TRP A 636 HIS 0.007 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00625 (25026) covalent geometry : angle 0.68213 (34353) hydrogen bonds : bond 0.04356 ( 1736) hydrogen bonds : angle 4.05783 ( 5184) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 312 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 352 LEU cc_start: 0.5246 (OUTLIER) cc_final: 0.4745 (tp) REVERT: D 973 LEU cc_start: 0.7245 (tp) cc_final: 0.7024 (tt) REVERT: C 242 ARG cc_start: 0.5670 (tpm170) cc_final: 0.4959 (tpm170) REVERT: C 361 TRP cc_start: 0.5698 (OUTLIER) cc_final: 0.5416 (m-10) REVERT: C 723 TRP cc_start: 0.6588 (t60) cc_final: 0.6291 (t60) REVERT: A 242 ARG cc_start: 0.5780 (OUTLIER) cc_final: 0.5283 (tpt170) REVERT: A 316 LEU cc_start: 0.5667 (tp) cc_final: 0.5459 (tp) REVERT: A 723 TRP cc_start: 0.6579 (t60) cc_final: 0.6359 (t60) REVERT: B 352 LEU cc_start: 0.4961 (OUTLIER) cc_final: 0.4579 (tp) REVERT: B 361 TRP cc_start: 0.5793 (OUTLIER) cc_final: 0.5469 (m-10) REVERT: B 384 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7231 (pp20) REVERT: B 792 THR cc_start: 0.4138 (OUTLIER) cc_final: 0.3929 (m) REVERT: B 1073 GLU cc_start: 0.6663 (mm-30) cc_final: 0.6408 (mm-30) outliers start: 83 outliers final: 58 residues processed: 373 average time/residue: 0.1531 time to fit residues: 92.7656 Evaluate side-chains 356 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 291 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 253 TRP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 878 PHE Chi-restraints excluded: chain D residue 882 TRP Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 253 TRP Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 361 TRP Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 878 PHE Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 882 TRP Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 361 TRP Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 878 PHE Chi-restraints excluded: chain B residue 882 TRP Chi-restraints excluded: chain B residue 968 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 50.0000 chunk 49 optimal weight: 0.7980 chunk 301 optimal weight: 10.0000 chunk 305 optimal weight: 0.9990 chunk 90 optimal weight: 80.0000 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 348 optimal weight: 20.0000 chunk 263 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 50.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** 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 = 0.4624 r_free = 0.4624 target = 0.224076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.212836 restraints weight = 36295.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.210088 restraints weight = 50657.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.209050 restraints weight = 51995.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.208488 restraints weight = 51351.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.207686 restraints weight = 51898.945| |-----------------------------------------------------------------------------| r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25026 Z= 0.157 Angle : 0.601 11.684 34353 Z= 0.298 Chirality : 0.039 0.210 4195 Planarity : 0.005 0.053 4377 Dihedral : 4.101 18.728 3694 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.44 % Allowed : 19.51 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.15), residues: 3477 helix: 1.55 (0.11), residues: 2447 sheet: -0.13 (0.41), residues: 165 loop : -2.78 (0.18), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1078 TYR 0.017 0.001 TYR B 535 PHE 0.014 0.001 PHE D 653 TRP 0.019 0.001 TRP B 773 HIS 0.007 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00363 (25026) covalent geometry : angle 0.60111 (34353) hydrogen bonds : bond 0.03610 ( 1736) hydrogen bonds : angle 3.75772 ( 5184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 311 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: C 242 ARG cc_start: 0.5430 (tpm170) cc_final: 0.5197 (tpm170) REVERT: C 361 TRP cc_start: 0.5648 (OUTLIER) cc_final: 0.5357 (m-10) REVERT: C 723 TRP cc_start: 0.6510 (t60) cc_final: 0.6215 (t60) REVERT: A 242 ARG cc_start: 0.5757 (OUTLIER) cc_final: 0.5215 (tpt170) REVERT: A 723 TRP cc_start: 0.6509 (t60) cc_final: 0.6282 (t60) REVERT: A 792 THR cc_start: 0.5472 (OUTLIER) cc_final: 0.5258 (m) REVERT: B 361 TRP cc_start: 0.5707 (OUTLIER) cc_final: 0.5425 (m-10) REVERT: B 792 THR cc_start: 