Starting phenix.real_space_refine on Thu May 29 05:35:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9goa_51495/05_2025/9goa_51495.cif Found real_map, /net/cci-nas-00/data/ceres_data/9goa_51495/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9goa_51495/05_2025/9goa_51495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9goa_51495/05_2025/9goa_51495.map" model { file = "/net/cci-nas-00/data/ceres_data/9goa_51495/05_2025/9goa_51495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9goa_51495/05_2025/9goa_51495.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.007 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): 2.72s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 8, 'HIS:plan': 8, 'TYR:plan': 11, 'ASN:plan1': 15, 'ASP:plan': 15, 'PHE:plan': 10, 'GLU:plan': 10, 'ARG:plan': 8} 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: {'GLN:plan1': 8, 'HIS:plan': 8, 'TYR:plan': 11, 'ASN:plan1': 15, 'ASP:plan': 15, 'PHE:plan': 10, 'GLU:plan': 10, 'ARG:plan': 8} 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: {'GLN:plan1': 8, 'HIS:plan': 8, 'TYR:plan': 11, 'ASN:plan1': 15, 'ASP:plan': 15, 'PHE:plan': 10, 'GLU:plan': 10, 'ARG:plan': 8} 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: {'GLN:plan1': 8, 'HIS:plan': 8, 'TYR:plan': 11, 'ASN:plan1': 15, 'ASP:plan': 15, 'PHE:plan': 10, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 379 Time building chain proxies: 20.31, per 1000 atoms: 0.64 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: 7.83 Conformation dependent library (CDL) restraints added in 4.4 seconds 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: 3.97 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: 12.22 Time building geometry restraints manager: 9.09 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: 0.08 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: 13.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.780 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 71.980 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.150 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.000 ------------------------------------------------------------------------------- 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 : 9.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (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 TRP 0.029 0.001 TRP A 640 HIS 0.008 0.001 HIS A 801 PHE 0.033 0.002 PHE A 217 TYR 0.025 0.001 TYR A 764 ARG 0.008 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.14496 ( 1756) hydrogen bonds : angle 5.61579 ( 5223) covalent geometry : bond 0.00437 (32156) covalent geometry : angle 0.70884 (43692) *********************** 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 : 3.348 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: 0.4035 time to fit residues: 411.3356 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 : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 0.7980 chunk 327 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 338 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 205 optimal weight: 40.0000 chunk 252 optimal weight: 2.9990 chunk 392 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 351 GLN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN A 785 GLN ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 553 ASN C 638 ASN 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 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4702 r_free = 0.4702 target = 0.200643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.161455 restraints weight = 55740.216| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 3.91 r_work: 0.3933 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32156 Z= 0.176 Angle : 0.630 9.478 43692 Z= 0.332 Chirality : 0.043 0.209 5072 Planarity : 0.005 0.072 5768 Dihedral : 4.146 43.505 4568 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.62 % Favored : 96.36 % Rotamer: Outliers : 1.83 % Allowed : 9.83 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.12), residues: 4312 helix: 0.96 (0.10), residues: 2585 sheet: 0.03 (0.42), residues: 156 loop : -0.89 (0.14), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 640 HIS 0.007 0.001 HIS A 496 PHE 0.044 0.002 PHE C 882 TYR 0.030 0.002 TYR C 914 ARG 0.007 0.001 ARG C 382 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 1756) hydrogen bonds : angle 4.50873 ( 5223) covalent geometry : bond 0.00410 (32156) covalent geometry : angle 0.63050 (43692) *********************** 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 611 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 556 time to evaluate : 3.470 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 407 SER cc_start: 0.8752 (m) cc_final: 0.8539 (p) REVERT: A 704 ILE cc_start: 0.6670 (mt) cc_final: 0.6437 (mt) REVERT: B 142 MET cc_start: 0.7388 (ptt) cc_final: 0.7176 (ptt) REVERT: B 150 MET cc_start: 0.7080 (mpp) cc_final: 0.6782 (mpp) REVERT: B 489 ASP cc_start: 0.7763 (t0) cc_final: 0.7438 (t0) REVERT: B 538 ASN cc_start: 0.8440 (m110) cc_final: 0.8139 (m110) REVERT: B 916 PHE cc_start: 0.7943 (m-80) cc_final: 0.7098 (m-80) REVERT: C 142 MET cc_start: 0.7543 (ptt) cc_final: 0.7319 (ppp) REVERT: C 248 THR cc_start: 0.8425 (p) cc_final: 0.8181 (t) REVERT: C 492 ARG cc_start: 