Starting phenix.real_space_refine on Mon Aug 25 12:33:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ymy_33947/08_2025/7ymy_33947.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymy_33947/08_2025/7ymy_33947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ymy_33947/08_2025/7ymy_33947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymy_33947/08_2025/7ymy_33947.map" model { file = "/net/cci-nas-00/data/ceres_data/7ymy_33947/08_2025/7ymy_33947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymy_33947/08_2025/7ymy_33947.cif" } resolution = 4.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.118 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 153 5.16 5 C 17546 2.51 5 N 4504 2.21 5 O 5474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27677 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "B" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "C" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.04, per 1000 atoms: 0.25 Number of scatterers: 27677 At special positions: 0 Unit cell: (155.1, 161.7, 179.3, 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 153 16.00 O 5474 8.00 N 4504 7.00 C 17546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.04 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.04 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.02 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.02 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.02 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.04 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 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 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A1401 " - " ASN A 166 " " NAG A1402 " - " ASN A 236 " " NAG A1403 " - " ASN A 619 " " NAG A1404 " - " ASN A 719 " " NAG A1405 " - " ASN A 785 " " NAG A1406 " - " ASN A 870 " " NAG A1407 " - " ASN A1213 " " NAG B1401 " - " ASN B 719 " " NAG B1402 " - " ASN B 785 " " NAG B1403 " - " ASN B 870 " " NAG B1404 " - " ASN B 619 " " NAG B1405 " - " ASN B1213 " " NAG C1401 " - " ASN C 619 " " NAG C1402 " - " ASN C1213 " " NAG C1403 " - " ASN C 166 " " NAG C1404 " - " ASN C 870 " " NAG C1405 " - " ASN C 719 " " NAG C1406 " - " ASN C 236 " " NAG C1407 " - " ASN C 785 " " NAG D 1 " - " ASN A 66 " " NAG E 1 " - " ASN A 125 " " NAG F 1 " - " ASN A 222 " " NAG G 1 " - " ASN B 125 " " NAG H 1 " - " ASN B 222 " " NAG I 1 " - " ASN B 66 " " NAG J 1 " - " ASN C 66 " " NAG K 1 " - " ASN C 222 " " NAG L 1 " - " ASN C 125 " Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6510 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 54 sheets defined 25.4% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.797A pdb=" N PHE A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 218 through 221 removed outlier: 4.216A pdb=" N ARG A 221 " --> pdb=" O ASN A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.883A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.776A pdb=" N GLN A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.196A pdb=" N LEU A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.577A pdb=" N LEU A 415 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER A 416 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 417 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 removed outlier: 3.706A pdb=" N ILE A 433 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA A 434 " --> pdb=" O ALA A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 434' Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.543A pdb=" N MET A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 457 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.950A pdb=" N SER A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 529 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.910A pdb=" N LEU A 600 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 812 removed outlier: 3.618A pdb=" N TYR A 809 " --> pdb=" O ASP A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 removed outlier: 3.671A pdb=" N ARG A 822 " --> pdb=" O GLU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 854 removed outlier: 3.978A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 896 Processing helix chain 'A' and resid 907 through 913 Processing helix chain 'A' and resid 940 through 959 removed outlier: 3.770A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 983 Processing helix chain 'A' and resid 986 through 993 removed outlier: 3.613A pdb=" N LEU A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1011 Processing helix chain 'A' and resid 1016 through 1039 removed outlier: 3.699A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1106 removed outlier: 4.096A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.849A pdb=" N PHE B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 removed outlier: 