Starting phenix.real_space_refine on Mon Aug 25 23:42:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9goa_51495/08_2025/9goa_51495.cif Found real_map, /net/cci-nas-00/data/ceres_data/9goa_51495/08_2025/9goa_51495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9goa_51495/08_2025/9goa_51495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9goa_51495/08_2025/9goa_51495.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9goa_51495/08_2025/9goa_51495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9goa_51495/08_2025/9goa_51495.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.007 sd= 1.201 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 19932 2.51 5 N 5496 2.21 5 O 6120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31628 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 7907 Classifications: {'peptide': 1080} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PTRANS': 32, 'TRANS': 1047} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 679 Unresolved non-hydrogen angles: 875 Unresolved non-hydrogen dihedrals: 555 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'HIS:plan': 8, 'PHE:plan': 10, 'ASP:plan': 15, 'GLN:plan1': 8, 'ARG:plan': 8, 'GLU:plan': 10, 'TYR:plan': 11, 'ASN:plan1': 15} Unresolved non-hydrogen planarities: 379 Chain: "B" Number of atoms: 7907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 7907 Classifications: {'peptide': 1080} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PTRANS': 32, 'TRANS': 1047} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 679 Unresolved non-hydrogen angles: 875 Unresolved non-hydrogen dihedrals: 555 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'HIS:plan': 8, 'PHE:plan': 10, 'ASP:plan': 15, 'GLN:plan1': 8, 'ARG:plan': 8, 'GLU:plan': 10, 'TYR:plan': 11, 'ASN:plan1': 15} Unresolved non-hydrogen planarities: 379 Chain: "C" Number of atoms: 7907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 7907 Classifications: {'peptide': 1080} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PTRANS': 32, 'TRANS': 1047} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 679 Unresolved non-hydrogen angles: 875 Unresolved non-hydrogen dihedrals: 555 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'HIS:plan': 8, 'PHE:plan': 10, 'ASP:plan': 15, 'GLN:plan1': 8, 'ARG:plan': 8, 'GLU:plan': 10, 'TYR:plan': 11, 'ASN:plan1': 15} Unresolved non-hydrogen planarities: 379 Chain: "D" Number of atoms: 7907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 7907 Classifications: {'peptide': 1080} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PTRANS': 32, 'TRANS': 1047} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 679 Unresolved non-hydrogen angles: 875 Unresolved non-hydrogen dihedrals: 555 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'HIS:plan': 8, 'PHE:plan': 10, 'ASP:plan': 15, 'GLN:plan1': 8, 'ARG:plan': 8, 'GLU:plan': 10, 'TYR:plan': 11, 'ASN:plan1': 15} Unresolved non-hydrogen planarities: 379 Time building chain proxies: 7.33, per 1000 atoms: 0.23 Number of scatterers: 31628 At special positions: 0 Unit cell: (178.06, 175.74, 160.08, 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 6120 8.00 N 5496 7.00 C 19932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8168 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 12 sheets defined 62.4% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 116 through 182 Proline residue: A 160 - end of helix removed outlier: 3.698A pdb=" N GLU A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.640A pdb=" N HIS A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 234 through 269 removed outlier: 3.653A pdb=" N VAL A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 295 removed outlier: 3.577A pdb=" N TYR A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 326 through 350 Processing helix chain 'A' and resid 456 through 463 Processing helix chain 'A' and resid 467 through 481 Processing helix chain 'A' and resid 493 through 502 Processing helix chain 'A' and resid 503 through 512 removed outlier: 3.733A pdb=" N PHE A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.663A pdb=" N LEU A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 515 through 520' Processing helix chain 'A' and resid 528 through 537 Processing helix chain 'A' and resid 538 through 549 removed outlier: 3.557A pdb=" N VAL A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 572 through 581 Processing helix chain 'A' and resid 596 through 605 removed outlier: 3.599A pdb=" N TYR A 600 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 615 removed outlier: 3.800A pdb=" N GLN A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 637 removed outlier: 3.637A pdb=" N LEU A 633 " --> pdb=" O THR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.886A pdb=" N LYS A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 672 Processing helix chain 'A' and resid 673 through 684 removed outlier: 3.616A pdb=" N THR A 677 " --> pdb=" O TYR A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 705 Processing helix chain 'A' and resid 708 through 718 removed outlier: 3.635A pdb=" N ALA A 712 " --> pdb=" O HIS A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 743 through 753 Processing helix chain 'A' and resid 765 through 771 Processing helix chain 'A' and resid 776 through 786 removed outlier: 3.901A pdb=" N GLN A 780 " --> pdb=" O PRO A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 807 Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 831 through 840 removed outlier: 3.596A pdb=" N GLY A 835 " --> pdb=" O MET A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 852 Processing helix chain 'A' and resid 853 through 858 Processing helix chain 'A' and resid 865 through 874 Processing helix chain 'A' and resid 875 through 884 Processing helix chain 'A' and resid 898 through 907 removed outlier: 3.667A pdb=" N ALA A 902 " --> pdb=" O ALA A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 919 Processing helix chain 'A' and resid 931 through 939 Processing helix chain 'A' and resid 941 through 951 removed outlier: 3.659A pdb=" N GLU A 951 " --> pdb=" O TYR A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 968 removed outlier: 3.594A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 986 removed outlier: 3.523A pdb=" N PHE A 978 " --> pdb=" O ALA A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 999 removed outlier: 3.517A pdb=" N VAL A 992 " --> pdb=" O ARG A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1015 Processing helix chain 'A' and resid 1016 through 1026 Processing helix chain 'A' and resid 1038 through 1047 removed outlier: 4.286A pdb=" N TYR A1042 " --> pdb=" O THR A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1059 Processing helix chain 'A' and resid 1071 through 1080 removed outlier: 4.370A pdb=" N LYS A1075 " --> pdb=" O THR A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1092 removed outlier: 4.094A pdb=" N VAL A1085 " --> pdb=" O HIS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1112 Processing helix chain 'A' and resid 1114 through 1125 Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.996A pdb=" N LEU A1144 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1160 Processing helix chain 'A' and resid 1174 through 1180 removed outlier: 3.713A pdb=" N ASP A1180 " --> pdb=" O ASP A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1193 removed outlier: 3.712A pdb=" N LYS A1193 " --> pdb=" O TYR A1189 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 182 Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 183 through 192 Processing helix chain 'B' and resid 196 through 204 removed outlier: 3.728A pdb=" N HIS B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 223 removed outlier: 3.547A pdb=" N LEU B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 270 removed outlier: 3.698A pdb=" N VAL B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 270 " --> pdb=" O HIS B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 295 Processing helix chain 'B' and resid 303 through 319 removed outlier: 4.344A pdb=" N ASP B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG B 308 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 350 Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 467 through 481 Processing helix chain 'B' and resid 493 through 502 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.620A pdb=" N PHE B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 removed outlier: 3.963A pdb=" N LEU B 519 " --> pdb=" O LYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 537 Processing helix chain 'B' and resid 538 through 549 removed outlier: 3.601A pdb=" N VAL B 542 " --> pdb=" O ASN B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 571 removed outlier: 3.666A pdb=" N LEU B 566 " --> pdb=" O THR B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 582 removed outlier: 3.997A pdb=" N PHE B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 582 " --> pdb=" O ARG B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 605 removed outlier: 4.465A pdb=" N ARG B 603 " --> pdb=" O HIS B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 615 removed outlier: 3.754A pdb=" N GLN B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 637 removed outlier: 4.143A pdb=" N LEU B 633 " --> pdb=" O THR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 650 removed outlier: 3.659A pdb=" N ALA B 643 " --> pdb=" O ASP B 639 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 672 removed outlier: 3.511A pdb=" N TYR B 667 " --> pdb=" O THR B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 684 removed outlier: 3.770A pdb=" N THR B 677 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS B 684 " --> pdb=" O LEU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 705 Processing helix chain 'B' and resid 708 through 718 removed outlier: 3.597A pdb=" N ALA B 712 " --> pdb=" O HIS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 741 removed outlier: 3.754A pdb=" N LEU B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 753 Processing helix chain 'B' and resid 765 through 773 Processing helix chain 'B' and resid 776 through 786 Processing helix chain 'B' and resid 798 through 806 Processing helix chain 'B' and resid 808 through 818 Processing helix chain 'B' and resid 831 through 839 removed outlier: 4.003A pdb=" N GLY B 835 " --> pdb=" O MET B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 852 Processing helix chain 'B' and resid 853 through 857 removed outlier: 3.856A pdb=" N VAL B 856 " --> pdb=" O ALA B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 874 removed outlier: 4.113A pdb=" N LEU B 869 " --> pdb=" O THR B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 885 Processing helix chain 'B' and resid 898 through 907 Processing helix chain 'B' and resid 909 through 918 Processing helix chain 'B' and resid 931 through 940 removed outlier: 3.608A pdb=" N TYR B 935 " --> pdb=" O ASN B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 951 Processing helix chain 'B' and resid 961 through 968 Processing helix chain 'B' and resid 974 through 986 Processing helix chain 'B' and resid 988 through 999 Processing helix chain 'B' and resid 1006 through 1015 Processing helix chain 'B' and resid 1017 through 1026 Processing helix chain 'B' and resid 1038 through 1047 removed outlier: 4.527A pdb=" N TYR B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1058 Processing helix chain 'B' and resid 1072 through 1079 Processing helix chain 'B' and resid 1081 through 1092 removed outlier: 3.988A pdb=" N GLY B1092 " --> pdb=" O LEU B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1112 Processing helix chain 'B' and resid 1114 through 1125 Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.231A pdb=" N LEU B1144 " --> pdb=" O THR B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1159 Processing helix chain 'B' and resid 1184 through 1193 Processing helix chain 'C' and resid 117 through 181 Proline residue: C 160 - end of helix Processing helix chain 'C' and resid 183 through 192 Processing helix chain 'C' and resid 196 through 204 removed outlier: 3.641A pdb=" N HIS C 200 " --> pdb=" O GLY C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 234 through 271 removed outlier: 3.779A pdb=" N LYS C 270 " --> pdb=" O HIS C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 295 removed outlier: 3.594A pdb=" N GLU C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 320 removed outlier: 3.562A pdb=" N GLU C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 350 Processing helix chain 'C' and resid 453 through 463 Processing helix chain 'C' and resid 467 through 481 Processing helix chain 'C' and resid 493 through 502 Processing helix chain 'C' and resid 503 through 512 removed outlier: 3.639A pdb=" N MET C 507 " --> pdb=" O ASN C 503 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 512 " --> pdb=" O PHE C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 520 Processing helix chain 'C' and resid 528 through 537 Processing helix chain 'C' and resid 539 through 548 Processing helix chain 'C' and resid 562 through 571 Processing helix chain 'C' and resid 572 through 580 removed outlier: 3.645A pdb=" N PHE C 576 " --> pdb=" O PHE C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 605 removed outlier: 3.647A pdb=" N TYR C 600 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG C 603 " --> pdb=" O HIS C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 615 removed outlier: 3.558A pdb=" N GLN C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 636 Processing helix chain 'C' and resid 639 through 650 removed outlier: 3.523A pdb=" N ALA C 643 " --> pdb=" O ASP C 639 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 672 Processing helix chain 'C' and resid 673 through 684 Processing helix chain 'C' and resid 698 through 705 Processing helix chain 'C' and resid 708 through 718 removed outlier: 3.593A pdb=" N ALA C 712 " --> pdb=" O HIS C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 741 Processing helix chain 'C' and resid 742 through 753 removed outlier: 3.949A pdb=" N LEU C 746 " --> pdb=" O ARG C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 765 through 772 Processing helix chain 'C' and resid 776 through 786 removed outlier: 3.699A pdb=" N GLN C 780 " --> pdb=" O PRO C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 807 Processing helix chain 'C' and resid 808 through 818 Processing helix chain 'C' and resid 831 through 840 removed outlier: 3.882A pdb=" N GLY C 835 " --> pdb=" O MET C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 852 Processing helix chain 'C' and resid 853 through 858 removed outlier: 3.511A pdb=" N VAL C 856 " --> pdb=" O ALA C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 874 Processing helix chain 'C' and resid 875 through 886 removed outlier: 3.516A pdb=" N ILE C 879 " --> pdb=" O HIS C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 907 Processing helix chain 'C' and resid 908 through 918 Processing helix chain 'C' and resid 931 through 940 removed outlier: 3.817A pdb=" N TYR C 935 " --> pdb=" O ASN C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 951 removed outlier: 3.663A pdb=" N VAL C 945 " --> pdb=" O HIS C 941 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU C 951 " --> pdb=" O TYR C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 968 Processing helix chain 'C' and resid 974 through 986 Processing helix chain 'C' and resid 988 through 999 Processing helix chain 'C' and resid 1006 through 1015 Processing helix chain 'C' and resid 1016 through 1026 Processing helix chain 'C' and resid 1038 through 1047 removed outlier: 3.928A pdb=" N TYR C1042 " --> pdb=" O THR C1038 " (cutoff:3.500A) Processing helix chain 'C' and resid 1048 through 1058 Processing helix chain 'C' and resid 1071 through 1079 