Starting phenix.real_space_refine on Fri Jun 27 10:36:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9goa_51495/06_2025/9goa_51495.cif Found real_map, /net/cci-nas-00/data/ceres_data/9goa_51495/06_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_51495/06_2025/9goa_51495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9goa_51495/06_2025/9goa_51495.map" model { file = "/net/cci-nas-00/data/ceres_data/9goa_51495/06_2025/9goa_51495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9goa_51495/06_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): 2.99s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 23.70, per 1000 atoms: 0.75 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: 16.54 Conformation dependent library (CDL) restraints added in 7.2 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: 6.24 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: 18.41 Time building geometry restraints manager: 17.21 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: 309.340 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: 0.050 Extract box with map and model: 1.540 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 101.340 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:3.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 418.030 ------------------------------------------------------------------------------- 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 : 4.757 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: 0.4532 time to fit residues: 462.3898 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 : 3.881 ------------------------------------------------------------------------------- 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 = 55740.225| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 3.91 r_work: 0.3933 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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 : 3.653 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: 0.8762 (m) cc_final: 0.8544 (p) REVERT: A 704 ILE cc_start: 0.6669 (mt) cc_final: 0.6435 (mt) REVERT: B 142 MET cc_start: 0.7382 (ptt) cc_final: 0.7169 (ptt) REVERT: B 150 MET cc_start: 0.7086 (mpp) cc_final: 0.6787 (mpp) REVERT: B 489 ASP cc_start: 0.7761 (t0) cc_final: 0.7443 (t0) REVERT: B 538 ASN cc_start: 0.8451 (m110) cc_final: 0.8148 (m110) REVERT: B 916 PHE cc_start: 0.7941 (m-80) cc_final: 0.7097 (m-80) REVERT: C 142 MET cc_start: 0.7545 (ptt) cc_final: 0.7317 (ppp) REVERT: C 248 THR cc_start: 0.8449 (p) cc_final: 0.8196 (t) REVERT: C 492 ARG cc_start: 0.7972 (tpp80) cc_final: 0.7682 (mmm-85) REVERT: C 910 ASP cc_start: 0.8832 (t70) cc_final: 0.7809 (t70) REVERT: D 821 ASN cc_start: 0.6061 (t0) cc_final: 0.5858 (p0) outliers start: 55 outliers final: 41 residues processed: 589 average time/residue: 0.4044 time to fit residues: 387.6274 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 : 3.510 ------------------------------------------------------------------------------- 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: 0.6980 chunk 174 optimal weight: 0.4980 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: 0.6380 ------------------------------------------------------------------------------- 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 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 HIS C 553 ASN C 873 ASN D 166 ASN D 213 GLN D 638 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.201720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.158014 restraints weight = 55051.526| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 3.85 r_work: 0.3983 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32156 Z= 0.115 Angle : 0.565 10.395 43692 Z= 0.295 Chirality : 0.040 0.194 5072 Planarity : 0.004 0.063 5768 Dihedral : 3.877 36.966 4568 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 1.67 % Allowed : 13.93 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.12), residues: 4312 helix: 1.17 (0.10), residues: 2591 sheet: 0.16 (0.43), residues: 152 loop : -0.85 (0.14), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 640 HIS 0.006 0.001 HIS C 599 PHE 0.040 0.002 PHE C 882 TYR 0.036 0.001 TYR C 914 ARG 0.006 0.000 ARG D 205 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 1756) hydrogen bonds : angle 4.27493 ( 5223) covalent geometry : bond 0.00253 (32156) covalent geometry : angle 0.56518 (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 602 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 552 time to evaluate : 3.263 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 407 SER cc_start: 0.8729 (m) cc_final: 0.8528 (p) REVERT: A 766 PRO cc_start: 0.7519 (Cg_exo) cc_final: 0.7131 (Cg_endo) REVERT: A 805 PHE cc_start: 0.8378 (m-10) cc_final: 0.8139 (m-80) REVERT: B 916 PHE cc_start: 0.8057 (m-80) cc_final: 0.7588 (m-80) REVERT: C 142 MET cc_start: 0.7450 (ptt) cc_final: 0.7229 (ppp) REVERT: C 161 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.6766 (tt) REVERT: C 248 THR cc_start: 0.8543 (p) cc_final: 0.8148 (t) REVERT: C 492 ARG cc_start: 0.8120 (tpp80) cc_final: 0.7741 (mmm-85) REVERT: C 881 TYR cc_start: 0.8478 (t80) cc_final: 0.8152 (t80) REVERT: C 910 ASP cc_start: 0.8741 (t70) cc_final: 0.8040 (t0) REVERT: D 548 ARG cc_start: 0.8240 (tpt90) cc_final: 0.7493 (tpp-160) REVERT: D 744 GLN cc_start: 0.8416 (mp10) cc_final: 0.8128 (tp-100) outliers start: 50 outliers final: 36 residues processed: 581 average time/residue: 0.4198 time to fit residues: 396.4803 Evaluate side-chains 529 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 492 time to evaluate : 3.385 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 381 optimal weight: 8.9990 chunk 255 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 252 optimal weight: 2.9990 chunk 422 optimal weight: 3.9990 chunk 216 optimal weight: 20.0000 chunk 320 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 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 569 GLN ** 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 C 553 ASN ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 HIS ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 818 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.193663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.151523 restraints weight = 59687.710| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 4.10 r_work: 0.3790 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 32156 Z= 0.243 Angle : 0.681 9.371 43692 Z= 0.359 Chirality : 0.044 0.215 5072 Planarity : 0.005 0.065 5768 Dihedral : 4.351 28.383 4568 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.90 % Favored : 96.08 % Rotamer: Outliers : 2.67 % Allowed : 16.13 % Favored : 81.20 % 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: 0.32 (0.12), residues: 4312 helix: 0.94 (0.10), residues: 2601 sheet: 0.05 (0.42), residues: 147 loop : -0.93 (0.14), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 640 HIS 0.009 0.002 HIS A 496 PHE 0.037 0.003 PHE C 882 TYR 0.036 0.002 TYR C 914 ARG 0.007 0.001 ARG D 205 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 1756) hydrogen bonds : angle 4.54621 ( 5223) covalent geometry : bond 0.00575 (32156) covalent geometry : angle 0.68076 (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 600 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 520 time to evaluate : 3.410 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 331 GLU cc_start: 0.8582 (pp20) cc_final: 0.7634 (pp20) REVERT: A 370 ASP cc_start: 0.7381 (p0) cc_final: 0.7024 (p0) REVERT: A 766 PRO cc_start: 0.7648 (Cg_exo) cc_final: 0.7356 (Cg_endo) REVERT: B 150 MET cc_start: 0.7367 (mpp) cc_final: 0.7061 (mpp) REVERT: B 175 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7091 (mm-30) REVERT: B 383 GLU cc_start: 0.8264 (pp20) cc_final: 0.8014 (pt0) REVERT: B 592 LYS cc_start: 0.8874 (tttt) cc_final: 0.8439 (ttpp) REVERT: B 745 ILE cc_start: 0.3773 (OUTLIER) cc_final: 0.3508 (tp) REVERT: B 916 PHE cc_start: 0.8127 (m-80) cc_final: 0.7636 (m-80) REVERT: B 949 MET cc_start: 0.8338 (mmm) cc_final: 0.7578 (ptp) REVERT: C 142 MET cc_start: 0.7538 (ptt) cc_final: 0.7279 (ppp) REVERT: C 217 PHE cc_start: 0.8130 (m-80) cc_final: 0.7623 (m-80) REVERT: C 492 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7897 (mmm-85) REVERT: C 746 LEU cc_start: 0.7973 (tt) cc_final: 0.7618 (mp) REVERT: C 910 ASP cc_start: 0.8743 (t70) cc_final: 0.8211 (t0) REVERT: C 912 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7891 (t) REVERT: D 177 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8385 (pm20) REVERT: D 240 TYR cc_start: 0.8108 (m-10) cc_final: 0.7901 (m-10) REVERT: D 351 GLN cc_start: 0.7847 (tt0) cc_final: 0.7619 (mm-40) REVERT: D 512 PHE cc_start: 0.5304 (OUTLIER) cc_final: 0.4204 (m-10) REVERT: D 548 ARG cc_start: 0.8374 (tpt90) cc_final: 0.7653 (tpp-160) outliers start: 80 outliers final: 51 residues processed: 568 average time/residue: 0.4109 time to fit residues: 378.0991 Evaluate side-chains 534 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 479 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 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 746 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 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 912 VAL 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 512 PHE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 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: 6.9990 chunk 414 optimal weight: 9.9990 chunk 99 optimal weight: 30.0000 chunk 126 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 chunk 407 optimal weight: 6.9990 chunk 362 optimal weight: 4.9990 chunk 264 optimal weight: 0.9980 chunk 393 optimal weight: 8.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 A 801 HIS ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 818 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.195934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.155023 restraints weight = 57694.454| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 4.17 r_work: 0.3866 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32156 Z= 0.125 Angle : 0.586 13.388 43692 Z= 0.308 Chirality : 0.041 0.195 5072 Planarity : 0.005 0.060 5768 Dihedral : 4.043 22.328 4568 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.13 % Favored : 96.85 % Rotamer: Outliers : 2.27 % Allowed : 17.07 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.12), residues: 4312 helix: 1.13 (0.10), residues: 2599 sheet: 0.00 (0.40), residues: 148 loop : -0.85 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 640 HIS 0.004 0.001 HIS A 801 PHE 0.033 0.002 PHE C 882 TYR 0.037 0.002 TYR C 914 ARG 0.005 0.000 ARG D 205 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 1756) hydrogen bonds : angle 4.30949 ( 5223) covalent geometry : bond 0.00282 (32156) covalent geometry : angle 0.58596 (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 592 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 524 time to evaluate : 5.760 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 331 GLU cc_start: 0.8187 (pp20) cc_final: 0.7665 (pp20) REVERT: A 370 ASP cc_start: 0.7212 (p0) cc_final: 0.6836 (p0) REVERT: A 555 LYS cc_start: 0.8455 (mtpp) cc_final: 0.8197 (ttmt) REVERT: B 150 MET cc_start: 0.7128 (mpp) cc_final: 0.6807 (mpp) REVERT: B 175 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7055 (mm-30) REVERT: B 577 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6809 (mp10) REVERT: B 584 GLU cc_start: 0.8653 (pm20) cc_final: 0.7720 (tm-30) REVERT: B 592 LYS cc_start: 0.8846 (tttt) cc_final: 0.8432 (ttpp) REVERT: B 745 ILE cc_start: 0.3544 (OUTLIER) cc_final: 0.3183 (tp) REVERT: B 916 PHE cc_start: 0.8024 (m-80) cc_final: 0.7487 (m-80) REVERT: C 142 MET cc_start: 0.7372 (ptt) cc_final: 0.7166 (ppp) REVERT: C 217 PHE cc_start: 0.8142 (m-80) cc_final: 0.7604 (m-80) REVERT: C 342 LYS cc_start: 0.8759 (tptt) cc_final: 0.8458 (mttm) REVERT: C 492 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7841 (mmm-85) REVERT: C 746 LEU cc_start: 0.8045 (tt) cc_final: 0.7717 (mp) REVERT: C 910 ASP cc_start: 0.8798 (t70) cc_final: 0.8276 (t0) REVERT: C 912 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7352 (t) REVERT: D 240 TYR cc_start: 0.8118 (m-10) cc_final: 0.7888 (m-10) REVERT: D 269 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6968 (mm-30) REVERT: D 351 GLN cc_start: 0.7778 (tt0) cc_final: 0.7548 (mm-40) REVERT: D 548 ARG cc_start: 0.8296 (tpt90) cc_final: 0.7507 (tpp-160) REVERT: D 633 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8096 (mt) REVERT: D 667 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6989 (m-80) REVERT: D 744 GLN cc_start: 0.8497 (mp10) cc_final: 0.8084 (tp-100) outliers start: 68 outliers final: 41 residues processed: 566 average time/residue: 0.5228 time to fit residues: 488.9385 Evaluate side-chains 543 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 496 time to evaluate : 3.