Starting phenix.real_space_refine on Sat Jun 21 02:13:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sla_40576/06_2025/8sla_40576.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sla_40576/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sla_40576/06_2025/8sla_40576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sla_40576/06_2025/8sla_40576.map" model { file = "/net/cci-nas-00/data/ceres_data/8sla_40576/06_2025/8sla_40576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sla_40576/06_2025/8sla_40576.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 19, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 15, 'TRP:plan': 3, 'ASP:plan': 25, 'PHE:plan': 16, 'GLU:plan': 38, 'ARG:plan': 28} 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: {'GLN:plan1': 19, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 15, 'TRP:plan': 3, 'ASP:plan': 25, 'PHE:plan': 16, 'GLU:plan': 38, 'ARG:plan': 28} 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: {'GLN:plan1': 19, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 15, 'TRP:plan': 3, 'ASP:plan': 25, 'PHE:plan': 16, 'GLU:plan': 38, 'ARG:plan': 28} 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: {'GLN:plan1': 19, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 15, 'TRP:plan': 3, 'ASP:plan': 25, 'PHE:plan': 16, 'GLU:plan': 38, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 694 Time building chain proxies: 15.34, per 1000 atoms: 0.63 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: 6.21 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 2.88 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: 9.39 Time building geometry restraints manager: 7.37 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: 2.710 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: 0.030 Extract box with map and model: 1.030 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 57.300 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.760 ------------------------------------------------------------------------------- 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 : 10.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.002 TRP A 636 HIS 0.007 0.001 HIS C1004 PHE 0.022 0.002 PHE B 878 TYR 0.018 0.001 TYR A 535 ARG 0.003 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.11918 ( 1736) hydrogen bonds : angle 5.54073 ( 5184) covalent geometry : bond 0.00387 (25026) covalent geometry : angle 0.65757 (34353) *********************** 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 : 2.578 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: 0.6175 (mm-30) REVERT: C 723 TRP cc_start: 0.6829 (t60) cc_final: 0.6379 (t60) REVERT: C 786 PHE cc_start: 0.6489 (m-10) cc_final: 0.6252 (m-10) REVERT: C 825 MET cc_start: 0.6264 (mmm) cc_final: 0.5839 (mpp) REVERT: A 602 ASN cc_start: 0.7779 (m-40) cc_final: 0.7514 (m110) REVERT: A 723 TRP cc_start: 0.6725 (t60) cc_final: 0.6343 (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: 0.7492 (tp) REVERT: B 1073 GLU cc_start: 0.6534 (mm-30) cc_final: 0.6332 (mm-30) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.3627 time to fit residues: 211.1851 Evaluate side-chains 292 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 1.9990 chunk 272 optimal weight: 0.4980 chunk 151 optimal weight: 0.1980 chunk 93 optimal weight: 30.0000 chunk 184 optimal weight: 40.0000 chunk 145 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 chunk 109 optimal weight: 0.0670 chunk 171 optimal weight: 0.5980 chunk 210 optimal weight: 0.0870 chunk 326 optimal weight: 1.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 210 HIS C 210 HIS C 314 HIS C 344 HIS ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 HIS B 210 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.226917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.213900 restraints weight = 35597.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.213103 restraints weight = 72069.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.213107 restraints weight = 64503.817| |-----------------------------------------------------------------------------| r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25026 Z= 0.118 Angle : 0.561 11.773 34353 Z= 0.285 Chirality : 0.038 0.132 4195 Planarity : 0.005 0.062 4377 Dihedral : 4.316 17.998 3694 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.44 % Allowed : 13.04 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3477 helix: 0.81 (0.10), residues: 2419 sheet: -1.22 (0.33), residues: 184 loop : -3.04 (0.18), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 773 HIS 0.007 0.001 HIS C 344 PHE 0.024 0.001 PHE A 402 TYR 0.014 0.001 TYR A 801 ARG 0.012 0.001 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 1736) hydrogen bonds : angle 3.89326 ( 5184) covalent