0.7964 (tpp80) cc_final: 0.7672 (mmm-85) REVERT: C 910 ASP cc_start: 0.8835 (t70) cc_final: 0.7813 (t70) REVERT: D 821 ASN cc_start: 0.6056 (t0) cc_final: 0.5853 (p0) outliers start: 55 outliers final: 41 residues processed: 589 average time/residue: 0.4128 time to fit residues: 391.9786 Evaluate side-chains 538 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 497 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 408 VAL 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 642 VAL 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 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 559 PHE 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 546 ILE Chi-restraints excluded: chain C residue 586 ASN Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 728 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 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 286 optimal weight: 0.9980 chunk 109 optimal weight: 20.0000 chunk 249 optimal weight: 0.1980 chunk 174 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 410 optimal weight: 5.9990 chunk 147 optimal weight: 0.1980 chunk 191 optimal weight: 2.9990 chunk 420 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 553 ASN A 586 ASN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 569 GLN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 HIS C 553 ASN C 873 ASN D 166 ASN ** D 213 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.200976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.156914 restraints weight = 55492.619| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 3.91 r_work: 0.3964 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32156 Z= 0.123 Angle : 0.573 9.492 43692 Z= 0.300 Chirality : 0.040 0.197 5072 Planarity : 0.005 0.062 5768 Dihedral : 3.918 37.561 4568 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 1.77 % Allowed : 13.77 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.12), residues: 4312 helix: 1.13 (0.10), residues: 2592 sheet: 0.13 (0.43), residues: 152 loop : -0.87 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 640 HIS 0.006 0.001 HIS A 801 PHE 0.038 0.002 PHE C 882 TYR 0.039 0.002 TYR C 914 ARG 0.017 0.000 ARG B 892 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 1756) hydrogen bonds : angle 4.31061 ( 5223) covalent geometry : bond 0.00277 (32156) covalent geometry : angle 0.57277 (43692) *********************** 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 598 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 545 time to evaluate : 3.611 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: A 407 SER cc_start: 0.8728 (m) cc_final: 0.8512 (p) REVERT: A 766 PRO cc_start: 0.7519 (Cg_exo) cc_final: 0.7144 (Cg_endo) REVERT: A 805 PHE cc_start: 0.8504 (m-10) cc_final: 0.8255 (m-80) REVERT: A 935 TYR cc_start: 0.8943 (t80) cc_final: 0.8697 (t80) REVERT: B 150 MET cc_start: 0.7115 (mpp) cc_final: 0.6845 (mpp) REVERT: B 538 ASN cc_start: 0.8422 (m110) cc_final: 0.8207 (m110) REVERT: B 916 PHE cc_start: 0.8168 (m-80) cc_final: 0.7685 (m-80) REVERT: C 142 MET cc_start: 0.7344 (ptt) cc_final: 0.7136 (ppp) REVERT: C 161 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.6843 (tt) REVERT: C 248 THR cc_start: 0.8617 (p) cc_final: 0.8220 (t) REVERT: C 342 LYS cc_start: 0.8763 (tptt) cc_final: 0.8382 (mttm) REVERT: C 492 ARG cc_start: 0.8100 (tpp80) cc_final: 0.7698 (mmm-85) REVERT: C 881 TYR cc_start: 0.8584 (t80) cc_final: 0.8266 (t80) REVERT: C 910 ASP cc_start: 0.8845 (t70) cc_final: 0.8122 (t0) REVERT: D 548 ARG cc_start: 0.8247 (tpt90) cc_final: 0.7486 (tpp-160) REVERT: D 639 ASP cc_start: 0.7521 (t0) cc_final: 0.7305 (t0) REVERT: D 744 GLN cc_start: 0.8422 (mp10) cc_final: 0.8077 (tp-100) outliers start: 53 outliers final: 38 residues processed: 574 average time/residue: 0.3911 time to fit residues: 362.7380 Evaluate side-chains 534 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 495 time to evaluate : 3.338 ------------------------------------------------------------------------------- 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 450 ASN Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 LEU 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 294 LEU 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 501 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 365 ILE 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 553 ASN 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 428 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 355 optimal weight: 4.9990 chunk 381 optimal weight: 0.9980 chunk 255 optimal weight: 4.9990 chunk 198 optimal weight: 9.9990 chunk 117 optimal weight: 0.0670 chunk 252 optimal weight: 2.9990 chunk 422 optimal weight: 8.9990 chunk 216 optimal weight: 40.0000 chunk 320 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- 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 351 GLN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN D 389 GLN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 818 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.195346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.153445 restraints weight = 58419.088| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 4.36 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 32156 