3.801A pdb=" N ARG B 221 " --> pdb=" O ASN B 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 395 through 399 removed outlier: 4.012A pdb=" N PHE B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.259A pdb=" N ILE B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 removed outlier: 4.253A pdb=" N SER B 457 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 524 through 530 removed outlier: 3.760A pdb=" N SER B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 529 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 600 removed outlier: 4.100A pdb=" N LEU B 600 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 812 Processing helix chain 'B' and resid 814 through 822 removed outlier: 3.835A pdb=" N ARG B 822 " --> pdb=" O GLU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 825 No H-bonds generated for 'chain 'B' and resid 823 through 825' Processing helix chain 'B' and resid 826 through 854 Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 908 through 915 Processing helix chain 'B' and resid 924 through 930 removed outlier: 4.166A pdb=" N TYR B 928 " --> pdb=" O CYS B 925 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 929 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 930 " --> pdb=" O GLN B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 959 removed outlier: 3.691A pdb=" N GLU B 944 " --> pdb=" O ASP B 940 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 982 Processing helix chain 'B' and resid 986 through 993 Processing helix chain 'B' and resid 993 through 1008 removed outlier: 3.516A pdb=" N ILE B 997 " --> pdb=" O ASN B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1039 removed outlier: 4.005A pdb=" N GLN B1020 " --> pdb=" O ASN B1016 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1056 Processing helix chain 'B' and resid 1059 through 1106 Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.714A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 342 through 350 removed outlier: 3.762A pdb=" N GLN C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.793A pdb=" N LEU C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 414 removed outlier: 3.531A pdb=" N LYS C 413 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 457 removed outlier: 3.724A pdb=" N MET C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER C 457 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 591 through 595 removed outlier: 3.792A pdb=" N LYS C 595 " --> pdb=" O ASN C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.772A pdb=" N LEU C 600 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 806 through 811 Processing helix chain 'C' and resid 814 through 825 removed outlier: 4.113A pdb=" N ARG C 822 " --> pdb=" O GLU C 818 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU C 823 " --> pdb=" O GLN C 819 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 854 removed outlier: 3.761A pdb=" N SER C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 875 Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 909 through 914 Processing helix chain 'C' and resid 940 through 956 Processing helix chain 'C' and resid 971 through 984 removed outlier: 3.599A pdb=" N SER C 975 " --> pdb=" O PRO C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 993 removed outlier: 3.608A pdb=" N LEU C 990 " --> pdb=" O THR C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1011 removed outlier: 3.867A pdb=" N ILE C 997 " --> pdb=" O ASN C 993 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET C1008 " --> pdb=" O ALA C1004 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN C1009 " --> pdb=" O LEU C1005 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C1011 " --> pdb=" O ALA C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1038 removed outlier: 3.652A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1041 No H-bonds generated for 'chain 'C' and resid 1039 through 1041' Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1106 removed outlier: 3.544A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS C1106 " --> pdb=" O LYS C1102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.141A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.507A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.566A pdb=" N LYS A 110 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 284 removed outlier: 5.271A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 155 removed outlier: 4.679A pdb=" N SER A 152 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 374 removed outlier: 6.698A pdb=" N GLY A 372 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N SER A 607 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 372 through 374 removed outlier: 6.698A pdb=" N GLY A 372 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N SER A 607 