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 576 PHE 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 492 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 700 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 912 VAL 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 633 LEU Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 667 TYR Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 784 ASP Chi-restraints excluded: chain D residue 927 ASN Chi-restraints excluded: chain D residue 942 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 154 optimal weight: 5.9990 chunk 230 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 396 optimal weight: 0.8980 chunk 259 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 175 optimal weight: 30.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 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** D 167 ASN D 520 ASN D 846 GLN D 873 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.196994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.152485 restraints weight = 57280.725| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 3.76 r_work: 0.3893 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3111 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= 0.117 Angle : 0.583 12.977 43692 Z= 0.305 Chirality : 0.040 0.233 5072 Planarity : 0.005 0.060 5768 Dihedral : 3.898 20.423 4568 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 2.30 % Allowed : 17.10 % Favored : 80.60 % 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: 0.70 (0.13), residues: 4312 helix: 1.26 (0.10), residues: 2591 sheet: 0.11 (0.41), residues: 148 loop : -0.80 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 640 HIS 0.006 0.001 HIS A 801 PHE 0.043 0.002 PHE C 882 TYR 0.038 0.001 TYR C 914 ARG 0.006 0.000 ARG D 205 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 1756) hydrogen bonds : angle 4.23817 ( 5223) covalent geometry : bond 0.00257 (32156) covalent geometry : angle 0.58308 (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 598 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 529 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ASP cc_start: 0.7193 (p0) cc_final: 0.6784 (p0) REVERT: A 555 LYS cc_start: 0.8310 (mtpp) cc_final: 0.8098 (ttmm) REVERT: A 780 GLN cc_start: 0.6262 (mm-40) cc_final: 0.5983 (mm-40) REVERT: B 166 ASN cc_start: 0.8715 (m110) cc_final: 0.8414 (m110) REVERT: B 183 LYS cc_start: 0.7910 (tmtt) cc_final: 0.7633 (mmmm) REVERT: B 577 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: B 592 LYS cc_start: 0.8816 (tttt) cc_final: 0.8372 (ttpp) REVERT: B 883 ILE cc_start: 0.8324 (pp) cc_final: 0.8095 (pp) REVERT: B 916 PHE cc_start: 0.8100 (m-80) cc_final: 0.7273 (m-80) REVERT: C 142 MET cc_start: 0.7351 (ptt) cc_final: 0.7117 (ppp) REVERT: C 161 ILE cc_start: 0.7349 (OUTLIER) cc_final: 0.6857 (tt) REVERT: C 217 PHE cc_start: 0.8119 (m-80) cc_final: 0.7657 (m-80) REVERT: C 492 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7862 (mmm-85) REVERT: C 912 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7482 (t) REVERT: C 916 PHE cc_start: 0.7822 (m-80) cc_final: 0.7480 (m-80) REVERT: D 240 TYR cc_start: 0.8016 (m-10) cc_final: 0.7814 (m-10) REVERT: D 269 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7074 (mm-30) REVERT: D 548 ARG cc_start: 0.8282 (tpt90) cc_final: 0.7533 (tpp-160) REVERT: D 633 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8081 (mt) REVERT: D 667 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.6987 (m-80) REVERT: D 914 TYR cc_start: 0.7812 (m-10) cc_final: 0.7597 (m-10) outliers start: 69 outliers final: 44 residues processed: 570 average time/residue: 0.4140 time to fit residues: 383.8834 Evaluate side-chains 540 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 490 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 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 365 ILE 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 602 ILE Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 932 PHE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 520 ASN 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 667 TYR Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 784 ASP Chi-restraints excluded: chain D residue 927 ASN Chi-restraints excluded: chain D residue 942 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 128 optimal weight: 0.0170 chunk 20 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 347 optimal weight: 2.9990 chunk 212 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 423 