Z= 0.193 Angle : 0.636 8.821 43692 Z= 0.335 Chirality : 0.043 0.210 5072 Planarity : 0.005 0.063 5768 Dihedral : 4.199 28.522 4568 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.06 % Rotamer: Outliers : 2.73 % Allowed : 15.57 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.12), residues: 4312 helix: 1.04 (0.10), residues: 2600 sheet: -0.04 (0.41), residues: 152 loop : -0.91 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 640 HIS 0.008 0.001 HIS A 496 PHE 0.035 0.002 PHE C 882 TYR 0.031 0.002 TYR C 914 ARG 0.008 0.001 ARG D 205 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 1756) hydrogen bonds : angle 4.43393 ( 5223) covalent geometry : bond 0.00456 (32156) covalent geometry : angle 0.63583 (43692) *********************** 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 609 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 527 time to evaluate : 4.794 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 256 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8435 (mp) REVERT: A 370 ASP cc_start: 0.7152 (p0) cc_final: 0.6695 (p0) REVERT: A 407 SER cc_start: 0.8604 (m) cc_final: 0.8393 (p) REVERT: A 555 LYS cc_start: 0.8205 (mtpp) cc_final: 0.7855 (ttmt) REVERT: A 766 PRO cc_start: 0.7667 (Cg_exo) cc_final: 0.7360 (Cg_endo) REVERT: A 805 PHE cc_start: 0.8651 (m-10) cc_final: 0.8438 (m-10) REVERT: A 935 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.8776 (t80) REVERT: B 150 MET cc_start: 0.7133 (mpp) cc_final: 0.6777 (mpp) REVERT: B 175 GLU cc_start: 0.7601 (mm-30) cc_final: 0.6727 (mm-30) REVERT: B 538 ASN cc_start: 0.8421 (m110) cc_final: 0.8116 (m110) REVERT: B 592 LYS cc_start: 0.8707 (tttt) cc_final: 0.8220 (ttpp) REVERT: B 745 ILE cc_start: 0.3642 (OUTLIER) cc_final: 0.3435 (tp) REVERT: B 916 PHE cc_start: 0.8082 (m-80) cc_final: 0.7551 (m-80) REVERT: C 142 MET cc_start: 0.7272 (ptt) cc_final: 0.7038 (ppp) REVERT: C 217 PHE cc_start: 0.7929 (m-80) cc_final: 0.7546 (m-80) REVERT: C 492 ARG cc_start: 0.7804 (tpp80) cc_final: 0.7489 (mmm-85) REVERT: C 746 LEU cc_start: 0.7962 (tt) cc_final: 0.7642 (mp) REVERT: C 910 ASP cc_start: 0.8818 (t70) cc_final: 0.8174 (t0) REVERT: C 943 ASN cc_start: 0.8042 (p0) cc_final: 0.7836 (p0) REVERT: D 177 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8230 (pm20) REVERT: D 240 TYR cc_start: 0.7595 (m-10) cc_final: 0.7340 (m-10) REVERT: D 914 TYR cc_start: 0.7840 (m-10) cc_final: 0.7638 (m-10) outliers start: 82 outliers final: 52 residues processed: 577 average time/residue: 0.4027 time to fit residues: 378.2703 Evaluate side-chains 540 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 484 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 408 VAL 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 587 ILE Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 642 VAL 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 A residue 935 TYR 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 596 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 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 546 ILE Chi-restraints excluded: chain C residue 586 ASN Chi-restraints excluded: chain C residue 588 ASN 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 177 GLU 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 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 784 ASP Chi-restraints excluded: chain D residue 927 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 325 optimal weight: 8.9990 chunk 414 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 407 optimal weight: 10.0000 chunk 362 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 393 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN C 553 ASN C 821 ASN D 496 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.198064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.154508 restraints weight = 58890.084| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 3.86 r_work: 0.3811 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 32156 Z= 0.200 Angle : 0.635 9.503 43692 Z= 0.335 Chirality : 0.043 0.208 5072 Planarity : 0.005 0.064 5768 Dihedral : 4.258 20.399 4568 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 2.97 % Allowed : 16.67 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.12), residues: 4312 helix: 1.02 (0.10), residues: 2603 sheet: -0.03 (0.41), residues: 142 loop : -0.91 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 640 HIS 0.007 0.001 HIS A 496 PHE 0.041 0.002 PHE C 916 TYR 0.038 0.002 TYR C 914 ARG 0.007 0.001 ARG D 205 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 1756) hydrogen bonds : angle 4.44745 ( 5223) covalent geometry : bond 0.00473 (32156) covalent geometry : angle 0.63496 (43692) *********************** 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 606 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 517 time to evaluate : 3.645 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: A 256 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8089 (mp) REVERT: A 331 GLU cc_start: 0.8595 (pp20) cc_final: 0.7974 (pp20) REVERT: A 370 ASP cc_start: 0.7385 (p0) cc_final: 0.7078 (p0) REVERT: A 525 LYS cc_start: 0.8553 (mttt) cc_final: 0.8328 (mtmm) REVERT: A 805 PHE cc_start: 0.8583 (m-10) cc_final: 0.8376 (m-10) REVERT: B 150 MET cc_start: 