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 648 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.136A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 515 removed outlier: 4.659A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 659 through 664 removed outlier: 4.098A pdb=" N THR A 669 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 724 removed outlier: 6.333A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.161A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 778 through 782 removed outlier: 4.767A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 785 through 795 removed outlier: 5.563A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB8, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AB9, first strand: chain 'A' and resid 1155 through 1157 removed outlier: 3.683A pdb=" N ILE A1214 " --> pdb=" O CYS A1156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1164 through 1167 Processing sheet with id=AC2, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.498A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.748A pdb=" N TYR B 314 " --> pdb=" O ARG B 119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AC5, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.148A pdb=" N LYS B 110 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 126 through 129 removed outlier: 4.182A pdb=" N SER B 126 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AC8, first strand: chain 'B' and resid 207 through 208 Processing sheet with id=AC9, first strand: chain 'B' and resid 359 through 362 removed outlier: 3.763A pdb=" N THR B 669 " --> pdb=" O ASP B 664 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 372 through 373 removed outlier: 6.974A pdb=" N GLY B 372 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N SER B 607 " --> pdb=" O GLY B 372 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 400 through 404 Processing sheet with id=AD3, first strand: chain 'B' and resid 407 through 409 removed outlier: 3.690A pdb=" N CYS B 585 " --> pdb=" O CYS B 407 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 513 through 515 removed outlier: 4.809A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 717 through 724 removed outlier: 3.617A pdb=" N VAL B 718 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 720 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER B 761 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 722 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 737 " --> pdb=" O PRO B 730 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.477A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 778 through 795 removed outlier: 6.449A pdb=" N ASN B1145 " --> pdb=" O THR B 784 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE B 786 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE B 788 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TYR B1141 " --> pdb=" O PHE B 788 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B 790 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B1139 " --> pdb=" O VAL B 790 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN B 792 " --> pdb=" O MET B1137 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N MET B1137 " --> pdb=" O GLN B 792 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B 794 " --> pdb=" O TYR B1135 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR B1135 " --> pdb=" O TYR B 794 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AD9, first strand: chain 'B' and resid 1164 through 1167 removed outlier: 3.664A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1170 through 1174 Processing sheet with id=AE2, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.262A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.353A pdb=" N VAL C 263 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR C 283 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 265 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 279 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AE5, first strand: chain 'C' and resid 110 through 111 removed outlier: 3.881A pdb=" N LYS C 110 " --> pdb=" O TYR C 293 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA C 146 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE C 147 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 126 through 129 removed outlier: 3.881A pdb=" N SER C 126 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 152 through 155 removed outlier: 4.222A pdb=" N SER C 152 " --> pdb=" O PHE C 165 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 3.952A pdb=" N THR C 669 " --> pdb=" O ASP C 664 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 373 through 374 Processing sheet with id=AF1, first strand: chain 'C' and resid 403 through 404 removed outlier: 6.347A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 