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 280 optimal weight: 0.0270 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 361 ASN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 588 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 758 GLN D 490 HIS D 520 ASN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.199527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.158669 restraints weight = 57369.020| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 3.92 r_work: 0.3872 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32156 Z= 0.153 Angle : 0.627 12.147 43692 Z= 0.326 Chirality : 0.042 0.308 5072 Planarity : 0.005 0.060 5768 Dihedral : 4.025 22.503 4568 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.43 % Rotamer: Outliers : 2.73 % Allowed : 17.80 % Favored : 79.47 % 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: 0.64 (0.13), residues: 4312 helix: 1.20 (0.10), residues: 2608 sheet: -0.16 (0.41), residues: 142 loop : -0.80 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 640 HIS 0.006 0.001 HIS B 632 PHE 0.045 0.002 PHE C 882 TYR 0.030 0.002 TYR C 914 ARG 0.007 0.000 ARG D 205 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 1756) hydrogen bonds : angle 4.31912 ( 5223) covalent geometry : bond 0.00356 (32156) covalent geometry : angle 0.62678 (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 593 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 511 time to evaluate : 4.352 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 370 ASP cc_start: 0.7285 (p0) cc_final: 0.6903 (p0) REVERT: A 555 LYS cc_start: 0.8405 (mtpp) cc_final: 0.8193 (tttp) REVERT: A 667 TYR cc_start: 0.7231 (m-10) cc_final: 0.7026 (m-80) REVERT: A 766 PRO cc_start: 0.7492 (Cg_exo) cc_final: 0.7235 (Cg_endo) REVERT: B 175 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7033 (mm-30) REVERT: B 383 GLU cc_start: 0.8194 (pp20) cc_final: 0.7978 (pt0) REVERT: B 577 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: B 580 MET cc_start: 0.7775 (mmt) cc_final: 0.7463 (mmp) REVERT: B 584 GLU cc_start: 0.8514 (pm20) cc_final: 0.7743 (tm-30) REVERT: B 592 LYS cc_start: 0.8848 (tttt) cc_final: 0.8444 (ttpp) REVERT: B 916 PHE cc_start: 0.8117 (m-80) cc_final: 0.7561 (m-80) REVERT: B 949 MET cc_start: 0.8228 (mmm) cc_final: 0.7585 (ptp) REVERT: C 142 MET cc_start: 0.7339 (ptt) cc_final: 0.7134 (ppp) REVERT: C 259 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7940 (mt0) REVERT: C 332 MET cc_start: 0.8034 (pmm) cc_final: 0.7779 (pmm) REVERT: C 409 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8364 (ttm170) REVERT: C 525 LYS cc_start: 0.8550 (mmtp) cc_final: 0.8099 (pttt) REVERT: C 746 LEU cc_start: 0.8027 (tt) cc_final: 0.7679 (mp) REVERT: C 910 ASP cc_start: 0.8767 (t70) cc_final: 0.8392 (t0) REVERT: C 912 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7388 (t) REVERT: D 269 GLU cc_start: 0.7248 (mm-30) cc_final: 0.7033 (mm-30) REVERT: D 548 ARG cc_start: 0.8310 (tpt90) cc_final: 0.7510 (tpp-160) REVERT: D 633 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8033 (mt) outliers start: 82 outliers final: 52 residues processed: 561 average time/residue: 0.4362 time to fit residues: 398.4619 Evaluate side-chains 548 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 491 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 544 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 639 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL 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 544 LEU Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 354 THR 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 700 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 932 PHE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 375 ILE 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 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 661 ASN Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 784 ASP Chi-restraints excluded: chain D residue 927 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 294 optimal weight: 30.0000 chunk 38 optimal weight: 0.7980 chunk 311 optimal weight: 9.9990 chunk 256 optimal weight: 0.4980 chunk 210 optimal weight: 30.0000 chunk 16 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 92 optimal weight: 50.0000 chunk 334 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 553 ASN ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 HIS D 520 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 = 0.4657 r_free = 0.4657 target = 0.195819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.154094 restraints weight = 60563.628| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 4.57 r_work: 0.3794 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 32156 Z= 0.221 Angle : 0.714 13.956 43692 Z= 0.372 Chirality : 0.045 0.300 5072 Planarity : 0.005 0.062 5768 Dihedral : 4.406 24.621 4568 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.29 % Favored : 95.69 % Rotamer: Outliers : 2.73 % Allowed : 18.60 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.10), residues: 2614 sheet: -0.19 (0.42), residues: 135 loop : -0.85 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 640 HIS 0.008 0.001 HIS A 496 PHE 0.048 0.003 PHE A 805 TYR 0.036 0.002 TYR D 775 ARG 0.009 0.001 ARG D 205 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 1756) hydrogen bonds : angle 4.56017 ( 5223) covalent geometry : bond 0.00523 (32156) covalent geometry : angle 0.71362 (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 576 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 494 time to evaluate : 5.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ASP cc_start: 0.7363 (p0) cc_final: 0.6913 (p0) REVERT: A 525 LYS cc_start: 0.8557 (mttt) cc_final: 0.8338 (mtmm) REVERT: A 731 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.7714 (tp) REVERT: A 766 PRO cc_start: 0.7619 (Cg_exo) cc_final: 0.7372 (Cg_endo) REVERT: A 780 GLN cc_start: 0.6608 (mm-40) cc_final: 0.6298 (mm-40) REVERT: B 150 MET cc_start: 0.6985 (mpp) cc_final: 0.6766 (mpp) REVERT: B 175 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7157 (mm-30) REVERT: B 583 PRO cc_start: 0.7555 (Cg_endo) cc_final: 0.6961 (Cg_endo) REVERT: B 584 GLU cc_start: 0.8516 (pm20) cc_final: 0.7754 (tm-30) REVERT: B 592 LYS cc_start: 0.8891 (tttt) cc_final: 0.8469 (ttpp) REVERT: B 916 PHE cc_start: 0.8562 (m-80) cc_final: 0.7849 (m-80) REVERT: B 949 MET cc_start: 0.8536 (mmm) cc_final: 0.7883 (ptp) REVERT: C 259 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8085 (mt0) REVERT: C 746 LEU cc_start: 0.7941 (tt) cc_final: 0.7588 (mp) REVERT: C 910 ASP cc_start: 0.8990 (t70) cc_final: 0.8709 (t0) REVERT: D 269 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6959 (mm-30) REVERT: D 512 PHE cc_start: 0.5183 (OUTLIER) cc_final: 0.4274 (m-80) REVERT: D 548 ARG cc_start: 0.8351 (tpt90) cc_final: 0.7578 (tpp-160) REVERT: D 633 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8033 (mt) REVERT: D 744 GLN cc_start: 0.8453 (mp10) cc_final: 0.7866 (tp-100) outliers start: 82 outliers final: 64 residues processed: 544 average time/residue: 0.6285 time to fit residues: 561.2221 Evaluate side-chains 547 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 479 time to evaluate : 4.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 361 ASN 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 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 639 ASP 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 238 VAL Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 310 LEU 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 543 ASN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 889 ILE Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 408 VAL 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 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 335 GLU Chi-restraints excluded: chain D residue 345 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 475 THR Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 520 ASN Chi-restraints excluded: chain D residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 424 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 408 optimal weight: 0.8980 chunk 39 optimal weight: 0.0060 chunk 279 optimal weight: 4.9990 chunk 223 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 386 optimal weight: 10.0000 chunk 374 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 430 optimal weight: 20.0000 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 768 HIS ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.198344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.156415 restraints weight = 52134.607| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 3.46 r_work: 0.3872 