Processing helix chain 'C' and resid 1081 through 1092 Processing helix chain 'C' and resid 1104 through 1112 Processing helix chain 'C' and resid 1114 through 1124 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.204A pdb=" N TYR C1147 " --> pdb=" O HIS C1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 1151 through 1160 Processing helix chain 'C' and resid 1174 through 1181 Processing helix chain 'C' and resid 1184 through 1194 Processing helix chain 'D' and resid 117 through 181 Proline residue: D 160 - end of helix removed outlier: 3.734A pdb=" N GLU D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 192 Processing helix chain 'D' and resid 196 through 204 Processing helix chain 'D' and resid 212 through 223 removed outlier: 3.956A pdb=" N LEU D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 270 removed outlier: 3.581A pdb=" N PHE D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU D 257 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU D 258 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN D 259 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS D 270 " --> pdb=" O HIS D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 295 removed outlier: 3.576A pdb=" N GLU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 320 removed outlier: 4.226A pdb=" N GLU D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 350 Processing helix chain 'D' and resid 457 through 463 Processing helix chain 'D' and resid 467 through 481 Processing helix chain 'D' and resid 493 through 502 Processing helix chain 'D' and resid 504 through 512 Processing helix chain 'D' and resid 515 through 520 removed outlier: 3.956A pdb=" N ASN D 520 " --> pdb=" O SER D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 537 Processing helix chain 'D' and resid 539 through 549 Processing helix chain 'D' and resid 562 through 571 Processing helix chain 'D' and resid 573 through 580 Processing helix chain 'D' and resid 596 through 605 removed outlier: 3.907A pdb=" N TYR D 600 " --> pdb=" O THR D 596 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG D 603 " --> pdb=" O HIS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 614 Processing helix chain 'D' and resid 629 through 638 Processing helix chain 'D' and resid 639 through 650 Processing helix chain 'D' and resid 663 through 672 removed outlier: 3.562A pdb=" N TYR D 667 " --> pdb=" O THR D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 684 removed outlier: 3.753A pdb=" N THR D 677 " --> pdb=" O TYR D 673 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS D 684 " --> pdb=" O LEU D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 705 Processing helix chain 'D' and resid 708 through 718 removed outlier: 3.642A pdb=" N ALA D 712 " --> pdb=" O HIS D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 731 removed outlier: 3.921A pdb=" N ILE D 731 " --> pdb=" O LEU D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 741 Processing helix chain 'D' and resid 742 through 753 Processing helix chain 'D' and resid 765 through 772 removed outlier: 3.825A pdb=" N ALA D 771 " --> pdb=" O LEU D 767 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET D 772 " --> pdb=" O HIS D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 786 removed outlier: 3.827A pdb=" N ILE D 781 " --> pdb=" O GLU D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 807 Processing helix chain 'D' and resid 808 through 818 Processing helix chain 'D' and resid 831 through 838 removed outlier: 3.851A pdb=" N MET D 838 " --> pdb=" O HIS D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 852 Processing helix chain 'D' and resid 853 through 858 removed outlier: 3.591A pdb=" N VAL D 856 " --> pdb=" O ALA D 853 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 858 " --> pdb=" O VAL D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 873 Processing helix chain 'D' and resid 875 through 884 Processing helix chain 'D' and resid 898 through 907 Processing helix chain 'D' and resid 909 through 918 removed outlier: 3.605A pdb=" N LYS D 918 " --> pdb=" O TYR D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 940 removed outlier: 3.953A pdb=" N TYR D 935 " --> pdb=" O ASN D 931 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY D 940 " --> pdb=" O ALA D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 941 through 951 removed outlier: 3.609A pdb=" N VAL D 945 " --> pdb=" O HIS D 941 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D 951 " --> pdb=" O TYR D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 968 Processing helix chain 'D' and resid 974 through 986 Processing helix chain 'D' and resid 989 through 999 Processing helix chain 'D' and resid 1006 through 1015 Processing helix chain 'D' and resid 1016 through 1026 removed outlier: 3.845A pdb=" N VAL D1020 " --> pdb=" O HIS D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1047 Processing helix chain 'D' and resid 1048 through 1058 Processing helix chain 'D' and resid 1071 through 1079 Processing helix chain 'D' and resid 1081 through 1091 Processing helix chain 'D' and resid 1104 through 1112 Processing helix chain 'D' and resid 1114 through 1125 Processing helix chain 'D' and resid 1141 through 1148 Processing helix chain 'D' and resid 1151 through 1161 Processing helix chain 'D' and resid 1174 through 1180 Processing helix chain 'D' and resid 1184 through 1191 removed outlier: 4.206A pdb=" N TYR D1189 " --> pdb=" O ASN D1185 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D1190 " --> pdb=" O ILE D1186 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS D1191 " --> pdb=" O VAL D1187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AA2, first strand: chain 'A' and resid 364 through 366 removed outlier: 3.513A pdb=" N GLN A 364 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 406 through 407 removed outlier: 6.409A pdb=" N VAL A 427 " --> pdb=" O GLU A 443 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU A 443 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A 429 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AA5, first strand: chain 'B' and resid 364 through 366 removed outlier: 3.829A pdb=" N GLN B 364 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 406 through 408 removed outlier: 4.507A pdb=" N ARG B 382 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 427 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU B 443 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 429 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AA8, first strand: chain 'C' and resid 364 through 366 removed outlier: 3.661A pdb=" N GLN C 364 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 384 through 390 removed outlier: 6.277A pdb=" N VAL C 427 " --> pdb=" O GLU C 443 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU C 443 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL C 429 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 354 through 355 Processing sheet with id=AB2, first strand: chain 'D' and resid 364 through 366 removed outlier: 3.701A pdb=" N GLN D 364 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 384 through 390 removed outlier: 6.442A pdb=" N VAL D 427 " --> pdb=" O GLU D 443 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU D 443 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 429 " --> pdb=" O VAL D 441 " (cutoff:3.500A) 1756 hydrogen bonds defined for protein. 