408 through 409 Processing sheet with id=AF3, first strand: chain 'C' and resid 513 through 514 removed outlier: 6.903A pdb=" N SER C 557 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N CYS C 503 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL C 555 " --> pdb=" O CYS C 503 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG C 505 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N TRP C 553 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 618 through 620 removed outlier: 4.054A pdb=" N TYR C 648 " --> pdb=" O CYS C 620 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 719 through 724 removed outlier: 5.589A pdb=" N LEU C 759 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU C 722 " --> pdb=" O LEU C 759 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 778 through 782 removed outlier: 4.648A pdb=" N VAL C1150 " --> pdb=" O LYS C1174 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 785 through 796 removed outlier: 6.067A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 802 through 804 removed outlier: 3.529A pdb=" N LYS C 933 " --> pdb=" O THR C 803 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1155 through 1156 removed outlier: 3.831A pdb=" N LEU C1155 " --> pdb=" O ILE C1165 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C1165 " --> pdb=" O LEU C1155 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 2736 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: 7.24 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6005 1.33 - 1.46: 8085 1.46 - 1.58: 14013 1.58 - 1.71: 0 1.71 - 1.84: 204 Bond restraints: 28307 Sorted by residual: bond pdb=" CA ARG C 221 " pdb=" C ARG C 221 " ideal model delta sigma weight residual 1.523 1.419 0.104 1.34e-02 5.57e+03 6.02e+01 bond pdb=" CA TYR B 270 " pdb=" C TYR B 270 " ideal model delta sigma weight residual 1.523 1.425 0.098 1.35e-02 5.49e+03 5.26e+01 bond pdb=" CA SER B 268 " pdb=" C SER B 268 " ideal model delta sigma weight residual 1.528 1.453 0.075 1.11e-02 8.12e+03 4.52e+01 bond pdb=" CA ASN C 220 " pdb=" C ASN C 220 " ideal model delta sigma weight residual 1.523 1.441 0.083 1.34e-02 5.57e+03 3.80e+01 bond pdb=" N VAL B 271 " pdb=" CA VAL B 271 " ideal model delta sigma weight residual 1.457 1.388 0.069 1.29e-02 6.01e+03 2.88e+01 ... (remaining 28302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 37413 2.48 - 4.95: 890 4.95 - 7.43: 166 7.43 - 9.91: 34 9.91 - 12.38: 6 Bond angle restraints: 38509 Sorted by residual: angle pdb=" N ARG B 269 " pdb=" CA ARG B 269 " pdb=" C ARG B 269 " ideal model delta sigma weight residual 111.40 100.13 11.27 1.22e+00 6.72e-01 8.54e+01 angle pdb=" N GLY A 866 " pdb=" CA GLY A 866 " pdb=" C GLY A 866 " ideal model delta sigma weight residual 114.67 102.29 12.38 1.41e+00 5.03e-01 7.71e+01 angle pdb=" C ILE C 57 " pdb=" N TYR C 58 " pdb=" CA TYR C 58 " ideal model delta sigma weight residual 120.68 132.57 -11.89 1.52e+00 4.33e-01 6.12e+01 angle pdb=" N LYS A 453 " pdb=" CA LYS A 453 " pdb=" C LYS A 453 " ideal model delta sigma weight residual 111.75 120.37 -8.62 1.28e+00 6.10e-01 4.54e+01 angle pdb=" C GLN A 319 " pdb=" N PRO A 320 " pdb=" CA PRO A 320 " ideal model delta sigma weight residual 119.90 113.62 6.28 1.05e+00 9.07e-01 3.57e+01 ... (remaining 38504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.66: 16337 24.66 - 49.32: 910 49.32 - 73.97: 138 73.97 - 98.63: 71 98.63 - 123.29: 22 Dihedral angle restraints: 17478 sinusoidal: 7287 harmonic: 10191 Sorted by residual: dihedral pdb=" CB CYS B 811 " pdb=" SG CYS B 811 " pdb=" SG CYS B 817 " pdb=" CB CYS B 817 " ideal model delta sinusoidal sigma weight residual -86.00 -162.44 76.44 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CB CYS C 811 " pdb=" SG CYS C 811 " pdb=" SG CYS C 817 " pdb=" CB CYS C 817 " ideal model delta sinusoidal sigma weight residual -86.00 -162.43 76.43 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CB CYS A 811 " pdb=" SG CYS A 811 " pdb=" SG CYS A 817 " pdb=" CB CYS A 817 " ideal model delta sinusoidal sigma weight residual -86.00 -160.96 74.96 1 1.00e+01 1.00e-02 7.11e+01 ... (remaining 17475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 4417 0.213 - 0.426: 20 0.426 - 0.639: 2 0.639 - 0.853: 0 0.853 - 1.066: 3 Chirality restraints: 4442 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 125 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.84e+01 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 222 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 125 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.44 -0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 4439 not shown) Planarity restraints: 4961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 875 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO B 876 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO B 876 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 876 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C1059 " -0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO C1060 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO C1060 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C1060 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 902 " -0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO C 903 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 903 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 903 " -0.047 5.00e-02 4.00e+02 ... (remaining 4958 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2890 2.74 - 3.28: 29272 3.28 - 3.82: 50296 3.82 - 4.36: 56709 4.36 - 4.90: 90998 Nonbonded interactions: 230165 Sorted by model distance: nonbonded pdb=" O PRO B 525 " pdb=" OG SER B 528 " model vdw 2.203 3.040 nonbonded pdb=" OG SER C 643 " pdb=" OD1 ASP C 645 " model vdw 2.205 3.040 nonbonded pdb=" OG SER C 268 " pdb=" O ASP C 272 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR A 397 " pdb=" O PRO A 531 " model vdw 2.212 3.040 nonbonded pdb=" NE2 GLN B 427 " pdb=" O ASN B 475 " model vdw 2.213 3.120 ... (remaining 230160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 19 through 1405) selection = chain 'B' selection = (chain 'C' and resid 19 through 1405) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 27.880 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.006 0.104 28401 Z= 0.313 Angle : 1.012 22.537 38743 Z= 0.526 Chirality : 0.064 1.066 4442 Planarity : 0.007 0.106 4933 Dihedral : 16.635 123.289 10824 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.64 % Favored : 91.19 % Rotamer: Outliers : 0.50 % Allowed : 0.80 % Favored : 98.70 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.13), residues: 3462 helix: -0.35 (0.19), residues: 697 sheet: -1.16 (0.18), residues: 728 loop : -1.88 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 181 TYR 0.038 0.002 TYR B 241 PHE 0.056 0.003 PHE C 266 TRP 0.028 0.002 TRP B1184 HIS 0.009 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00570 (28307) covalent geometry : angle 0.95899 (38509) SS BOND : bond 0.00373 ( 48) SS BOND : angle 1.78617 ( 96) hydrogen bonds : bond 0.14397 ( 1015) hydrogen bonds : angle 7.70331 ( 2736) link_ALPHA1-3 : bond 0.00424 ( 3) link_ALPHA1-3 : angle 2.06485 ( 9) link_ALPHA1-6 : bond 0.00285 ( 2) link_ALPHA1-6 : angle 1.88249 ( 6) link_BETA1-4 : bond 0.01328 ( 13) link_BETA1-4 : angle 3.94593 ( 39) link_NAG-ASN : bond 0.00820 ( 28) link_NAG-ASN : angle 6.26268 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8128 (m-10) cc_final: 0.7275 (m-80) REVERT: A 148 MET cc_start: 0.9710 (ppp) cc_final: 0.9505 (ppp) REVERT: A 169 LEU cc_start: 0.9664 (pp) cc_final: 0.9327 (tt) REVERT: A 171 LEU cc_start: 0.9436 (mp) cc_final: 0.9068 (pp) REVERT: A 240 MET cc_start: 0.7916 (mtm) cc_final: 0.7031 (mmm) REVERT: A 277 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8039 (p0) REVERT: A 757 MET cc_start: 0.8331 (tpp) cc_final: 0.7929 (tpp) REVERT: A 1062 GLU cc_start: 0.9537 (mm-30) cc_final: 0.9270 (mp0) REVERT: B 563 MET cc_start: 0.7525 (mmp) cc_final: 0.5645 (mmp) REVERT: B 569 MET cc_start: 0.9457 (mpp) cc_final: 0.9000 (mmp) REVERT: B 590 PHE cc_start: 0.8596 (m-10) cc_final: 0.8142 (t80) REVERT: B 757 MET cc_start: 0.8313 (tpp) cc_final: 0.7163 (mtt) REVERT: C 84 MET cc_start: 0.8936 (tmm) cc_final: 0.8643 (tmm) REVERT: C 161 MET cc_start: 0.9491 (ppp) cc_final: 0.9191 (ppp) REVERT: C 167 HIS cc_start: 0.8362 (OUTLIER) cc_final: 0.7958 (t70) REVERT: C 875 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8952 (tm-30) outliers start: 15 outliers final: 6 residues processed: 147 average time/residue: 0.1684 time to fit residues: 40.2193 Evaluate side-chains 96 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 50.0000 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 30.0000 overall best weight: 13.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN A1097 GLN A1129 ASN A1145 ASN A1169 ASN B 60 GLN B 521 ASN B 636 GLN B 812 ASN B1169 ASN C 60 GLN ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 GLN C 836 HIS ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 ASN C1145 ASN C1208 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.026409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.017926 restraints weight = 649342.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2362 r_free = 0.2362 target = 0.018089 restraints weight = 566808.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2369 r_free = 0.2369 target = 0.018200 restraints weight = 515961.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.018288 restraints weight = 480002.