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32156 Z= 0.139 Angle : 0.659 16.634 43692 Z= 0.343 Chirality : 0.042 0.325 5072 Planarity : 0.005 0.061 5768 Dihedral : 4.168 25.398 4568 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 2.07 % Allowed : 19.73 % Favored : 78.20 % 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 (0.13), residues: 4312 helix: 1.09 (0.10), residues: 2617 sheet: -0.05 (0.42), residues: 135 loop : -0.77 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 822 HIS 0.008 0.001 HIS A 801 PHE 0.041 0.002 PHE C 882 TYR 0.034 0.002 TYR C 914 ARG 0.010 0.000 ARG D 180 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 1756) hydrogen bonds : angle 4.37854 ( 5223) covalent geometry : bond 0.00318 (32156) covalent geometry : angle 0.65927 (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 586 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 524 time to evaluate : 3.436 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 228 LYS cc_start: 0.7733 (mptt) cc_final: 0.7467 (mptt) REVERT: A 370 ASP cc_start: 0.7306 (p0) cc_final: 0.6899 (p0) REVERT: A 766 PRO cc_start: 0.7628 (Cg_exo) cc_final: 0.7369 (Cg_endo) REVERT: A 780 GLN cc_start: 0.6319 (mm-40) cc_final: 0.5980 (mm-40) REVERT: B 577 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7261 (mp10) REVERT: B 583 PRO cc_start: 0.7391 (Cg_endo) cc_final: 0.6942 (Cg_endo) REVERT: B 584 GLU cc_start: 0.8338 (pm20) cc_final: 0.7748 (tm-30) REVERT: B 592 LYS cc_start: 0.8859 (tttt) cc_final: 0.8412 (ttpp) REVERT: B 916 PHE cc_start: 0.8375 (m-80) cc_final: 0.7689 (m-80) REVERT: C 259 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: C 342 LYS cc_start: 0.8660 (mttp) cc_final: 0.8396 (mttp) REVERT: C 746 LEU cc_start: 0.7974 (tt) cc_final: 0.7642 (mp) REVERT: C 838 MET cc_start: 0.7845 (mmp) cc_final: 0.7462 (ptt) REVERT: D 490 HIS cc_start: 0.7785 (m90) cc_final: 0.6829 (m-70) REVERT: D 512 PHE cc_start: 0.5111 (OUTLIER) cc_final: 0.4202 (m-80) REVERT: D 548 ARG cc_start: 0.8294 (tpt90) cc_final: 0.7508 (tpp-160) REVERT: D 633 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8029 (mt) REVERT: D 744 GLN cc_start: 0.8333 (mp10) cc_final: 0.7878 (tp-100) outliers start: 62 outliers final: 47 residues processed: 563 average time/residue: 0.4145 time to fit residues: 376.8751 Evaluate side-chains 549 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 498 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL 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 663 THR Chi-restraints excluded: chain B residue 680 LEU 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 602 ILE Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 932 PHE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 335 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 784 ASP Chi-restraints excluded: chain D residue 927 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 216 optimal weight: 40.0000 chunk 409 optimal weight: 30.0000 chunk 325 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 210 optimal weight: 0.0670 chunk 351 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 275 optimal weight: 4.9990 chunk 394 optimal weight: 0.0270 chunk 233 optimal weight: 1.9990 overall best weight: 1.5780 ------------------------------------------------------------------------------- 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 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN B 259 GLN B 588 ASN ** B 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.196174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.154345 restraints weight = 53199.315| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.30 r_work: 0.3855 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work: 0.3855 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32156 Z= 0.159 Angle : 0.684 15.009 43692 Z= 0.356 Chirality : 0.043 0.346 5072 Planarity : 0.005 0.062 5768 Dihedral : 4.194 26.276 4568 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.13 % Favored : 95.85 % Rotamer: Outliers : 1.90 % Allowed : 20.20 % Favored : 77.90 % 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: 0.52 (0.13), residues: 4312 helix: 1.09 (0.10), residues: 2614 sheet: -0.37 (0.42), residues: 133 loop : -0.78 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 822 HIS 0.010 0.001 HIS C 632 PHE 0.059 0.002 PHE A 805 TYR 0.041 0.002 TYR D 914 ARG 0.008 