geometry : bond 0.00246 (25026) covalent geometry : angle 0.56145 (34353) *********************** 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 344 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 317 time to evaluate : 2.706 Fit side-chains REVERT: D 723 TRP cc_start: 0.6243 (t60) cc_final: 0.5984 (t60) REVERT: C 242 ARG cc_start: 0.5708 (tpt170) cc_final: 0.5478 (tpm170) REVERT: C 723 TRP cc_start: 0.6532 (t60) cc_final: 0.6117 (t60) REVERT: C 825 MET cc_start: 0.6294 (mmm) cc_final: 0.5891 (mpp) REVERT: A 723 TRP cc_start: 0.6427 (t60) cc_final: 0.6037 (t60) REVERT: A 792 THR cc_start: 0.4878 (OUTLIER) cc_final: 0.4590 (m) REVERT: B 242 ARG cc_start: 0.6071 (tpt170) cc_final: 0.5864 (tpm170) REVERT: B 792 THR cc_start: 0.3800 (OUTLIER) cc_final: 0.3560 (m) REVERT: B 1073 GLU cc_start: 0.6573 (mm-30) cc_final: 0.6025 (mm-30) REVERT: B 1074 GLU cc_start: 0.6489 (mm-30) cc_final: 0.6208 (mm-30) outliers start: 27 outliers final: 15 residues processed: 334 average time/residue: 0.3309 time to fit residues: 178.4591 Evaluate side-chains 302 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 285 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 990 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 26 optimal weight: 20.0000 chunk 187 optimal weight: 7.9990 chunk 182 optimal weight: 20.0000 chunk 353 optimal weight: 4.9990 chunk 341 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 239 optimal weight: 3.9990 chunk 193 optimal weight: 30.0000 chunk 92 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 50.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 737 ASN C 344 HIS C 349 GLN C 737 ASN A 210 HIS A 344 HIS A 349 GLN A 737 ASN B 349 GLN B 737 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.211773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.204076 restraints weight = 35904.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.202101 restraints weight = 48616.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.201363 restraints weight = 61281.035| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.156 25026 Z= 0.678 Angle : 1.131 15.963 34353 Z= 0.597 Chirality : 0.063 0.322 4195 Planarity : 0.007 0.063 4377 Dihedral : 5.976 35.074 3694 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.71 % Favored : 92.06 % Rotamer: Outliers : 5.61 % Allowed : 17.74 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.13), residues: 3477 helix: -0.50 (0.10), residues: 2463 sheet: -0.71 (0.39), residues: 164 loop : -3.23 (0.18), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP B 636 HIS 0.011 0.002 HIS A1004 PHE 0.041 0.005 PHE A 622 TYR 0.041 0.004 TYR B 997 ARG 0.013 0.002 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.07318 ( 1736) hydrogen bonds : angle 5.90047 ( 5184) covalent geometry : bond 0.01594 (25026) covalent geometry : angle 1.13140 (34353) *********************** 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 412 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 307 time to evaluate : 2.649 Fit side-chains REVERT: D 352 LEU cc_start: 0.5308 (OUTLIER) cc_final: 0.4745 (tp) REVERT: D 361 TRP cc_start: 0.5908 (OUTLIER) cc_final: 0.5626 (m-10) REVERT: D 723 TRP cc_start: 0.6557 (t60) cc_final: 0.6251 (t60) REVERT: C 242 ARG cc_start: 0.5734 (OUTLIER) cc_final: 0.5502 (tpm170) REVERT: C 352 LEU cc_start: 0.5174 (OUTLIER) cc_final: 0.4738 (tp) REVERT: C 361 TRP cc_start: 0.5954 (OUTLIER) cc_final: 0.5679 (m-10) REVERT: C 825 MET cc_start: 0.6226 (mmm) cc_final: 0.5808 (mpp) REVERT: C 1074 GLU cc_start: 0.6574 (mm-30) cc_final: 0.6340 (mm-30) REVERT: A 316 LEU cc_start: 0.5611 (tp) cc_final: 0.5179 (tp) REVERT: A 352 LEU cc_start: 0.5227 (OUTLIER) cc_final: 0.4793 (tp) REVERT: A 361 TRP cc_start: 0.5902 (OUTLIER) cc_final: 0.5597 (m-10) REVERT: A 740 MET cc_start: 0.7764 (tpp) cc_final: 0.7508 (tpp) REVERT: A 1073 GLU cc_start: 0.6523 (mm-30) cc_final: 0.6088 (mm-30) REVERT: B 242 ARG cc_start: 0.6158 (OUTLIER) cc_final: 0.5933 (tpm170) REVERT: B 352 LEU cc_start: 0.5192 (OUTLIER) cc_final: 0.4601 (tp) REVERT: B 361 TRP cc_start: 0.5848 (OUTLIER) cc_final: 0.5494 (m-10) REVERT: B 723 TRP cc_start: 0.6831 (t60) cc_final: 0.6629 (t60) REVERT: B 1073 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6274 (mm-30) outliers start: 105 outliers final: 71 residues processed: 387 average time/residue: 0.3291 time to fit residues: 206.0082 Evaluate side-chains 375 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 294 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 223 SER 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 361 TRP Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 628 VAL 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 836 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 1084 