0.7041 (mpp) cc_final: 0.6755 (mpp) REVERT: B 175 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7095 (mm-30) REVERT: B 383 GLU cc_start: 0.8224 (pp20) cc_final: 0.8005 (pt0) REVERT: B 538 ASN cc_start: 0.8556 (m110) cc_final: 0.8233 (m110) REVERT: B 577 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: B 584 GLU cc_start: 0.8540 (pm20) cc_final: 0.7737 (tm-30) REVERT: B 592 LYS cc_start: 0.8883 (tttt) cc_final: 0.8440 (ttpp) REVERT: B 745 ILE cc_start: 0.3455 (OUTLIER) cc_final: 0.3086 (tp) REVERT: B 916 PHE cc_start: 0.8137 (m-80) cc_final: 0.7571 (m-80) REVERT: C 492 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7905 (mmm-85) REVERT: C 746 LEU cc_start: 0.7991 (tt) cc_final: 0.7662 (mp) REVERT: C 910 ASP cc_start: 0.8799 (t70) cc_final: 0.8224 (t0) REVERT: D 240 TYR cc_start: 0.8127 (m-10) cc_final: 0.7921 (m-10) REVERT: D 351 GLN cc_start: 0.7853 (tt0) cc_final: 0.7556 (mm-40) REVERT: D 512 PHE cc_start: 0.5416 (OUTLIER) cc_final: 0.4334 (m-10) REVERT: D 633 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8064 (mt) REVERT: D 744 GLN cc_start: 0.8577 (mp10) cc_final: 0.8157 (tp-100) outliers start: 89 outliers final: 64 residues processed: 570 average time/residue: 0.4003 time to fit residues: 369.2852 Evaluate side-chains 549 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 479 time to evaluate : 3.481 ------------------------------------------------------------------------------- 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 256 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 408 VAL 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 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 161 ILE 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 535 ASP Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 577 GLN 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 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 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 700 LEU Chi-restraints excluded: chain C residue 755 ASN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 932 PHE Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 375 ILE 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 457 ASP 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 588 ASN Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 633 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 154 optimal weight: 3.9990 chunk 230 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 396 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 336 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 175 optimal weight: 30.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** ** B 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 873 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.196832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.152578 restraints weight = 59094.282| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 3.89 r_work: 0.3788 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 32156 Z= 0.201 Angle : 0.652 9.783 43692 Z= 0.344 Chirality : 0.043 0.218 5072 Planarity : 0.005 0.065 5768 Dihedral : 4.332 21.952 4568 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.04 % Favored : 95.94 % Rotamer: Outliers : 3.60 % Allowed : 17.10 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.12), residues: 4312 helix: 0.98 (0.10), residues: 2609 sheet: -0.13 (0.41), residues: 142 loop : -0.88 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 640 HIS 0.007 0.001 HIS A 496 PHE 0.044 0.002 PHE C 882 TYR 0.039 0.002 TYR C 914 ARG 0.007 0.001 ARG D 205 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 1756) hydrogen bonds : angle 4.49720 ( 5223) covalent geometry : bond 0.00476 (32156) covalent geometry : angle 0.65189 (43692) *********************** 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 614 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 506 time to evaluate : 3.486 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: A 331 GLU cc_start: 0.8226 (pp20) cc_final: 0.7809 (pp20) REVERT: A 370 ASP cc_start: 0.7344 (p0) cc_final: 0.7028 (p0) REVERT: A 805 PHE cc_start: 0.8694 (m-10) cc_final: 0.8475 (m-10) REVERT: B 150 MET cc_start: 0.7051 (mpp) cc_final: 0.6738 (mpp) REVERT: B 175 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7147 (mm-30) REVERT: B 538 ASN cc_start: 0.8564 (m110) cc_final: 0.8249 (m110) REVERT: B 583 PRO cc_start: 0.7498 (Cg_endo) cc_final: 0.6971 (Cg_endo) REVERT: B 584 GLU cc_start: 0.8461 (pm20) cc_final: 0.7801 (tm-30) REVERT: B 592 LYS cc_start: 0.8887 (tttt) cc_final: 0.8422 (ttpp) REVERT: B 916 PHE cc_start: 0.8326 (m-80) cc_final: 0.7665 (m-80) REVERT: C 492 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7917 (mmm-85) REVERT: C 746 LEU cc_start: 0.7984 (tt) cc_final: 0.7603 (mp) REVERT: C 910 ASP cc_start: 0.8913 (t70) cc_final: 0.8545 (t70) REVERT: D 177 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: D 240 TYR cc_start: 0.8103 (m-10) cc_final: 0.7869 (m-10) REVERT: D 351 GLN cc_start: 0.7825 (tt0) cc_final: 0.7594 (mm-40) REVERT: D 512 PHE cc_start: 0.5397 (OUTLIER) cc_final: 0.4474 (m-80) REVERT: D 633 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8029 (mt) outliers start: 108 outliers final: 76 residues processed: 575 average