0.4117 (OUTLIER) cc_final: 0.3906 (m) REVERT: B 1073 GLU cc_start: 0.6513 (mm-30) cc_final: 0.6273 (mm-30) REVERT: B 1078 ARG cc_start: 0.6482 (mtt-85) cc_final: 0.5732 (mtt-85) outliers start: 83 outliers final: 69 residues processed: 371 average time/residue: 0.1616 time to fit residues: 97.5973 Evaluate side-chains 370 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 296 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 253 TRP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 642 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 878 PHE Chi-restraints excluded: chain D residue 882 TRP Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 979 TYR Chi-restraints excluded: chain C residue 253 TRP Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 361 TRP Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 878 PHE Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 882 TRP Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 979 TYR Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 361 TRP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 878 PHE Chi-restraints excluded: chain B residue 882 TRP Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 979 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 352 optimal weight: 0.8980 chunk 304 optimal weight: 0.7980 chunk 188 optimal weight: 50.0000 chunk 276 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 282 optimal weight: 40.0000 chunk 194 optimal weight: 50.0000 chunk 226 optimal weight: 10.0000 chunk 355 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 GLN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 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 = 0.4573 r_free = 0.4573 target = 0.218634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.209745 restraints weight = 34893.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.208823 restraints weight = 69761.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.208194 restraints weight = 70556.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.207547 restraints weight = 66241.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.207402 restraints weight = 54190.432| |-----------------------------------------------------------------------------| r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 25026 Z= 0.387 Angle : 0.829 11.857 34353 Z= 0.425 Chirality : 0.049 0.414 4195 Planarity : 0.006 0.061 4377 Dihedral : 4.952 28.884 3694 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.83 % Allowed : 19.51 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.14), residues: 3477 helix: 0.74 (0.11), residues: 2455 sheet: -0.09 (0.41), residues: 164 loop : -2.75 (0.18), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 363 TYR 0.021 0.002 TYR A1003 PHE 0.023 0.003 PHE C 734 TRP 0.026 0.002 TRP B 773 HIS 0.006 0.001 HIS C1004 Details of bonding type rmsd covalent geometry : bond 0.00912 (25026) covalent geometry : angle 0.82927 (34353) hydrogen bonds : bond 0.05292 ( 1736) hydrogen bonds : angle 4.62259 ( 5184) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 304 time to evaluate : 0.830 Fit side-chains REVERT: D 352 LEU cc_start: 0.5416 (OUTLIER) cc_final: 0.4875 (tp) REVERT: C 242 ARG cc_start: 0.5814 (tpm170) cc_final: 0.5471 (tpm170) REVERT: C 352 LEU cc_start: 0.5197 (OUTLIER) cc_final: 0.4819 (tp) REVERT: C 361 TRP cc_start: 0.5689 (OUTLIER) cc_final: 0.5320 (m-10) REVERT: C 723 TRP cc_start: 0.6746 (t60) cc_final: 0.6482 (t60) REVERT: A 242 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.5345 (tpt170) REVERT: A 352 LEU cc_start: 0.5228 (OUTLIER) cc_final: 0.4812 (tp) REVERT: A 723 TRP cc_start: 0.6699 (t60) cc_final: 0.6346 (t60) REVERT: A 740 MET cc_start: 0.7642 (tpp) cc_final: 0.7364 (tpp) REVERT: A 792 THR cc_start: 0.5052 (OUTLIER) cc_final: 0.4852 (m) REVERT: A 976 MET cc_start: 0.5598 (tmm) cc_final: 0.5033 (tmm) REVERT: B 316 LEU cc_start: 0.5857 (tp) cc_final: 0.5638 (tp) REVERT: B 361 TRP cc_start: 0.5704 (OUTLIER) cc_final: 0.5349 (m-10) REVERT: B 430 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6781 (tt) REVERT: B 792 THR cc_start: 0.4452 (OUTLIER) cc_final: 0.4229 (m) outliers start: 109 outliers final: 82 residues processed: 386 average time/residue: 0.1601 time to fit residues: 99.8749 Evaluate side-chains 390 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 299 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 253 