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 242 ARG 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 399 VAL Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 836 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 1076 VAL 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 331 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 361 TRP Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 544 VAL 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 843 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 1084 VAL Chi-restraints excluded: chain B residue 242 ARG 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 399 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 560 LEU 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 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 1084 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 156 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 164 optimal weight: 0.2980 chunk 135 optimal weight: 0.6980 chunk 245 optimal weight: 0.8980 chunk 144 optimal weight: 0.4980 chunk 25 optimal weight: 8.9990 chunk 353 optimal weight: 0.8980 chunk 358 optimal weight: 5.9990 chunk 251 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 528 ASN C 344 HIS C 528 ASN A 344 HIS A 528 ASN B 528 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.224462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.213137 restraints weight = 36165.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.210374 restraints weight = 48285.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.209775 restraints weight = 55901.291| |-----------------------------------------------------------------------------| r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5843 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25026 Z= 0.133 Angle : 0.588 11.128 34353 Z= 0.298 Chirality : 0.038 0.131 4195 Planarity : 0.005 0.056 4377 Dihedral : 4.562 20.294 3694 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.47 % Allowed : 19.56 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3477 helix: 1.03 (0.11), residues: 2413 sheet: -0.58 (0.39), residues: 165 loop : -2.87 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 636 HIS 0.010 0.001 HIS A 612 PHE 0.026 0.002 PHE B 402 TYR 0.014 0.001 TYR C 535 ARG 0.010 0.001 ARG C 363 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 1736) hydrogen bonds : angle 3.98192 ( 5184) covalent geometry : bond 0.00288 (25026) covalent geometry : angle 0.58755 (34353) *********************** 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 372 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 307 time to evaluate : 2.415 Fit side-chains revert: symmetry clash REVERT: D 361 TRP cc_start: 0.5562 (OUTLIER) cc_final: 0.5310 (m-10) REVERT: D 723 TRP cc_start: 0.6342 (t60) cc_final: 0.6041 (t60) REVERT: C 231 LEU cc_start: 0.4870 (mp) cc_final: 0.4643 (mp) REVERT: C 361 TRP cc_start: 0.5620 (OUTLIER) cc_final: 0.5238 (m-10) REVERT: C 723 TRP cc_start: 0.6607 (t60) cc_final: 0.6283 (t60) REVERT: C 825 MET cc_start: 0.6367 (mmm) cc_final: 0.5871 (mpp) REVERT: A 361 TRP cc_start: 0.5588 (OUTLIER) cc_final: 0.5357 (m-10) REVERT: A 723 TRP cc_start: 0.6479 (t60) cc_final: 0.6184 (t60) REVERT: A 792 THR cc_start: 0.5555 (OUTLIER) cc_final: 0.5333 (m) REVERT: A 1073 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6239 (mm-30) REVERT: B 242 ARG cc_start: 0.6047 (OUTLIER) cc_final: 0.5541 (tpm170) REVERT: B 361 TRP cc_start: 0.5529 (OUTLIER) cc_final: 0.5163 (m-10) REVERT: B 792 THR cc_start: 0.4417 (OUTLIER) cc_final: 0.4198 (m) outliers start: 65 outliers final: 35 residues processed: 352 average time/residue: 0.3627 time to fit residues: 208.2613 Evaluate side-chains 329 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 287 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 243 MET 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 584 SER Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 882 TRP Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain C residue 243 MET 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 584 SER Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 361 TRP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 882 TRP 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 357 LEU Chi-restraints excluded: chain B residue 361 TRP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 843 VAL 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 239 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 chunk 242 optimal weight: 9.9990 chunk 291 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 125 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 247 optimal weight: 6.9990 chunk 283 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 528 ASN C 528 ASN A 528 ASN B 528 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.220094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.207389 restraints weight = 36068.