time/residue: 0.4150 time to fit residues: 386.2784 Evaluate side-chains 561 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 481 time to evaluate : 3.448 ------------------------------------------------------------------------------- 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 198 LEU Chi-restraints excluded: chain A residue 211 SER 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 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 639 ASP 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 817 ASN Chi-restraints excluded: chain A residue 923 TYR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 307 ASP 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 579 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 620 VAL 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 889 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 492 ARG 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 586 ASN Chi-restraints excluded: chain C residue 588 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 697 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 177 GLU Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 375 ILE 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 457 ASP 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 588 ASN Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 663 THR 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 128 optimal weight: 4.9990 chunk 20 optimal weight: 0.0010 chunk 146 optimal weight: 1.9990 chunk 347 optimal weight: 2.9990 chunk 212 optimal weight: 40.0000 chunk 28 optimal weight: 0.1980 chunk 423 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 chunk 158 optimal weight: 0.0270 chunk 54 optimal weight: 0.7980 chunk 280 optimal weight: 6.9990 overall best weight: 0.6046 ------------------------------------------------------------------------------- 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 351 GLN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 758 GLN D 167 ASN D 389 GLN D 520 ASN D 638 ASN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 846 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.199468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.156257 restraints weight = 56902.051| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 4.16 r_work: 0.3865 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.3577 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= 0.120 Angle : 0.597 10.466 43692 Z= 0.313 Chirality : 0.041 0.258 5072 Planarity : 0.005 0.061 5768 Dihedral : 4.021 23.010 4568 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.90 % Favored : 97.08 % Rotamer: Outliers : 2.33 % Allowed : 18.73 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.13), residues: 4312 helix: 1.17 (0.10), residues: 2615 sheet: -0.05 (0.42), residues: 139 loop : -0.79 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 640 HIS 0.006 0.001 HIS B 834 PHE 0.041 0.002 PHE C 882 TYR 0.036 0.001 TYR C 914 ARG 0.005 0.000 ARG D 205 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1756) hydrogen bonds : angle 4.30169 ( 5223) covalent geometry : bond 0.00265 (32156) covalent geometry : angle 0.59690 (43692) *********************** 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 624 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 554 time to evaluate : 3.588 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: 0.7152 (p0) cc_final: 0.6760 (p0) REVERT: A 555 LYS cc_start: 0.8398 (mtpp) cc_final: 0.8120 (ttmt) REVERT: A 731 ILE cc_start: 0.8464 (mp) cc_final: 0.8058 (mm) REVERT: A 780 GLN cc_start: 0.6352 (mm-40) cc_final: 0.6025 (mm-40) REVERT: A 846 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8929 (mm110) REVERT: B 166 ASN cc_start: 0.8704 (m110) cc_final: 0.8380 (m110) REVERT: B 183 LYS cc_start: 0.8009 (tmtt) cc_final: 0.7691 (mmmm) REVERT: B 453 ASP cc_start: 0.7771 (t70) cc_final: 0.7515 (t70) REVERT: B 577 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: B 583 PRO cc_start: 0.7364 (Cg_endo) cc_final: 0.6894 (Cg_endo) REVERT: B 584 GLU cc_start: 0.8416 (pm20) cc_final: 0.7847 (tm-30) REVERT: B 592 LYS cc_start: 0.8870 (tttt) cc_final: 0.8443 (ttpp) REVERT: B 916 PHE cc_start: 0.8263 (m-80) cc_final: 0.7229 (m-80) REVERT: B 949 MET cc_start: 0.8275 (mmm) cc_final: 0.7737 (ptp) REVERT: C 161 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.6947 (tt) REVERT: C 217 PHE cc_start: 0.8133 (m-80) cc_final: 0.7580 (m-80) REVERT: C 259 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: C 332 MET cc_start: 0.8069 (pmm) cc_final: 0.7860 (pmm) REVERT: C 342 LYS cc_start: 0.8720 (tptt) cc_final: 0.8395 (mtmm) REVERT: C 409 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8283 (ttm170) REVERT: C 525 LYS cc_start: 0.8646 (mmtp) cc_final: 0.8108 (pttt) REVERT: D 351 GLN cc_start: 0.7782 (tt0) cc_final: 0.7504 (mm-40) REVERT: D 512 PHE cc_start: 0.5196 (OUTLIER) cc_final: 0.4288 (m-80) REVERT: D 633 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8001 (mt) REVERT: D 744 GLN cc_start: 0.8446 (mp10) cc_final: 0.7952 (tp-100) outliers start: 70 outliers final: 43 residues processed: 596 average time/residue: 0.3985 time to fit residues: 385.4701 Evaluate side-chains 560 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 511 time