5223 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.06 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 1 1.09 - 1.27: 5577 1.27 - 1.45: 8136 1.45 - 1.63: 18294 1.63 - 1.81: 148 Bond restraints: 32156 Sorted by residual: bond pdb=" CB PRO C 465 " pdb=" CG PRO C 465 " ideal model delta sigma weight residual 1.492 0.909 0.583 5.00e-02 4.00e+02 1.36e+02 bond pdb=" CG PRO C 465 " pdb=" CD PRO C 465 " ideal model delta sigma weight residual 1.503 1.231 0.272 3.40e-02 8.65e+02 6.39e+01 bond pdb=" CA PRO C 465 " pdb=" CB PRO C 465 " ideal model delta sigma weight residual 1.534 1.567 -0.033 1.40e-02 5.10e+03 5.68e+00 bond pdb=" CB PRO B 227 " pdb=" CG PRO B 227 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 3.97e+00 bond pdb=" CB PRO B 583 " pdb=" CG PRO B 583 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.35e+00 ... (remaining 32151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.66: 43689 14.66 - 29.31: 2 29.31 - 43.97: 0 43.97 - 58.63: 0 58.63 - 73.28: 1 Bond angle restraints: 43692 Sorted by residual: angle pdb=" CB PRO C 465 " pdb=" CG PRO C 465 " pdb=" CD PRO C 465 " ideal model delta sigma weight residual 106.10 179.38 -73.28 3.20e+00 9.77e-02 5.24e+02 angle pdb=" N PRO C 465 " pdb=" CD PRO C 465 " pdb=" CG PRO C 465 " ideal model delta sigma weight residual 103.20 78.72 24.48 1.50e+00 4.44e-01 2.66e+02 angle pdb=" CA PRO C 465 " pdb=" CB PRO C 465 " pdb=" CG PRO C 465 " ideal model delta sigma weight residual 104.50 75.74 28.76 1.90e+00 2.77e-01 2.29e+02 angle pdb=" CA PRO C 465 " pdb=" N PRO C 465 " pdb=" CD PRO C 465 " ideal model delta sigma weight residual 112.00 102.52 9.48 1.40e+00 5.10e-01 4.58e+01 angle pdb=" CA MET C 332 " pdb=" CB MET C 332 " pdb=" CG MET C 332 " ideal model delta sigma weight residual 114.10 123.31 -9.21 2.00e+00 2.50e-01 2.12e+01 ... (remaining 43687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17781 17.96 - 35.91: 1332 35.91 - 53.87: 204 53.87 - 71.82: 36 71.82 - 89.78: 23 Dihedral angle restraints: 19376 sinusoidal: 6764 harmonic: 12612 Sorted by residual: dihedral pdb=" CA LYS B 326 " pdb=" C LYS B 326 " pdb=" N ASN B 327 " pdb=" CA ASN B 327 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" N PRO C 465 " pdb=" CG PRO C 465 " pdb=" CD PRO C 465 " pdb=" CB PRO C 465 " ideal model delta sinusoidal sigma weight residual -30.00 -85.61 55.61 1 1.50e+01 4.44e-03 1.86e+01 dihedral pdb=" CA LYS A1182 " pdb=" C LYS A1182 " pdb=" N PHE A1183 " pdb=" CA PHE A1183 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 19373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3876 0.045 - 0.090: 991 0.090 - 0.134: 191 0.134 - 0.179: 9 0.179 - 0.224: 5 Chirality restraints: 5072 Sorted by residual: chirality pdb=" CA GLU B 584 " pdb=" N GLU B 584 " pdb=" C GLU B 584 " pdb=" CB GLU B 584 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA THR A 373 " pdb=" N THR A 373 " pdb=" C THR A 373 " pdb=" CB THR A 373 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" CA THR C 373 " pdb=" N THR C 373 " pdb=" C THR C 373 " pdb=" CB THR C 373 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.14e-01 ... (remaining 5069 not shown) Planarity restraints: 5768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 226 " -0.074 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO B 227 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO B 227 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 227 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 404 " 0.065 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO C 405 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO C 405 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 405 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 404 " -0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO A 405 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 405 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 405 " -0.048 5.00e-02 4.00e+02 ... (remaining 5765 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 296 2.63 - 3.20: 30568 3.20 - 3.77: 49012 3.77 - 4.33: 64137 4.33 - 4.90: 103005 Nonbonded interactions: 247018 Sorted by model distance: nonbonded pdb=" OD2 ASP A 173 " pdb=" OH TYR A 244 " model vdw 2.068 3.040 nonbonded pdb=" O VAL B 738 " pdb=" OH TYR B 775 " model vdw 2.070 3.040 nonbonded pdb=" O ASP C 155 " pdb=" OG SER C 159 " model vdw 2.108 3.040 nonbonded pdb=" O GLU A 203 " pdb=" OG1 THR A 206 " model vdw 2.150 3.040 nonbonded pdb=" OG SER A 536 " pdb=" OD1 ASN A 538 " model vdw 2.160 3.040 ... (remaining 247013 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.060 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 26.740 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 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 0.583 32156 Z= 0.142 Angle : 0.709 73.282 43692 Z= 0.348 Chirality : 0.040 0.224 5072 Planarity : 0.005 0.109 5768 Dihedral : 13.299 89.775 11208 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.12), residues: 4312 helix: 1.00 (0.10), residues: 2512 sheet: 0.64 (0.44), residues: 151 loop : -0.74 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 205 TYR 0.025 0.001 TYR A 764 PHE 0.033 0.002 PHE A 217 TRP 0.029 0.001 TRP A 640 HIS 0.008 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00437 (32156) covalent geometry : angle 0.70884 (43692) hydrogen bonds : bond 0.14496 ( 1756) hydrogen bonds : angle 5.61579 ( 5223) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 622 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 916 PHE cc_start: 0.7121 (m-80) cc_final: 0.6850 (m-80) REVERT: C 614 ASN cc_start: 0.7081 (t0) cc_final: 0.6794 (t0) REVERT: C 910 ASP cc_start: 0.8470 (t70) cc_final: 0.7114 (t70) outliers start: 0 outliers final: 0 residues processed: 622 average time/residue: 0.1966 time to fit residues: 202.2224 Evaluate side-chains 504 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 351 GLN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN A 785 GLN A 846 GLN B 200 HIS ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 868 ASN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN C 638 ASN ** C 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 873 ASN C 885 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN D 460 ASN D 490 HIS D 818 ASN D 939 ASN D 959 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.202256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.159181 restraints weight = 55928.392| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 3.72 r_work: 0.3992 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 32156 Z= 0.151 Angle : 0.601 9.248 43692 Z= 0.316 Chirality : 0.042 0.224 5072 Planarity : 0.005 0.070 5768 Dihedral : 3.989 43.775 4568 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 1.50 % Allowed : 9.57 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.12), residues: 4312 helix: 1.08 (0.10), residues: 2577 sheet: 0.14 (0.43), residues: 153 loop : -0.85 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 205 TYR 0.029 0.002 TYR C 914 PHE 0.044 0.002 PHE C 882 TRP 0.019 0.002 TRP A 640 HIS 0.008 0.001 HIS C 599 Details of bonding type rmsd covalent geometry : bond 0.00349 (32156) covalent geometry : angle 0.60094 (43692) hydrogen bonds : bond 0.03940 ( 1756) hydrogen bonds : angle 4.44174 ( 5223) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 554 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 SER cc_start: 0.8735 (m) cc_final: 0.8486 (p) REVERT: A 704 ILE cc_start: 0.6476 (mt) cc_final: 0.6250 (mt) REVERT: A 766 PRO cc_start: 0.7517 (Cg_exo) cc_final: 0.7098 (Cg_endo) REVERT: B 150 MET cc_start: 0.7113 (mpp) cc_final: 0.6770 (mpp) REVERT: B 166 ASN cc_start: 0.8584 (m110) cc_final: 0.8204 (m110) REVERT: B 489 ASP cc_start: 0.7670 (t0) cc_final: 0.7400 (t0) REVERT: B 538 ASN cc_start: 0.8426 (m110) cc_final: 0.8181 (m110) REVERT: B 547 GLN cc_start: 0.8027 (mt0) cc_final: 0.7381 (tm-30) REVERT: B 916 PHE cc_start: 0.8121 (m-80) cc_final: 0.7730 (m-80) REVERT: C 142 MET cc_start: 0.7502 (ptt) cc_final: 0.7237 (ppp) REVERT: C 248 THR cc_start: 0.8451 (p) cc_final: 0.8115 (t) REVERT: C 492 ARG cc_start: 0.7903 (tpp80) cc_final: 0.7603 (mmm-85) REVERT: C 910 ASP cc_start: 0.8905 (t70) cc_final: 0.7978 (t70) REVERT: C 941 HIS cc_start: 0.4885 (m170) cc_final: 0.4678 (m170) outliers start: 45 outliers final: 35 residues processed: 578 average time/residue: 0.2048 time to fit residues: 193.6229 Evaluate side-chains 536 