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.205830 restraints weight = 57212.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.204069 restraints weight = 52995.213| |-----------------------------------------------------------------------------| r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25026 Z= 0.231 Angle : 0.663 11.008 34353 Z= 0.336 Chirality : 0.042 0.147 4195 Planarity : 0.005 0.063 4377 Dihedral : 4.613 23.243 3694 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.06 % Allowed : 21.43 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3477 helix: 0.99 (0.11), residues: 2435 sheet: -0.44 (0.40), residues: 165 loop : -2.88 (0.18), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 636 HIS 0.007 0.001 HIS A 344 PHE 0.017 0.002 PHE B 583 TYR 0.021 0.002 TYR C 535 ARG 0.007 0.001 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 1736) hydrogen bonds : angle 4.16261 ( 5184) covalent geometry : bond 0.00543 (25026) covalent geometry : angle 0.66313 (34353) *********************** 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 370 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 294 time to evaluate : 2.588 Fit side-chains revert: symmetry clash REVERT: D 361 TRP cc_start: 0.5695 (OUTLIER) cc_final: 0.5437 (m-10) REVERT: D 723 TRP cc_start: 0.6420 (t60) cc_final: 0.6140 (t60) REVERT: C 361 TRP cc_start: 0.5710 (OUTLIER) cc_final: 0.5382 (m-10) REVERT: C 723 TRP cc_start: 0.6573 (t60) cc_final: 0.6280 (t60) REVERT: A 361 TRP cc_start: 0.5753 (OUTLIER) cc_final: 0.5538 (m-10) REVERT: A 401 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7652 (tt) REVERT: A 723 TRP cc_start: 0.6599 (t60) cc_final: 0.6343 (t60) REVERT: A 792 THR cc_start: 0.5678 (OUTLIER) cc_final: 0.5454 (m) REVERT: A 1073 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6391 (mm-30) REVERT: B 242 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.5389 (tpm170) REVERT: B 361 TRP cc_start: 0.5645 (OUTLIER) cc_final: 0.5309 (m-10) REVERT: B 792 THR cc_start: 0.4366 (OUTLIER) cc_final: 0.4139 (m) REVERT: B 1074 GLU cc_start: 0.6476 (mm-30) cc_final: 0.6084 (mm-30) outliers start: 76 outliers final: 48 residues processed: 352 average time/residue: 0.3221 time to fit residues: 183.5810 Evaluate side-chains 346 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 290 time to evaluate : 2.650 ------------------------------------------------------------------------------- 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 584 SER Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 851 ILE 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 331 THR Chi-restraints excluded: chain C residue 361 TRP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 843 VAL 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 270 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 361 TRP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 792 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 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 520 LEU Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 851 ILE 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 351 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 269 optimal weight: 0.9990 chunk 98 optimal weight: 50.0000 chunk 236 optimal weight: 4.9990 chunk 312 optimal weight: 0.0670 chunk 111 optimal weight: 2.9990 chunk 332 optimal weight: 6.9990 chunk 167 optimal weight: 50.0000 chunk 103 optimal weight: 50.0000 chunk 267 optimal weight: 0.7980 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.223044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.211782 restraints weight = 35509.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.209034 restraints weight = 48595.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.207593 restraints weight = 55917.331| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.2892 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= 0.127 Angle : 0.582 11.639 34353 Z= 0.287 Chirality : 0.038 0.165 4195 Planarity : 0.005 0.054 4377 Dihedral : 4.153 18.793 3694 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.28 % Allowed : 21.97 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3477 helix: 1.47 (0.11), residues: 2459 sheet: -0.25 (0.40), residues: 165 loop : -2.91 (0.18), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 773 HIS 0.009 0.001 HIS A 344 PHE 0.023 0.001 PHE B 653 TYR 0.015 0.001 TYR C 535 ARG 0.008 0.001 ARG D 242 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 1736) hydrogen bonds : angle 3.65393 ( 5184) covalent geometry : bond 0.00283 (25026) covalent geometry : angle 0.58177 (34353) *********************** 