to evaluate : 3.314 ------------------------------------------------------------------------------- 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 506 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 310 LEU 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 577 GLN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 620 VAL 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 889 ILE Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 161 ILE 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 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 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 501 SER Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 520 ASN Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 633 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 294 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 311 optimal weight: 10.0000 chunk 256 optimal weight: 0.5980 chunk 210 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 334 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 361 ASN A 364 GLN A 389 GLN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS B 143 ASN B 588 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 768 HIS ** C 334 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.200117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.157625 restraints weight = 57223.156| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.93 r_work: 0.3902 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 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 0.038 32156 Z= 0.121 Angle : 0.613 11.133 43692 Z= 0.321 Chirality : 0.041 0.306 5072 Planarity : 0.005 0.060 5768 Dihedral : 3.977 23.466 4568 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.34 % Favored : 96.64 % Rotamer: Outliers : 1.93 % Allowed : 20.20 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.13), residues: 4312 helix: 1.28 (0.10), residues: 2600 sheet: 0.08 (0.42), residues: 140 loop : -0.77 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 640 HIS 0.009 0.001 HIS A 801 PHE 0.043 0.002 PHE C 882 TYR 0.049 0.001 TYR C 914 ARG 0.005 0.000 ARG D 205 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 1756) hydrogen bonds : angle 4.24211 ( 5223) covalent geometry : bond 0.00264 (32156) covalent geometry : angle 0.61339 (43692) *********************** 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 580 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 522 time to evaluate : 3.491 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 244 TYR cc_start: 0.7276 (t80) cc_final: 0.6995 (t80) REVERT: A 370 ASP cc_start: 0.7164 (p0) cc_final: 0.6768 (p0) REVERT: A 555 LYS cc_start: 0.8369 (mtpp) cc_final: 0.8092 (ttmm) REVERT: A 731 ILE cc_start: 0.8386 (mp) cc_final: 0.8007 (mm) REVERT: A 766 PRO cc_start: 0.7496 (Cg_exo) cc_final: 0.7149 (Cg_endo) REVERT: A 846 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8804 (mm110) REVERT: B 166 ASN cc_start: 0.8662 (m110) cc_final: 0.8328 (m110) REVERT: B 183 LYS cc_start: 0.7976 (tmtt) cc_final: 0.7681 (mmmm) REVERT: B 453 ASP cc_start: 0.7674 (t70) cc_final: 0.7426 (t70) REVERT: B 577 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7194 (mp10) REVERT: B 583 PRO cc_start: 0.7321 (Cg_endo) cc_final: 0.6868 (Cg_endo) REVERT: B 584 GLU cc_start: 0.8358 (pm20) cc_final: 0.7811 (tm-30) REVERT: B 592 LYS cc_start: 0.8836 (tttt) cc_final: 0.8425 (ttpp) REVERT: B 916 PHE cc_start: 0.8180 (m-80) cc_final: 0.7480 (m-80) REVERT: B 949 MET cc_start: 0.8258 (mmm) cc_final: 0.7721 (ptp) REVERT: C 161 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.6857 (tt) REVERT: C 217 PHE cc_start: 0.8118 (m-80) cc_final: 0.7570 (m-80) REVERT: C 259 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: C 342 LYS cc_start: 0.8664 (tptt) cc_final: 0.8405 (mttp) REVERT: C 409 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8212 (ttm170) REVERT: C 525 LYS cc_start: 0.8448 (mmtp) cc_final: 0.8054 (pttt) REVERT: C 838 MET cc_start: 0.7594 (mmp) cc_final: 0.7351 (ptt) REVERT: C 910 ASP cc_start: 0.8700 (t70) cc_final: 0.8484 (t0) REVERT: D 351 GLN cc_start: 0.7771 (tt0) cc_final: 0.7556 (mm-40) REVERT: D 512 PHE cc_start: 0.5200 (OUTLIER) cc_final: 0.4236 (m-80) REVERT: D 581 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7890 (mm-30) REVERT: D 633 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7973 (mt) outliers start: 58 outliers final: 44 residues processed: 557 average time/residue: 0.4140 time to fit residues: 373.8810 Evaluate side-chains 555 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 505 time to evaluate : 3.863 ------------------------------------------------------------------------------- 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 335 GLU Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 564 LEU 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 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 511 THR Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 161 ILE 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 602 ILE Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 728 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 345 GLU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 705 LEU 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 424 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 408 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 223 optimal weight: 0.9990 chunk 156 optimal weight: 0.5980 chunk 386 optimal weight: 9.9990 chunk 374 optimal weight: 0.0060 chunk 163 optimal weight: 0.5980 chunk 430 optimal weight: 4.