TRP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 642 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 878 PHE Chi-restraints excluded: chain D residue 882 TRP Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 979 TYR Chi-restraints excluded: chain D residue 1059 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 253 TRP Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 361 TRP Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 878 PHE Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 882 TRP Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 979 TYR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 361 TRP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 878 PHE Chi-restraints excluded: chain B residue 882 TRP Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 979 TYR Chi-restraints excluded: chain B residue 1059 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 329 optimal weight: 0.7980 chunk 76 optimal weight: 40.0000 chunk 289 optimal weight: 8.9990 chunk 328 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 221 optimal weight: 0.5980 chunk 225 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 11 optimal weight: 0.0000 chunk 262 optimal weight: 0.6980 chunk 304 optimal weight: 0.5980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 602 ASN C 602 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.225513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.213842 restraints weight = 36243.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.210580 restraints weight = 46470.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.209568 restraints weight = 57895.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.208966 restraints weight = 56220.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.207859 restraints weight = 54757.215| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5879 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25026 Z= 0.117 Angle : 0.597 13.154 34353 Z= 0.291 Chirality : 0.039 0.334 4195 Planarity : 0.005 0.094 4377 Dihedral : 4.111 18.963 3694 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.69 % Allowed : 21.70 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.15), residues: 3477 helix: 1.61 (0.11), residues: 2447 sheet: -0.11 (0.41), residues: 164 loop : -2.71 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B1078 TYR 0.013 0.001 TYR D 535 PHE 0.024 0.001 PHE B 875 TRP 0.020 0.001 TRP B 773 HIS 0.009 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00256 (25026) covalent geometry : angle 0.59743 (34353) hydrogen bonds : bond 0.03330 ( 1736) hydrogen bonds : angle 3.71104 ( 5184) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 317 time to evaluate : 0.928 Fit side-chains REVERT: D 976 MET cc_start: 0.5693 (tmm) cc_final: 0.5298 (tmm) REVERT: C 242 ARG cc_start: 0.5660 (tpm170) cc_final: 0.5320 (tpm170) REVERT: C 723 TRP cc_start: 0.6472 (t60) cc_final: 0.6191 (t60) REVERT: C 740 MET cc_start: 0.7482 (tpp) cc_final: 0.7197 (tpp) REVERT: C 976 MET cc_start: 0.5909 (tmm) cc_final: 0.5372 (tmm) REVERT: A 242 ARG cc_start: 0.5833 (OUTLIER) cc_final: 0.5254 (tpt170) REVERT: A 723 TRP cc_start: 0.6505 (t60) cc_final: 0.6234 (t60) REVERT: A 740 MET cc_start: 0.7355 (tpp) cc_final: 0.7142 (tpp) REVERT: A 792 THR cc_start: 0.5440 (OUTLIER) cc_final: 0.5204 (m) REVERT: A 976 MET cc_start: 0.5631 (tmm) cc_final: 0.5352 (tmm) REVERT: B 242 ARG cc_start: 0.5561 (OUTLIER) cc_final: 0.5356 (tpm170) REVERT: B 361 TRP cc_start: 0.5518 (OUTLIER) cc_final: 0.5227 (m-10) REVERT: B 792 THR cc_start: 0.4311 (OUTLIER) cc_final: 0.4071 (m) outliers start: 69 outliers final: 54 residues processed: 360 average time/residue: 0.1573 time to fit residues: 91.8408 Evaluate side-chains 360 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 301 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 253 TRP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 642 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 792 THR Chi-restraints excluded: chain D residue 878 PHE Chi-restraints excluded: chain D residue 882 TRP Chi-restraints excluded: chain D residue 979 TYR Chi-restraints excluded: chain C residue 253 TRP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 878 PHE Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 979 TYR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 882 TRP Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 979 TYR Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 361 TRP Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 878 PHE Chi-restraints excluded: chain B residue 882 TRP Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 979 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 116 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 17 optimal weight: 50.0000 chunk 202 optimal weight: 20.0000 chunk 314 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 337 optimal weight: 0.3980 chunk 27 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 291 optimal weight: 0.0010 overall best weight: 1.