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 501 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 854 THR Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 586 ASN Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 885 GLN Chi-restraints excluded: chain C residue 932 PHE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 784 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 412 optimal weight: 30.0000 chunk 99 optimal weight: 50.0000 chunk 312 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 344 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 332 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 392 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 284 ASN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN B 941 HIS C 553 ASN C 873 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 HIS D 638 ASN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 818 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.198004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.152580 restraints weight = 57023.343| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 3.64 r_work: 0.3877 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32156 Z= 0.179 Angle : 0.613 8.771 43692 Z= 0.323 Chirality : 0.042 0.207 5072 Planarity : 0.005 0.063 5768 Dihedral : 4.078 35.950 4568 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 2.33 % Allowed : 13.40 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.12), residues: 4312 helix: 1.06 (0.10), residues: 2594 sheet: 0.02 (0.40), residues: 159 loop : -0.90 (0.14), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 205 TYR 0.037 0.002 TYR C 914 PHE 0.032 0.002 PHE C 882 TRP 0.014 0.002 TRP A 640 HIS 0.007 0.001 HIS A 496 Details of bonding type rmsd covalent geometry : bond 0.00421 (32156) covalent geometry : angle 0.61265 (43692) hydrogen bonds : bond 0.04150 ( 1756) hydrogen bonds : angle 4.40768 ( 5223) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 535 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ASP cc_start: 0.7284 (p0) cc_final: 0.7070 (p0) REVERT: A 766 PRO cc_start: 0.7613 (Cg_exo) cc_final: 0.7253 (Cg_endo) REVERT: A 805 PHE cc_start: 0.8431 (m-10) cc_final: 0.8188 (m-80) REVERT: B 142 MET cc_start: 0.7377 (ptt) cc_final: 0.7084 (ptm) REVERT: B 150 MET cc_start: 0.7188 (mpp) cc_final: 0.6868 (mpp) REVERT: B 538 ASN cc_start: 0.8474 (m110) cc_final: 0.8233 (m110) REVERT: B 564 LEU cc_start: 0.8106 (mt) cc_final: 0.7815 (mt) REVERT: B 592 LYS cc_start: 0.8778 (tttt) cc_final: 0.8334 (ttpp) REVERT: B 916 PHE cc_start: 0.8001 (m-80) cc_final: 0.6861 (m-80) REVERT: B 949 MET cc_start: 0.7822 (mmp) cc_final: 0.7365 (mtm) REVERT: C 142 MET cc_start: 0.7415 (ptt) cc_final: 0.7149 (ppp) REVERT: C 248 THR cc_start: 0.8454 (p) cc_final: 0.8168 (t) REVERT: C 492 ARG cc_start: 0.8117 (tpp80) cc_final: 0.7777 (mmm-85) REVERT: C 888 ASP cc_start: 0.4956 (t70) cc_final: 0.4712 (t70) REVERT: C 910 ASP cc_start: 0.8834 (t70) cc_final: 0.8051 (t70) REVERT: D 269 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6966 (mm-30) REVERT: D 548 ARG cc_start: 0.8258 (tpt90) cc_final: 0.7616 (tpp-160) REVERT: D 744 GLN cc_start: 0.8458 (mp10) cc_final: 0.8151 (tp-100) outliers start: 70 outliers final: 48 residues processed: 577 average time/residue: 0.2031 time to fit residues: 190.5846 Evaluate side-chains 539 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 491 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 932 PHE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 784 ASP Chi-restraints excluded: chain D residue 927 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 214 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 345 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 263 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 332 optimal weight: 1.9990 chunk 409 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 553 ASN ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN D 213 GLN ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 ASN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 818 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.197963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.152818 restraints weight = 56195.849| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 3.89 r_work: 0.3877 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32156 Z= 0.136 Angle : 0.579 9.104 43692 Z= 0.304 Chirality : 0.041 0.200 5072 Planarity : 0.005 0.061 5768 Dihedral : 3.972 28.740 4568 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 2.47 % Allowed : 15.30 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.12), residues: 4312 helix: 1.19 (0.10), residues: 2591 sheet: -0.04 (0.41), residues: 152 loop : -0.86 (0.14), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 892 TYR 0.038 0.002 TYR C 914 PHE 0.036 0.002 PHE C 882 TRP 0.012 0.002 TRP B 640 HIS 0.004 0.001 HIS A 496 Details of bonding type rmsd covalent geometry : bond 0.00314 (32156) covalent geometry : angle 0.57859 (43692) hydrogen bonds : bond 0.03746 ( 1756) hydrogen bonds : angle 4.26403 ( 5223) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 536 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 TYR cc_start: 0.7321 (t80) cc_final: 0.7102 (t80) REVERT: A 370 ASP cc_start: 0.7203 (p0) cc_final: 0.6770 (p0) REVERT: A 555 LYS cc_start: 0.8331 (mtpp) cc_final: 0.8028 (tttp) REVERT: A 766 PRO cc_start: 0.7581 (Cg_exo) cc_final: 0.7285 (Cg_endo) REVERT: A 805 PHE cc_start: 0.8546 (m-10) cc_final: 0.8344 (m-10) REVERT: B 150 MET cc_start: 0.7156 (mpp) cc_final: 0.6829 (mpp) REVERT: B 592 LYS cc_start: 0.8799 (tttt) cc_final: 0.8353 (ttpp) REVERT: B 745 ILE cc_start: 0.3693 (OUTLIER) cc_final: 0.3321 (tp) REVERT: B 916 PHE cc_start: 0.8125 (m-80) cc_final: 0.7539 (m-80) REVERT: C 142 MET cc_start: 0.7320 (ptt) cc_final: 0.7104 (ppp) REVERT: C 161 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.6904 (tt) REVERT: C 248 THR cc_start: 0.8537 (p) cc_final: 0.8136 (t) REVERT: C 409 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8317 (ttm170) REVERT: C 492 ARG cc_start: 0.8237 (tpp80) cc_final: 0.7837 (mmm-85) REVERT: C 821 ASN cc_start: 0.7892 (m-40) cc_final: 0.7662 (m-40) REVERT: C 910 ASP cc_start: 0.8816 (t70) cc_final: 0.8179 (t0) REVERT: D 548 ARG cc_start: 0.8237 (tpt90) cc_final: 0.7532 (tpp-160) outliers start: 74 outliers final: 53 residues processed: 587 average time/residue: 0.1928 time to fit residues: 185.4631 Evaluate side-chains 552 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 496 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 409 ARG Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 586 ASN Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 918 LYS Chi-restraints excluded: chain C residue 932 PHE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 784 ASP Chi-restraints excluded: chain D residue 927 ASN Chi-restraints excluded: chain D residue 942 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 327 optimal weight: 5.9990 chunk 391 optimal weight: 5.9990 chunk 289 optimal weight: 2.9990 chunk 340 optimal weight: 3.9990 chunk 390 optimal weight: 3.9990 chunk 329 optimal weight: 3.9990 chunk 95 optimal weight: 0.0050 chunk 162 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 167 ASN A 553 ASN A 586 ASN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN C 553 ASN ** C 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 HIS ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 818 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.196230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.155682 restraints weight = 58301.617| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 4.80 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32156 Z= 0.151 Angle : 0.598 9.424 43692 Z= 0.314 Chirality : 0.041 0.224 5072 Planarity : 0.005 0.061 5768 Dihedral : 3.991 22.310 4568 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.62 % Favored : 96.36 % Rotamer: Outliers : 3.00 % Allowed : 15.90 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.12), residues: 4312 helix: 1.20 (0.10), residues: 2598 sheet: -0.04 (0.40), residues: 152 loop : -0.84 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 424 TYR 0.041 0.002 TYR C 914 PHE 0.036 0.002 PHE C 882 TRP 0.013 0.002 TRP B 640 HIS 0.005 0.001 HIS A 496 Details of bonding type rmsd covalent geometry : bond 0.00352 (32156) covalent geometry : angle 0.59774 (43692) hydrogen bonds : bond 0.03829 ( 1756) hydrogen bonds : angle 4.28951 ( 5223) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 517 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 GLU cc_start: 0.8526 (pp20) cc_final: 0.7618 (pp20) REVERT: A 370 ASP cc_start: 0.6965 (p0) cc_final: 0.6506 (p0) REVERT: A 780 GLN cc_start: 0.6348 (mm-40) cc_final: 0.6026 (mm-40) REVERT: A 805 PHE cc_start: 0.8662 (m-10) cc_final: 0.8422 (m-10) REVERT: B 150 MET cc_start: 0.6978 (mpp) cc_final: 0.6616 (mpp) REVERT: B 175 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6616 (mm-30) REVERT: B 222 GLU cc_start: 0.7715 (pt0) cc_final: 0.7488 (pt0) REVERT: B 577 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7099 (mp10) REVERT: B 592 LYS cc_start: 0.8723 (tttt) cc_final: 0.8238 (ttpp) REVERT: B 716 MET cc_start: 0.5451 (ptt) cc_final: 0.5236 (ptt) REVERT: B 916 PHE cc_start: 0.8192 (m-80) cc_final: 0.7588 (m-80) REVERT: C 248 THR cc_start: 0.8801 (p) cc_final: 0.8544 (m) REVERT: C 409 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7737 (ttm170) REVERT: C 492 ARG cc_start: 0.7807 (tpp80) cc_final: 0.7486 (mmm-85) REVERT: C 881 TYR cc_start: 0.8706 (t80) cc_final: 0.8236 (t80) REVERT: C 910 ASP cc_start: 0.8901 (t70) cc_final: 0.8303 (t0) REVERT: D 512 PHE cc_start: 0.5249 (OUTLIER) cc_final: 0.4167 (m-80) REVERT: D 580 MET cc_start: 0.8554 (mmm) cc_final: 0.8320 (mmp) REVERT: D 667 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: D 673 TYR cc_start: 0.7827 (m-80) cc_final: 0.7589 (m-80) REVERT: D 744 GLN cc_start: 0.8521 (mp10) cc_final: 0.8070 (tp-100) outliers start: 90 outliers final: 62 residues processed: 571 average time/residue: 0.1997 time to fit residues: 185.5768 Evaluate side-chains 556 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 490 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 409 ARG Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 586 ASN Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 930 MET Chi-restraints excluded: chain C residue 932 PHE Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 667 TYR Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 784 ASP Chi-restraints excluded: chain D residue 927 ASN Chi-restraints excluded: chain D residue 942 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 315 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 431 optimal weight: 7.9990 chunk 284 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 141 optimal weight: 0.0050 chunk 307 optimal weight: 7.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 167 ASN A 351 GLN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 553 ASN D 520 ASN D 638 ASN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 818 ASN D 846 GLN D 873 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.199140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.156467 restraints weight = 57899.825| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 4.10 r_work: 0.3831 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32156 Z= 0.172 Angle : 0.619 9.412 43692 Z= 0.325 Chirality : 0.042 0.217 5072 Planarity : 0.005 0.063 5768 Dihedral : 4.107 19.845 4568 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 3.03 % Allowed : 16.57 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.12), residues: 4312 helix: 1.17 (0.10), residues: 2608 sheet: -0.06 (0.41), residues: 147 loop : -0.83 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 205 TYR 0.040 0.002 TYR C 914 PHE 0.039 0.002 PHE C 882 TRP 0.015 0.002 TRP B 640 HIS 0.007 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00406 (32156) covalent geometry : angle 0.61938 (43692) hydrogen bonds : bond 0.04023 ( 1756) hydrogen bonds : angle 4.35369 ( 5223) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 511 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ASP cc_start: 0.7252 (p0) cc_final: 0.6819 (p0) REVERT: A 525 LYS cc_start: 0.8539 (mttt) cc_final: 0.8312 (mtmm) REVERT: A 805 PHE cc_start: 0.8655 (m-10) cc_final: 0.8454 (m-10) REVERT: B 150 MET cc_start: 0.7036 (mpp) cc_final: 0.6760 (mpp) REVERT: B 175 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7074 (mm-30) REVERT: B 577 GLN cc_start: 0.7565 (mp10) cc_final: 0.7334 (mp10) REVERT: B 584 GLU cc_start: 0.8516 (pm20) cc_final: 0.7676 (tm-30) REVERT: B 592 LYS cc_start: 0.8832 (tttt) cc_final: 0.8404 (ttpp) REVERT: B 745 ILE cc_start: 0.3647 (OUTLIER) cc_final: 0.3323 (tp) REVERT: B 916 PHE cc_start: 0.8212 (m-80) cc_final: 0.7584 (m-80) REVERT: C 342 LYS cc_start: 0.8615 (mttp) cc_final: 0.8405 (mttp) REVERT: C 492 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7881 (mmm-85) REVERT: C 746 LEU cc_start: 0.8009 (tt) cc_final: 0.7692 (mp) REVERT: C 838 MET cc_start: 0.7838 (mmp) cc_final: 0.7580 (ptt) REVERT: C 881 TYR cc_start: 0.8696 (t80) cc_final: 0.8448 (t80) REVERT: C 910 ASP cc_start: 0.8964 (t70) cc_final: 0.8402 (t0) REVERT: D 512 PHE cc_start: 0.5393 (OUTLIER) cc_final: 0.4316 (m-10) REVERT: D 667 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.7047 (m-80) REVERT: D 673 TYR cc_start: 0.8173 (m-80) cc_final: 0.7964 (m-80) REVERT: D 914 TYR cc_start: 0.7835 (m-10) cc_final: 0.7634 (m-10) outliers start: 91 outliers final: 64 residues processed: 567 average time/residue: 0.1657 time to fit residues: 153.4587 Evaluate side-chains 547 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 479 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 409 ARG Chi-restraints excluded: chain C residue 492 ARG Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 586 ASN Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 918 LYS Chi-restraints excluded: chain C residue 932 PHE Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 520 ASN Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 667 TYR Chi-restraints excluded: chain D residue 784 ASP Chi-restraints excluded: chain D residue 927 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 304 optimal weight: 20.0000 chunk 214 optimal weight: 0.9990 chunk 366 optimal weight: 0.7980 chunk 293 optimal weight: 8.9990 chunk 254 optimal weight: 0.1980 chunk 395 optimal weight: 0.4980 chunk 196 optimal weight: 5.9990 chunk 428 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 351 GLN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 768 HIS C 311 GLN C 553 ASN D 195 ASN D 638 ASN D 818 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.200786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.161382 restraints weight = 56665.484| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 3.87 r_work: 0.3903 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32156 Z= 0.121 Angle : 0.593 11.543 43692 Z= 0.310 Chirality : 0.041 0.297 5072 Planarity : 0.005 0.062 5768 Dihedral : 3.939 20.518 4568 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.13 % Favored : 96.85 % Rotamer: Outliers : 2.23 % Allowed : 18.13 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.13), residues: 4312 helix: 1.29 (0.10), residues: 2605 sheet: 0.21 (0.40), residues: 147 loop : -0.80 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 205 TYR 0.039 0.001 TYR C 914 PHE 0.043 0.002 PHE D 576 TRP 0.012 0.001 TRP B 640 HIS 0.004 0.001 HIS B 632 Details of bonding type rmsd covalent geometry : bond 0.00269 (32156) covalent geometry : angle 0.59298 (43692) hydrogen bonds : bond 0.03617 ( 1756) hydrogen bonds : angle 4.21774 ( 5223) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 534 