0.000 ARG D 205 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 1756) hydrogen bonds : angle 4.44465 ( 5223) covalent geometry : bond 0.00371 (32156) covalent geometry : angle 0.68383 (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 566 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 509 time to evaluate : 3.579 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: 0.7748 (mptt) cc_final: 0.7486 (mptt) REVERT: A 370 ASP cc_start: 0.7324 (p0) cc_final: 0.6906 (p0) REVERT: A 731 ILE cc_start: 0.8473 (mp) cc_final: 0.7990 (mm) REVERT: A 766 PRO cc_start: 0.7677 (Cg_exo) cc_final: 0.7435 (Cg_endo) REVERT: A 780 GLN cc_start: 0.6318 (mm-40) cc_final: 0.5974 (mm-40) REVERT: A 846 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8687 (mm110) REVERT: B 175 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7076 (mm-30) REVERT: B 577 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7310 (mp10) REVERT: B 583 PRO cc_start: 0.7458 (Cg_endo) cc_final: 0.7006 (Cg_endo) REVERT: B 584 GLU cc_start: 0.8366 (pm20) cc_final: 0.7773 (tm-30) REVERT: B 592 LYS cc_start: 0.8862 (tttt) cc_final: 0.8421 (ttpp) REVERT: B 678 LYS cc_start: 0.8230 (mmtp) cc_final: 0.7862 (mmtm) REVERT: B 916 PHE cc_start: 0.8137 (m-80) cc_final: 0.7481 (m-80) REVERT: C 259 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: C 342 LYS cc_start: 0.8650 (mttp) cc_final: 0.8402 (mttp) REVERT: C 525 LYS cc_start: 0.8428 (mmtp) cc_final: 0.7993 (pttt) REVERT: C 614 ASN cc_start: 0.7585 (t0) cc_final: 0.7336 (t0) REVERT: C 838 MET cc_start: 0.7882 (mmp) cc_final: 0.7655 (ptt) REVERT: C 854 THR cc_start: 0.7413 (m) cc_final: 0.7166 (p) REVERT: D 489 ASP cc_start: 0.7374 (t0) cc_final: 0.7129 (t0) REVERT: D 490 HIS cc_start: 0.7766 (m90) cc_final: 0.6921 (m-70) REVERT: D 512 PHE cc_start: 0.5316 (OUTLIER) cc_final: 0.4409 (m-80) REVERT: D 548 ARG cc_start: 0.8268 (tpt90) cc_final: 0.7537 (tpp-160) REVERT: D 633 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8040 (mt) REVERT: D 914 TYR cc_start: 0.7659 (m-80) cc_final: 0.7401 (m-80) outliers start: 57 outliers final: 50 residues processed: 545 average time/residue: 0.4144 time to fit residues: 365.7895 Evaluate side-chains 549 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 495 time to evaluate : 3.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 238 VAL 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 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 663 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 917 ASP Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 408 VAL 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 697 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 932 PHE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 335 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 784 ASP Chi-restraints excluded: chain D residue 927 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 69 optimal weight: 20.0000 chunk 395 optimal weight: 20.0000 chunk 134 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 chunk 174 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 368 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 520 ASN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.196484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.153961 restraints weight = 52815.744| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 3.40 r_work: 0.3862 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32156 Z= 0.150 Angle : 0.677 14.969 43692 Z= 0.353 Chirality : 0.043 0.316 5072 Planarity : 0.005 0.062 5768 Dihedral : 4.153 26.319 4568 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.71 % Favored : 96.27 % Rotamer: Outliers : 2.00 % Allowed : 20.17 % Favored : 77.83 % 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: 0.59 (0.13), residues: 4312 helix: 1.12 (0.10), residues: 2616 sheet: -0.15 (0.43), residues: 128 loop : -0.74 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 822 HIS 0.010 0.001 HIS C 632 PHE 0.044 0.002 PHE C 882 TYR 0.039 0.002 TYR C 914 ARG 0.007 0.000 ARG D 180 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 1756) hydrogen bonds : angle 4.43377 ( 5223) covalent geometry : bond 0.00349 (32156) covalent geometry : angle 0.67743 (43692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25857.02 seconds wall clock time: 453 minutes 28.97 seconds (27208.97 seconds total)