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 391 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 311 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 352 LEU cc_start: 0.5145 (OUTLIER) cc_final: 0.4841 (tp) REVERT: D 723 TRP cc_start: 0.6319 (t60) cc_final: 0.6036 (t60) REVERT: C 242 ARG cc_start: 0.5232 (tpm170) cc_final: 0.5031 (tpm170) REVERT: C 723 TRP cc_start: 0.6469 (t60) cc_final: 0.6153 (t60) REVERT: A 723 TRP cc_start: 0.6459 (t60) cc_final: 0.6163 (t60) REVERT: A 792 THR cc_start: 0.5527 (OUTLIER) cc_final: 0.5299 (m) REVERT: A 1073 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6280 (mm-30) REVERT: B 352 LEU cc_start: 0.4945 (OUTLIER) cc_final: 0.4641 (tp) REVERT: B 792 THR cc_start: 0.4381 (OUTLIER) cc_final: 0.4152 (m) outliers start: 80 outliers final: 54 residues processed: 370 average time/residue: 0.3536 time to fit residues: 213.5401 Evaluate side-chains 356 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 298 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 253 TRP Chi-restraints excluded: chain D residue 270 VAL 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 430 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 851 ILE 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 331 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 843 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 253 TRP Chi-restraints excluded: chain A residue 270 VAL 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 584 SER Chi-restraints excluded: chain A residue 628 VAL 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 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 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 352 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 843 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 217 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 280 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 5 optimal weight: 50.0000 chunk 248 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.221783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.209906 restraints weight = 35488.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.207865 restraints weight = 55640.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.207496 restraints weight = 45610.004| |-----------------------------------------------------------------------------| r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25026 Z= 0.150 Angle : 0.599 11.691 34353 Z= 0.296 Chirality : 0.039 0.183 4195 Planarity : 0.005 0.053 4377 Dihedral : 4.107 18.712 3694 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.33 % Allowed : 22.55 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3477 helix: 1.58 (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 TRP 0.022 0.001 TRP B 636 HIS 0.008 0.001 HIS A 344 PHE 0.022 0.002 PHE C 977 TYR 0.018 0.001 TYR C 535 ARG 0.008 0.001 ARG B1078 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 1736) hydrogen bonds : angle 3.64925 ( 5184) covalent geometry : bond 0.00343 (25026) covalent geometry : angle 0.59862 (34353) *********************** 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 392 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 311 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 352 LEU cc_start: 0.4807 (OUTLIER) cc_final: 0.4490 (tp) REVERT: D 361 TRP cc_start: 0.5709 (OUTLIER) cc_final: 0.5464 (m-10) REVERT: D 723 TRP cc_start: 0.6313 (t60) cc_final: 0.6059 (t60) REVERT: C 723 TRP cc_start: 0.6443 (t60) cc_final: 0.6166 (t60) REVERT: A 723 TRP cc_start: 0.6490 (t60) cc_final: 0.6214 (t60) REVERT: A 792 THR cc_start: 0.5437 (OUTLIER) cc_final: 0.5179 (m) REVERT: A 1073 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6386 (mm-30) REVERT: B 352 LEU cc_start: 0.5080 (OUTLIER) cc_final: 0.4826 (tp) REVERT: B 361 TRP cc_start: 0.5570 (OUTLIER) cc_final: 0.5285 (m-10) REVERT: B 792 THR cc_start: 0.4592 (OUTLIER) cc_final: 0.4369 (m) outliers start: 81 outliers final: 60 residues processed: 370 average time/residue: 0.3181 time to fit residues: 191.6739 Evaluate side-chains 362 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 296 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 211 ILE 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 361 TRP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 843 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 357 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 628 VAL 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 843 VAL 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 84 LEU Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 270 VAL 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 584 SER Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 745 LEU 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 