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ASP cc_start: 0.7409 (p0) cc_final: 0.6946 (p0) REVERT: A 525 LYS cc_start: 0.8469 (mttt) cc_final: 0.8235 (mtmm) REVERT: A 731 ILE cc_start: 0.8491 (mp) cc_final: 0.8106 (mm) REVERT: A 780 GLN cc_start: 0.6211 (mm-40) cc_final: 0.5897 (mm-40) REVERT: A 846 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8863 (mm110) REVERT: B 166 ASN cc_start: 0.8752 (m110) cc_final: 0.8391 (m110) REVERT: B 183 LYS cc_start: 0.8018 (tmtt) cc_final: 0.7698 (mmmm) REVERT: B 577 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7175 (mp10) REVERT: B 583 PRO cc_start: 0.7296 (Cg_endo) cc_final: 0.6695 (Cg_endo) REVERT: B 584 GLU cc_start: 0.8416 (pm20) cc_final: 0.7682 (tm-30) REVERT: B 592 LYS cc_start: 0.8835 (tttt) cc_final: 0.8430 (ttpp) REVERT: B 745 ILE cc_start: 0.3551 (OUTLIER) cc_final: 0.3262 (tp) REVERT: B 916 PHE cc_start: 0.8053 (m-80) cc_final: 0.7433 (m-80) REVERT: C 161 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.6911 (tt) REVERT: C 332 MET cc_start: 0.8183 (pmm) cc_final: 0.7967 (pmm) REVERT: C 409 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8098 (ttm170) REVERT: C 525 LYS cc_start: 0.8497 (mmtp) cc_final: 0.8078 (pttt) REVERT: C 910 ASP cc_start: 0.8811 (t70) cc_final: 0.8373 (t0) REVERT: D 512 PHE cc_start: 0.5156 (OUTLIER) cc_final: 0.4149 (m-10) REVERT: D 667 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.7071 (m-80) REVERT: D 673 TYR cc_start: 0.8021 (m-80) cc_final: 0.7792 (m-80) REVERT: D 744 GLN cc_start: 0.8315 (mp10) cc_final: 0.8006 (tp-100) outliers start: 67 outliers final: 44 residues processed: 577 average time/residue: 0.1712 time to fit residues: 161.2953 Evaluate side-chains 548 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 498 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 409 ARG Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 586 ASN Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 932 PHE Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 667 TYR Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 784 ASP Chi-restraints excluded: chain D residue 927 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 293 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 401 optimal weight: 6.9990 chunk 230 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 227 optimal weight: 0.0870 chunk 425 optimal weight: 50.0000 chunk 386 optimal weight: 9.9990 chunk 275 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 538 ASN A 553 ASN A 586 ASN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS B 143 ASN B 259 GLN B 588 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 553 ASN C 758 GLN ** C 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 ASN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 818 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.198060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.156671 restraints weight = 58421.782| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 3.82 r_work: 0.3840 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32156 Z= 0.172 Angle : 0.648 13.921 43692 Z= 0.339 Chirality : 0.043 0.336 5072 Planarity : 0.005 0.062 5768 Dihedral : 4.154 23.068 4568 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.22 % Favored : 95.76 % Rotamer: Outliers : 2.50 % Allowed : 18.63 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.13), residues: 4312 helix: 1.14 (0.10), residues: 2613 sheet: -0.05 (0.41), residues: 147 loop : -0.79 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 205 TYR 0.036 0.002 TYR C 914 PHE 0.038 0.002 PHE C 882 TRP 0.017 0.002 TRP B 640 HIS 0.006 0.001 HIS A 496 Details of bonding type rmsd covalent geometry : bond 0.00405 (32156) covalent geometry : angle 0.64755 (43692) hydrogen bonds : bond 0.04077 ( 1756) hydrogen bonds : angle 4.37122 ( 5223) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 517 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ASP cc_start: 0.7368 (p0) cc_final: 0.6918 (p0) REVERT: A 525 LYS cc_start: 0.8536 (mttt) cc_final: 0.8308 (mtmm) REVERT: A 731 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8095 (mm) REVERT: A 766 PRO cc_start: 0.7491 (Cg_exo) cc_final: 0.7143 (Cg_endo) REVERT: A 846 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8799 (mm110) REVERT: B 175 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7074 (mm-30) REVERT: B 577 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7200 (mp10) REVERT: B 592 LYS cc_start: 0.8867 (tttt) cc_final: 0.8447 (ttpp) REVERT: B 745 ILE cc_start: 0.3478 (OUTLIER) cc_final: 0.3211 (tp) REVERT: B 916 PHE cc_start: 0.7995 (m-80) cc_final: 0.7344 (m-80) REVERT: B 949 MET cc_start: 0.8218 (mmm) cc_final: 0.7659 (ptp) REVERT: C 259 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: C 332 MET cc_start: 0.8158 (pmm) cc_final: 0.7928 (pmm) REVERT: C 342 LYS cc_start: 0.8603 (mttm) cc_final: 0.8358 (mttp) REVERT: C 525 LYS cc_start: 0.8562 (mmtp) cc_final: 0.8127 (pttt) REVERT: C 746 LEU cc_start: 0.8022 (tt) cc_final: 0.7690 (mp) REVERT: C 910 ASP cc_start: 0.8752 (t70) cc_final: 0.8429 (t0) REVERT: D 512 PHE cc_start: 0.5313 (OUTLIER) cc_final: 0.4307 (m-80) REVERT: D 667 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.7224 (m-80) outliers start: 75 outliers final: 55 residues processed: 565 average time/residue: 0.1733 time to fit residues: 160.0738 Evaluate side-chains 563 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 502 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 586 ASN Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 932 PHE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 667 TYR Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 784 ASP Chi-restraints excluded: chain D residue 927 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 252 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 287 optimal weight: 6.9990 chunk 165 optimal weight: 0.0870 chunk 60 optimal weight: 8.9990 chunk 334 optimal weight: 3.9990 chunk 337 optimal weight: 0.5980 chunk 292 optimal weight: 1.9990 chunk 361 optimal weight: 2.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 351 GLN A 364 GLN A 538 ASN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 588 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 ASN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.200084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.158496 restraints weight = 57328.760| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 4.05 r_work: 0.3893 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32156 Z= 0.128 Angle : 0.626 14.052 43692 Z= 0.327 Chirality : 0.042 0.333 5072 Planarity : 0.005 0.068 5768 Dihedral : 4.021 23.545 4568 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 2.30 % Allowed : 18.90 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.13), residues: 4312 helix: 1.28 (0.10), residues: 2599 sheet: 0.12 (0.42), residues: 135 loop : -0.74 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 139 TYR 0.040 0.002 TYR C 914 PHE 0.042 0.002 PHE C 882 TRP 0.011 0.001 TRP B 640 HIS 0.010 0.001 HIS C 632 Details of bonding type rmsd covalent geometry : bond 0.00288 (32156) covalent geometry : angle 0.62649 (43692) hydrogen bonds : bond 0.03690 ( 1756) hydrogen bonds : angle 4.26384 ( 5223) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 529 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LYS cc_start: 0.7865 (mptt) cc_final: 0.7624 (mptt) REVERT: A 370 ASP cc_start: 0.7078 (p0) cc_final: 0.6699 (p0) REVERT: A 731 ILE cc_start: 0.8325 (mp) cc_final: 0.7952 (mm) REVERT: A 766 PRO cc_start: 0.7426 (Cg_exo) cc_final: 0.7146 (Cg_endo) REVERT: A 846 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8760 (mm110) REVERT: B 166 ASN cc_start: 0.8747 (m110) cc_final: 0.8427 (m110) REVERT: B 175 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7054 (mm-30) REVERT: B 183 LYS cc_start: 0.7982 (tmtt) cc_final: 0.7719 (mmmm) REVERT: B 577 