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.224669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.212631 restraints weight = 35209.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.209465 restraints weight = 45387.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.208982 restraints weight = 50893.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.208419 restraints weight = 44754.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.207990 restraints weight = 48432.743| |-----------------------------------------------------------------------------| r_work (final): 0.4480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25026 Z= 0.138 Angle : 0.615 13.375 34353 Z= 0.297 Chirality : 0.039 0.350 4195 Planarity : 0.005 0.055 4377 Dihedral : 3.981 17.559 3694 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.22 % Allowed : 21.81 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.15), residues: 3477 helix: 1.73 (0.11), residues: 2447 sheet: -0.17 (0.40), residues: 164 loop : -2.63 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 363 TYR 0.018 0.001 TYR B 535 PHE 0.017 0.001 PHE D 653 TRP 0.019 0.001 TRP A 636 HIS 0.008 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00317 (25026) covalent geometry : angle 0.61466 (34353) hydrogen bonds : bond 0.03416 ( 1736) hydrogen bonds : angle 3.66608 ( 5184) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 304 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: D 976 MET cc_start: 0.5634 (tmm) cc_final: 0.5278 (tmm) REVERT: C 242 ARG cc_start: 0.5631 (tpm170) cc_final: 0.5298 (tpm170) REVERT: C 723 TRP cc_start: 0.6481 (t60) cc_final: 0.6207 (t60) REVERT: C 740 MET cc_start: 0.7527 (tpp) cc_final: 0.7290 (tpp) REVERT: C 976 MET cc_start: 0.5753 (tmm) cc_final: 0.5313 (tmm) REVERT: A 242 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.5368 (tpt170) REVERT: A 723 TRP cc_start: 0.6511 (t60) cc_final: 0.6244 (t60) REVERT: A 740 MET cc_start: 0.7451 (tpp) cc_final: 0.7227 (tpp) REVERT: A 792 THR cc_start: 0.5513 (OUTLIER) cc_final: 0.5278 (m) REVERT: A 976 MET cc_start: 0.5524 (tmm) cc_final: 0.5320 (tmm) REVERT: B 361 TRP cc_start: 0.5449 (OUTLIER) cc_final: 0.5175 (m-10) REVERT: B 792 THR cc_start: 0.4478 (OUTLIER) cc_final: 0.4215 (m) outliers start: 79 outliers final: 66 residues processed: 360 average time/residue: 0.1567 time to fit residues: 92.3227 Evaluate side-chains 362 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 292 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 253 TRP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 642 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 792 THR Chi-restraints excluded: chain D residue 878 PHE Chi-restraints excluded: chain D residue 882 TRP Chi-restraints excluded: chain D residue 963 LEU Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain C residue 253 TRP Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 851 ILE Chi-restraints excluded: chain C residue 878 PHE Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 882 TRP Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 979 TYR Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 361 TRP Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 878 PHE Chi-restraints excluded: chain B residue 882 TRP Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 979 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 302 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 255 optimal weight: 50.0000 chunk 357 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 251 optimal weight: 20.0000 chunk 270 optimal weight: 90.0000 chunk 2 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.220802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.208603 restraints weight = 34763.