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 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 352 LEU 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 553 ILE Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 628 VAL 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 843 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 103 optimal weight: 10.0000 chunk 289 optimal weight: 20.0000 chunk 335 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 359 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 317 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 344 HIS C 349 GLN A 344 HIS A 349 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.221989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.210354 restraints weight = 36040.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.207351 restraints weight = 49863.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.206793 restraints weight = 57278.958| |-----------------------------------------------------------------------------| r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.3146 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= 0.200 Angle : 0.649 12.117 34353 Z= 0.322 Chirality : 0.041 0.166 4195 Planarity : 0.005 0.056 4377 Dihedral : 4.280 20.712 3694 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 5.24 % Allowed : 22.18 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3477 helix: 1.45 (0.11), residues: 2456 sheet: -0.16 (0.40), residues: 164 loop : -2.71 (0.18), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 636 HIS 0.008 0.001 HIS C 344 PHE 0.023 0.002 PHE D 977 TYR 0.019 0.001 TYR C 535 ARG 0.010 0.001 ARG B 346 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 1736) hydrogen bonds : angle 3.83316 ( 5184) covalent geometry : bond 0.00470 (25026) covalent geometry : angle 0.64897 (34353) *********************** 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 396 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 298 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 352 LEU cc_start: 0.5277 (OUTLIER) cc_final: 0.4855 (tp) REVERT: D 361 TRP cc_start: 0.5701 (OUTLIER) cc_final: 0.5475 (m-10) REVERT: D 723 TRP cc_start: 0.6355 (t60) cc_final: 0.6109 (t60) REVERT: D 740 MET cc_start: 0.7567 (tpp) cc_final: 0.7225 (tpp) REVERT: D 976 MET cc_start: 0.5745 (tmm) cc_final: 0.5324 (tmm) REVERT: C 723 TRP cc_start: 0.6541 (t60) cc_final: 0.6251 (t60) REVERT: C 976 MET cc_start: 0.5876 (tmm) cc_final: 0.5313 (tmm) REVERT: A 361 TRP cc_start: 0.5771 (OUTLIER) cc_final: 0.5504 (m-10) REVERT: A 723 TRP cc_start: 0.6535 (t60) cc_final: 0.6259 (t60) REVERT: A 792 THR cc_start: 0.5442 (OUTLIER) cc_final: 0.5177 (m) REVERT: B 229 LEU cc_start: 0.6029 (tt) cc_final: 0.5643 (tp) REVERT: B 352 LEU cc_start: 0.5105 (OUTLIER) cc_final: 0.4726 (tp) REVERT: B 361 TRP cc_start: 0.5602 (OUTLIER) cc_final: 0.5304 (m-10) outliers start: 98 outliers final: 78 residues processed: 373 average time/residue: 0.3212 time to fit residues: 195.7974 Evaluate side-chains 375 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 291 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 211 ILE 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 361 TRP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 415 TYR Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 584 SER 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 745 LEU Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 851 ILE 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 357 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 584 SER 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 745 LEU Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 843 VAL 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 84 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 361 TRP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 584 SER 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 745 LEU 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 809 CYS Chi-restraints excluded: chain A residue 821 VAL 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 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 352 LEU 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 553 ILE Chi-restraints excluded: chain B residue 584 SER 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 768 VAL Chi-restraints excluded: chain B residue 809 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 843 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 356 optimal weight: 0.9990 chunk 256 optimal weight: 50.0000 chunk 132 optimal weight: 0.0050 chunk 329 optimal weight: 4.9990 chunk 112 optimal weight: 30.0000 chunk 224 optimal weight: 0.5980 chunk 154 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 307 optimal weight: 3.9990 chunk 341 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 overall best weight: 2.