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- 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** B 143 ASN B 259 GLN B 588 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** C 334 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.195585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.154195 restraints weight = 58075.861| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 3.75 r_work: 0.3884 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32156 Z= 0.131 Angle : 0.627 10.809 43692 Z= 0.328 Chirality : 0.041 0.311 5072 Planarity : 0.005 0.060 5768 Dihedral : 3.980 24.379 4568 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 2.10 % Allowed : 20.30 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.13), residues: 4312 helix: 1.29 (0.10), residues: 2599 sheet: 0.05 (0.41), residues: 140 loop : -0.75 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 640 HIS 0.009 0.001 HIS C 632 PHE 0.044 0.002 PHE C 882 TYR 0.046 0.002 TYR C 914 ARG 0.006 0.000 ARG D 205 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 1756) hydrogen bonds : angle 4.26886 ( 5223) covalent geometry : bond 0.00299 (32156) covalent geometry : angle 0.62747 (43692) *********************** 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 580 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 517 time to evaluate : 3.497 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: A 370 ASP cc_start: 0.7241 (p0) cc_final: 0.6801 (p0) REVERT: A 555 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8186 (ttmm) REVERT: A 731 ILE cc_start: 0.8380 (mp) cc_final: 0.8004 (mm) REVERT: A 766 PRO cc_start: 0.7484 (Cg_exo) cc_final: 0.7159 (Cg_endo) REVERT: B 166 ASN cc_start: 0.8684 (m110) cc_final: 0.8366 (m110) REVERT: B 183 LYS cc_start: 0.8000 (tmtt) cc_final: 0.7683 (mmmm) REVERT: B 453 ASP cc_start: 0.7732 (t70) cc_final: 0.7493 (t70) REVERT: B 577 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: B 583 PRO cc_start: 0.7361 (Cg_endo) cc_final: 0.6876 (Cg_endo) REVERT: B 584 GLU cc_start: 0.8452 (pm20) cc_final: 0.7826 (tm-30) REVERT: B 592 LYS cc_start: 0.8807 (tttt) cc_final: 0.8390 (ttpp) REVERT: B 678 LYS cc_start: 0.8348 (mttm) cc_final: 0.7604 (mmtt) REVERT: B 916 PHE cc_start: 0.8062 (m-80) cc_final: 0.7358 (m-80) REVERT: B 949 MET cc_start: 0.8245 (mmm) cc_final: 0.7726 (ptp) REVERT: C 161 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.6948 (tt) REVERT: C 224 TYR cc_start: 0.8108 (m-80) cc_final: 0.7856 (m-80) REVERT: C 342 LYS cc_start: 0.8648 (tptt) cc_final: 0.8426 (mttp) REVERT: C 409 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8281 (ttm170) REVERT: C 525 LYS cc_start: 0.8460 (mmtp) cc_final: 0.8010 (pttt) REVERT: D 512 PHE cc_start: 0.5168 (OUTLIER) cc_final: 0.4215 (m-80) REVERT: D 581 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7876 (mm-30) REVERT: D 633 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7993 (mt) REVERT: D 744 GLN cc_start: 0.8488 (mp10) cc_final: 0.8047 (tp-100) REVERT: D 914 TYR cc_start: 0.7557 (m-80) cc_final: 0.7338 (m-80) REVERT: D 930 MET cc_start: 0.6229 (mmm) cc_final: 0.5765 (mmm) outliers start: 63 outliers final: 53 residues processed: 554 average time/residue: 0.4160 time to fit residues: 372.7693 Evaluate side-chains 565 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 507 time to evaluate : 3.597 ------------------------------------------------------------------------------- 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 335 GLU Chi-restraints excluded: chain A residue 384 VAL 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 626 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 725 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 289 ASP 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 511 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 161 ILE 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 588 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 690 VAL Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 728 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 345 GLU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 633 LEU 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 927 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 216 optimal weight: 50.0000 chunk 409 optimal weight: 8.9990 chunk 325 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 210 optimal weight: 30.0000 chunk 351 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 275 optimal weight: 6.9990 chunk 394 optimal weight: 8.9990 chunk 233 optimal weight: 0.5980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN ** A 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN D 638 ASN ** 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 = 0.4658 r_free = 0.4658 target = 0.196101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.154791 restraints weight = 53798.478| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 3.67 r_work: 0.3813 