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.205965 restraints weight = 48008.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.204700 restraints weight = 51775.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.204061 restraints weight = 47889.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.202912 restraints weight = 49354.604| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 25026 Z= 0.283 Angle : 0.744 13.188 34353 Z= 0.372 Chirality : 0.045 0.336 4195 Planarity : 0.005 0.060 4377 Dihedral : 4.468 23.982 3694 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.22 % Allowed : 22.39 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.15), residues: 3477 helix: 1.32 (0.11), residues: 2432 sheet: -0.25 (0.40), residues: 164 loop : -2.66 (0.18), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 346 TYR 0.020 0.002 TYR C 535 PHE 0.017 0.002 PHE C 878 TRP 0.031 0.002 TRP D 517 HIS 0.006 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00670 (25026) covalent geometry : angle 0.74371 (34353) hydrogen bonds : bond 0.04361 ( 1736) hydrogen bonds : angle 4.16087 ( 5184) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 294 time to evaluate : 1.121 Fit side-chains REVERT: D 740 MET cc_start: 0.7739 (tpp) cc_final: 0.7353 (tpp) REVERT: D 976 MET cc_start: 0.5755 (tmm) cc_final: 0.5481 (tmm) REVERT: C 242 ARG cc_start: 0.5737 (tpm170) cc_final: 0.5397 (tpm170) REVERT: C 723 TRP cc_start: 0.6621 (t60) cc_final: 0.6330 (t60) REVERT: A 242 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.5469 (tpt170) REVERT: A 723 TRP cc_start: 0.6627 (t60) cc_final: 0.6353 (t60) REVERT: A 740 MET cc_start: 0.7606 (tpp) cc_final: 0.7367 (tpp) REVERT: A 792 THR cc_start: 0.5141 (OUTLIER) cc_final: 0.4886 (m) REVERT: B 361 TRP cc_start: 0.5521 (OUTLIER) cc_final: 0.5189 (m-10) REVERT: B 792 THR cc_start: 0.4225 (OUTLIER) cc_final: 0.4020 (m) outliers start: 79 outliers final: 72 residues processed: 350 average time/residue: 0.1591 time to fit residues: 90.8419 Evaluate side-chains 366 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 290 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 253 TRP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 642 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 878 PHE Chi-restraints excluded: chain D residue 882 TRP Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain C residue 253 TRP Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 851 ILE Chi-restraints excluded: chain C residue 878 PHE Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 882 TRP Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 979 TYR Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 361 TRP Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 878 PHE Chi-restraints excluded: chain B residue 882 TRP Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 979 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.1735 > 50: distance: 14 - 17: 27.395 distance: 17 - 18: 24.322 distance: 18 - 19: 12.525 distance: 18 - 21: 21.132 distance: 19 - 20: 15.819 distance: 19 - 22: 31.513 distance: 22 - 23: 9.967 distance: 23 - 24: 19.330 distance: 23 - 26: 11.276 distance: 24 - 25: 28.924 distance: 24 - 27: 14.594 distance: 27 - 28: 11.299 distance: 28 - 29: 15.178 distance: 28 - 31: 15.887 distance: 29 - 30: 17.497 distance: 29 - 32: 24.707 distance: 32 - 33: 17.861 distance: 33 - 34: 4.175 distance: 33 - 36: 29.573 distance: 34 - 35: 8.863 distance: 37 - 38: 13.706 distance: 38 - 39: 15.453 distance: 38 - 41: 9.767 distance: 39 - 40: 11.869 distance: 39 - 42: 16.077 distance: 42 - 43: 10.613 distance: 43 - 44: 23.024 distance: 43 - 46: 13.457 distance: 44 - 45: 21.948 distance: 44 - 47: 10.268 distance: 47 - 48: 17.889 distance: 47 - 53: 18.964 distance: 48 - 49: 8.188 distance: 48 - 51: 15.567 distance: 49 - 50: 10.914 distance: 49 - 54: 3.764 distance: 51 - 52: 17.844 distance: 52 - 53: 19.974 distance: 54 - 55: 11.849 distance: 55 - 56: 7.213 distance: 55 - 58: 6.451 distance: 56 - 57: 5.665 distance: 56 - 62: 21.348 distance: 58 - 59: 10.585 distance: 59 - 60: 31.765 distance: 59 - 61: 24.182 distance: 62 - 63: 26.571 distance: 63 - 64: 12.019 distance: 63 - 66: 19.865 distance: 64 - 65: 28.608 distance: 64 - 70: 25.277 distance: 66 - 67: 34.438 distance: 67 - 68: 5.495 distance: 67 - 69: 16.875 distance: 70 - 71: 23.193 distance: 71 - 72: 25.611 distance: 71 - 74: 9.411 distance: 72 - 73: 10.924 distance: 72 - 75: 14.084