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 344 HIS A 344 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.221453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.209735 restraints weight = 36122.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.206917 restraints weight = 49074.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.205253 restraints weight = 57125.745| |-----------------------------------------------------------------------------| r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25026 Z= 0.209 Angle : 0.665 12.335 34353 Z= 0.330 Chirality : 0.041 0.240 4195 Planarity : 0.005 0.057 4377 Dihedral : 4.343 21.535 3694 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.86 % Allowed : 23.25 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3477 helix: 1.40 (0.11), residues: 2459 sheet: -0.26 (0.40), residues: 164 loop : -2.71 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 636 HIS 0.010 0.001 HIS A 344 PHE 0.025 0.002 PHE D 977 TYR 0.018 0.002 TYR C 535 ARG 0.009 0.001 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 1736) hydrogen bonds : angle 3.87316 ( 5184) covalent geometry : bond 0.00492 (25026) covalent geometry : angle 0.66465 (34353) *********************** 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 393 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 302 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 352 LEU cc_start: 0.5329 (OUTLIER) cc_final: 0.4916 (tp) REVERT: D 361 TRP cc_start: 0.5610 (OUTLIER) cc_final: 0.5389 (m-10) REVERT: D 723 TRP cc_start: 0.6406 (t60) cc_final: 0.6115 (t60) REVERT: D 976 MET cc_start: 0.5709 (tmm) cc_final: 0.5445 (tmm) REVERT: C 723 TRP cc_start: 0.6575 (t60) cc_final: 0.6277 (t60) REVERT: A 361 TRP cc_start: 0.5809 (OUTLIER) cc_final: 0.5543 (m-10) REVERT: A 723 TRP cc_start: 0.6555 (t60) cc_final: 0.6277 (t60) REVERT: A 792 THR cc_start: 0.5457 (OUTLIER) cc_final: 0.5203 (m) REVERT: B 229 LEU cc_start: 0.6030 (tt) cc_final: 0.5552 (tp) REVERT: B 352 LEU cc_start: 0.5122 (OUTLIER) cc_final: 0.4714 (tp) REVERT: B 361 TRP cc_start: 0.5554 (OUTLIER) cc_final: 0.5267 (m-10) outliers start: 91 outliers final: 80 residues processed: 369 average time/residue: 0.3261 time to fit residues: 196.7166 Evaluate side-chains 382 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 296 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 211 ILE 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 361 TRP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 415 TYR Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 584 SER 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 745 LEU Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 851 ILE 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 357 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 584 SER 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 745 LEU Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 809 CYS Chi-restraints excluded: chain C residue 843 VAL 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 103 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 361 TRP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 584 SER 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 745 LEU 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 809 CYS 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 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 352 LEU 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 553 ILE Chi-restraints excluded: chain B residue 584 SER 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 745 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 809 CYS Chi-restraints excluded: chain B residue 843 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 311 optimal weight: 0.6980 chunk 5 optimal weight: 50.0000 chunk 322 optimal weight: 0.5980 chunk 196 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 13 optimal weight: 0.0030 chunk 126 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 chunk 192 optimal weight: 30.0000 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 344 HIS A 344 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.223406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.211775 restraints weight = 35734.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.208179 restraints weight = 45611.