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: B 584 GLU cc_start: 0.8408 (pm20) cc_final: 0.7857 (tm-30) REVERT: B 592 LYS cc_start: 0.8849 (tttt) cc_final: 0.8439 (ttpp) REVERT: B 745 ILE cc_start: 0.3384 (OUTLIER) cc_final: 0.3038 (tp) REVERT: B 916 PHE cc_start: 0.7886 (m-80) cc_final: 0.7249 (m-80) REVERT: C 259 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: C 342 LYS cc_start: 0.8537 (mttm) cc_final: 0.8316 (mttp) REVERT: C 409 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8333 (ttm170) REVERT: C 525 LYS cc_start: 0.8445 (mmtp) cc_final: 0.8081 (pttt) REVERT: C 910 ASP cc_start: 0.8646 (t70) cc_final: 0.8413 (t0) REVERT: D 512 PHE cc_start: 0.5319 (OUTLIER) cc_final: 0.4328 (m-80) REVERT: D 581 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7918 (mm-30) REVERT: D 667 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.7238 (m-80) REVERT: D 914 TYR cc_start: 0.7498 (m-80) cc_final: 0.7242 (m-80) REVERT: D 930 MET cc_start: 0.6159 (mmm) cc_final: 0.5713 (mmm) outliers start: 69 outliers final: 54 residues processed: 571 average time/residue: 0.1618 time to fit residues: 150.7399 Evaluate side-chains 573 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 513 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 409 ARG Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 586 ASN Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 932 PHE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 667 TYR Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 775 TYR Chi-restraints excluded: chain D residue 784 ASP Chi-restraints excluded: chain D residue 927 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 221 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 282 optimal weight: 5.9990 chunk 296 optimal weight: 0.0050 chunk 424 optimal weight: 20.0000 chunk 412 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 48 optimal weight: 0.0670 chunk 131 optimal weight: 3.9990 overall best weight: 1.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 351 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 588 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.195896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.153734 restraints weight = 57930.035| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 4.04 r_work: 0.3847 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32156 Z= 0.139 Angle : 0.657 18.423 43692 Z= 0.341 Chirality : 0.042 0.339 5072 Planarity : 0.005 0.062 5768 Dihedral : 4.050 25.135 4568 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.76 % Favored : 96.22 % Rotamer: Outliers : 2.13 % Allowed : 19.47 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.13), residues: 4312 helix: 1.28 (0.10), residues: 2597 sheet: 0.04 (0.41), residues: 137 loop : -0.73 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 139 TYR 0.042 0.002 TYR C 914 PHE 0.041 0.002 PHE C 882 TRP 0.013 0.001 TRP B 640 HIS 0.010 0.001 HIS C 632 Details of bonding type rmsd covalent geometry : bond 0.00319 (32156) covalent geometry : angle 0.65710 (43692) hydrogen bonds : bond 0.03772 ( 1756) hydrogen bonds : angle 4.31270 ( 5223) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 523 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LYS cc_start: 0.7833 (mptt) cc_final: 0.7560 (mptt) REVERT: A 370 ASP cc_start: 0.7170 (p0) cc_final: 0.6774 (p0) REVERT: A 731 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8073 (mm) REVERT: A 766 PRO cc_start: 0.7421 (Cg_exo) cc_final: 0.7145 (Cg_endo) REVERT: A 846 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8912 (mm110) REVERT: B 175 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7075 (mm-30) REVERT: B 183 LYS cc_start: 0.8065 (tmtt) cc_final: 0.7697 (mmmm) REVERT: B 577 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7211 (mp10) REVERT: B 584 GLU cc_start: 0.8429 (pm20) cc_final: 0.7782 (tm-30) REVERT: B 592 LYS cc_start: 0.8825 (tttt) cc_final: 0.8417 (ttpp) REVERT: B 745 ILE cc_start: 0.3057 (OUTLIER) cc_final: 0.2793 (tp) REVERT: B 916 PHE cc_start: 0.8249 (m-80) cc_final: 0.7595 (m-80) REVERT: C 259 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: C 342 LYS cc_start: 0.8618 (mttm) cc_final: 0.8382 (mttp) REVERT: C 525 LYS cc_start: 0.8487 (mmtp) cc_final: 0.8014 (pttt) REVERT: D 512 PHE cc_start: 0.5204 (OUTLIER) cc_final: 0.4219 (m-80) REVERT: D 581 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7969 (mm-30) REVERT: D 667 TYR cc_start: 0.7367 (OUTLIER) cc_final: 0.7111 (m-80) REVERT: D 914 TYR cc_start: 0.7823 (m-80) cc_final: 0.7558 (m-80) REVERT: D 930 MET cc_start: 0.6273 (mmm) cc_final: 0.5816 (mmm) outliers start: 64 outliers final: 51 residues processed: 563 average time/residue: 0.1688 time to fit residues: 155.6363 Evaluate side-chains 571 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 514 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 586 ASN Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 932 PHE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 667 TYR Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 784 ASP Chi-restraints excluded: chain D residue 927 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 156 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 409 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 426 optimal weight: 40.0000 chunk 308 optimal weight: 30.0000 chunk 292 optimal weight: 0.9980 chunk 299 optimal weight: 8.9990 chunk 425 optimal weight: 30.0000 chunk 193 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 538 ASN A 586 ASN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 HIS B 588 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 GLN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.198243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.198027 restraints weight = 51490.236| |-----------------------------------------------------------------------------| r_work (start): 0.4679 rms_B_bonded: 0.11 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.5000 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.2500 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.1250 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0625 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0312 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0156 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0078 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0039 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0020 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0010 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0005 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0002 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0001 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0001 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0000 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0000 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0000 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0000 r_work: 0.4676 rms_B_bonded: 0.11 restraints_weight: 0.0000 r_work (final): 0.4676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32156 Z= 0.155 Angle : 0.677 15.161 43692 Z= 0.351 Chirality : 0.043 0.346 5072 Planarity : 0.005 0.060 5768 Dihedral : 4.131 25.825 4568 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 2.17 % Allowed : 19.73 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.13), residues: 4312 helix: 1.21 (0.10), residues: 2605 sheet: 0.14 (0.41), residues: 142 loop : -0.75 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 139 TYR 0.045 0.002 TYR C 914 PHE 0.042 0.002 PHE C 882 TRP 0.015 0.002 TRP B 640 HIS 0.010 0.001 HIS C 632 Details of bonding type rmsd covalent geometry : bond 0.00362 (32156) covalent geometry : angle 0.67738 (43692) hydrogen bonds : bond 0.03931 ( 1756) hydrogen bonds : angle 4.39066 ( 5223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11647.14 seconds wall clock time: 199 minutes 9.25 seconds (11949.25 seconds total)