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 32156 Z= 0.207 Angle : 0.704 11.756 43692 Z= 0.369 Chirality : 0.045 0.318 5072 Planarity : 0.005 0.073 5768 Dihedral : 4.316 25.889 4568 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.22 % Favored : 95.76 % Rotamer: Outliers : 2.07 % Allowed : 20.93 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.13), residues: 4312 helix: 1.03 (0.10), residues: 2622 sheet: -0.19 (0.41), residues: 147 loop : -0.80 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 640 HIS 0.010 0.001 HIS C 632 PHE 0.044 0.003 PHE C 882 TYR 0.052 0.002 TYR C 914 ARG 0.011 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 1756) hydrogen bonds : angle 4.51697 ( 5223) covalent geometry : bond 0.00489 (32156) covalent geometry : angle 0.70364 (43692) ********************** 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 571 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 509 time to evaluate : 3.349 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 228 LYS cc_start: 0.7746 (mptt) cc_final: 0.7490 (mptt) REVERT: A 370 ASP cc_start: 0.7239 (p0) cc_final: 0.6828 (p0) REVERT: A 555 LYS cc_start: 0.8391 (mtpp) cc_final: 0.8088 (ttmt) REVERT: A 731 ILE cc_start: 0.8524 (mp) cc_final: 0.8159 (mm) REVERT: A 766 PRO cc_start: 0.7551 (Cg_exo) cc_final: 0.7237 (Cg_endo) REVERT: A 846 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8887 (mm110) REVERT: B 150 MET cc_start: 0.7018 (mpp) cc_final: 0.6758 (mpp) REVERT: B 175 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7116 (mm-30) REVERT: B 453 ASP cc_start: 0.7691 (t70) cc_final: 0.7395 (t70) REVERT: B 577 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.6774 (mp10) REVERT: B 583 PRO cc_start: 0.7412 (Cg_endo) cc_final: 0.6954 (Cg_endo) REVERT: B 584 GLU cc_start: 0.8351 (pm20) cc_final: 0.7788 (tm-30) REVERT: B 592 LYS cc_start: 0.8886 (tttt) cc_final: 0.8448 (ttpp) REVERT: B 745 ILE cc_start: 0.3226 (OUTLIER) cc_final: 0.2959 (tp) REVERT: B 916 PHE cc_start: 0.8175 (m-80) cc_final: 0.7459 (m-80) REVERT: B 949 MET cc_start: 0.8283 (mmm) cc_final: 0.7815 (ptp) REVERT: C 224 TYR cc_start: 0.8124 (m-80) cc_final: 0.7817 (m-80) REVERT: C 259 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7893 (mt0) REVERT: C 342 LYS cc_start: 0.8759 (tptt) cc_final: 0.8481 (mttp) REVERT: C 525 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8072 (pttt) REVERT: C 746 LEU cc_start: 0.8013 (tt) cc_final: 0.7655 (mp) REVERT: C 854 THR cc_start: 0.7406 (m) cc_final: 0.7171 (p) REVERT: D 512 PHE cc_start: 0.5514 (OUTLIER) cc_final: 0.4613 (m-80) REVERT: D 633 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7990 (mt) REVERT: D 709 ASP cc_start: 0.7541 (t0) cc_final: 0.7326 (t0) outliers start: 62 outliers final: 54 residues processed: 549 average time/residue: 0.4089 time to fit residues: 361.2149 Evaluate side-chains 551 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 492 time to evaluate : 3.301 ------------------------------------------------------------------------------- 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 335 GLU Chi-restraints excluded: chain A residue 384 VAL 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 642 VAL 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 475 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 745 ILE 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 588 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 690 VAL Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 728 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 345 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 475 THR Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 633 LEU 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 927 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 69 optimal weight: 5.9990 chunk 395 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 268 optimal weight: 0.6980 chunk 368 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 351 GLN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN A 708 HIS ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 GLN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN D 439 GLN D 460 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.198849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.159113 restraints weight = 51331.315| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 3.72 r_work: 0.3894 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32156 Z= 0.133 Angle : 0.657 11.298 43692 Z= 0.343 Chirality : 0.042 0.318 5072 Planarity : 0.005 0.060 5768 Dihedral : 4.130 25.921 4568 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 2.00 % Allowed : 21.30 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 4312 helix: 1.19 (0.10), residues: 2612 sheet: 0.05 (0.43), residues: 135 loop : -0.73 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 822 HIS 0.009 0.001 HIS C 632 PHE 0.051 0.002 PHE B 903 TYR 0.054 0.002 TYR C 914 ARG 0.007 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 1756) hydrogen bonds : angle 4.36952 ( 5223) covalent geometry : bond 0.00299 (32156) covalent geometry : angle 0.65695 (43692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23233.98 seconds wall clock time: 402 minutes 4.37 seconds (24124.37 seconds total)