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.207560 restraints weight = 54219.856| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 0.3444 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= 0.137 Angle : 0.609 13.216 34353 Z= 0.297 Chirality : 0.038 0.229 4195 Planarity : 0.005 0.055 4377 Dihedral : 4.064 21.640 3694 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.33 % Allowed : 23.62 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.15), residues: 3477 helix: 1.71 (0.11), residues: 2458 sheet: -0.20 (0.40), residues: 164 loop : -2.62 (0.18), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 806 HIS 0.015 0.001 HIS C 850 PHE 0.014 0.001 PHE A 878 TYR 0.017 0.001 TYR C 535 ARG 0.009 0.001 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 1736) hydrogen bonds : angle 3.60951 ( 5184) covalent geometry : bond 0.00314 (25026) covalent geometry : angle 0.60854 (34353) ********************** 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 388 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 307 time to evaluate : 2.546 Fit side-chains revert: symmetry clash REVERT: D 352 LEU cc_start: 0.5418 (OUTLIER) cc_final: 0.5014 (tp) REVERT: D 361 TRP cc_start: 0.5475 (OUTLIER) cc_final: 0.5234 (m-10) REVERT: D 723 TRP cc_start: 0.6341 (t60) cc_final: 0.6122 (t60) REVERT: C 723 TRP cc_start: 0.6397 (t60) cc_final: 0.6161 (t60) REVERT: C 976 MET cc_start: 0.5779 (tmm) cc_final: 0.5425 (tmm) REVERT: A 723 TRP cc_start: 0.6477 (t60) cc_final: 0.6204 (t60) REVERT: A 792 THR cc_start: 0.5367 (OUTLIER) cc_final: 0.5091 (m) REVERT: B 229 LEU cc_start: 0.5893 (tt) cc_final: 0.5547 (tp) REVERT: B 352 LEU cc_start: 0.5143 (OUTLIER) cc_final: 0.4741 (tp) REVERT: B 361 TRP cc_start: 0.5559 (OUTLIER) cc_final: 0.5249 (m-10) REVERT: B 740 MET cc_start: 0.7487 (tpp) cc_final: 0.7175 (tpp) outliers start: 81 outliers final: 72 residues processed: 367 average time/residue: 0.3314 time to fit residues: 197.5574 Evaluate side-chains 373 residues out of total 3151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 296 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 211 ILE 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 361 TRP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 415 TYR Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 584 SER 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 745 LEU Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 792 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 851 ILE 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 357 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 628 VAL 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 809 CYS Chi-restraints excluded: chain C residue 843 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 103 ILE Chi-restraints excluded: chain A residue 211 ILE 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 392 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 584 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 745 LEU 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 809 CYS 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 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 352 LEU Chi-restraints excluded: chain B residue 357 LEU 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 584 SER Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 843 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 77 optimal weight: 30.0000 chunk 311 optimal weight: 0.9990 chunk 255 optimal weight: 50.0000 chunk 1 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 276 optimal weight: 0.0980 chunk 352 optimal weight: 0.8980 chunk 308 optimal weight: 7.9990 chunk 53 optimal weight: 0.3980 chunk 271 optimal weight: 40.0000 chunk 340 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 344 HIS A 344 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.225009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.212617 restraints weight = 34753.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.210217 restraints weight = 46824.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.208500 restraints weight = 43757.035| |-----------------------------------------------------------------------------| r_work (final): 0.4480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25026 Z= 0.130 Angle : 0.612 13.658 34353 Z= 0.297 Chirality : 0.038 0.236 4195 Planarity : 0.005 0.055 4377 Dihedral : 3.953 19.913 3694 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.38 % Allowed : 23.68 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.15), residues: 3477 helix: 1.81 (0.11), residues: 2462 sheet: -0.09 (0.40), residues: 164 loop : -2.62 (0.18), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 636 HIS 0.010 0.001 HIS A 344 PHE 0.017 0.001 PHE B 402 TYR 0.022 0.001 TYR A 801 ARG 0.011 0.001 ARG D 346 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 1736) hydrogen bonds : angle 3.54010 ( 5184) covalent geometry : bond 0.00296 (25026) covalent geometry : angle 0.61179 (34353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6805.47 seconds wall clock time: 118 minutes 48.08 seconds (7128.08 seconds total)