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2381 r_free = 0.2381 target = 0.018395 restraints weight = 456838.145| |-----------------------------------------------------------------------------| r_work (final): 0.2281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 28401 Z= 0.298 Angle : 0.818 18.870 38743 Z= 0.416 Chirality : 0.049 0.771 4442 Planarity : 0.006 0.065 4933 Dihedral : 11.541 120.285 4734 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 25.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.65 % Favored : 92.32 % Rotamer: Outliers : 0.13 % Allowed : 6.95 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.13), residues: 3462 helix: 0.01 (0.18), residues: 695 sheet: -1.49 (0.18), residues: 736 loop : -1.75 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 334 TYR 0.021 0.002 TYR C1142 PHE 0.040 0.003 PHE C 165 TRP 0.012 0.002 TRP C1184 HIS 0.007 0.002 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00583 (28307) covalent geometry : angle 0.77366 (38509) SS BOND : bond 0.00605 ( 48) SS BOND : angle 1.50955 ( 96) hydrogen bonds : bond 0.05317 ( 1015) hydrogen bonds : angle 7.13733 ( 2736) link_ALPHA1-3 : bond 0.00878 ( 3) link_ALPHA1-3 : angle 5.44054 ( 9) link_ALPHA1-6 : bond 0.00172 ( 2) link_ALPHA1-6 : angle 2.60280 ( 6) link_BETA1-4 : bond 0.00840 ( 13) link_BETA1-4 : angle 2.80650 ( 39) link_NAG-ASN : bond 0.00777 ( 28) link_NAG-ASN : angle 4.89579 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.780 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: A 147 PHE cc_start: 0.8865 (m-10) cc_final: 0.8469 (m-80) REVERT: A 171 LEU cc_start: 0.9693 (mp) cc_final: 0.9410 (pp) REVERT: A 757 MET cc_start: 0.9533 (tpp) cc_final: 0.9111 (tpp) REVERT: B 569 MET cc_start: 0.9469 (mpp) cc_final: 0.9094 (mmp) REVERT: B 757 MET cc_start: 0.9465 (tpp) cc_final: 0.8007 (mtt) REVERT: B 824 TYR cc_start: 0.9259 (m-10) cc_final: 0.8956 (m-80) REVERT: B 939 MET cc_start: 0.9680 (mpp) cc_final: 0.9125 (mtp) REVERT: C 84 MET cc_start: 0.9238 (tmm) cc_final: 0.9010 (mmm) REVERT: C 161 MET cc_start: 0.8875 (ppp) cc_final: 0.8563 (ppp) REVERT: C 824 TYR cc_start: 0.9535 (m-10) cc_final: 0.9208 (m-80) REVERT: C 939 MET cc_start: 0.8692 (tpt) cc_final: 0.8431 (tpt) outliers start: 4 outliers final: 1 residues processed: 99 average time/residue: 0.1657 time to fit residues: 27.4313 Evaluate side-chains 78 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 307 optimal weight: 7.9990 chunk 217 optimal weight: 20.0000 chunk 318 optimal weight: 10.0000 chunk 244 optimal weight: 50.0000 chunk 104 optimal weight: 20.0000 chunk 304 optimal weight: 6.9990 chunk 187 optimal weight: 30.0000 chunk 51 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 334 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 overall best weight: 7.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 GLN A1016 ASN ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS C 261 GLN C 475 ASN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 GLN ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1208 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.027999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.019646 restraints weight = 616600.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.019893 restraints weight = 509159.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.020103 restraints weight = 450740.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.020210 restraints weight = 411889.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.020318 restraints weight = 380899.360| |-----------------------------------------------------------------------------| r_work (final): 0.2302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28401 Z= 0.179 Angle : 0.697 19.557 38743 Z= 0.347 Chirality : 0.048 0.709 4442 Planarity : 0.005 0.075 4933 Dihedral : 10.816 120.996 4734 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.14), residues: 3462 helix: 0.22 (0.19), residues: 705 sheet: -1.50 (0.18), residues: 707 loop : -1.71 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 334 TYR 0.025 0.002 TYR C 947 PHE 0.017 0.002 PHE A 204 TRP 0.020 0.001 TRP C 253 HIS 0.006 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00366 (28307) covalent geometry : angle 0.65189 (38509) SS BOND : bond 0.00371 ( 48) SS BOND : angle 1.27825 ( 96) hydrogen bonds : bond 0.04385 ( 1015) hydrogen bonds : angle 6.80346 ( 2736) link_ALPHA1-3 : bond 0.01252 ( 3) link_ALPHA1-3 : angle 3.78275 ( 9) link_ALPHA1-6 : bond 0.00525 ( 2) link_ALPHA1-6 : angle 1.86611 ( 6) link_BETA1-4 : bond 0.00672 ( 13) link_BETA1-4 : angle 2.49168 ( 39) link_NAG-ASN : bond 0.00739 ( 28) link_NAG-ASN : angle 4.79961 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.672 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: A 147 PHE cc_start: 0.8761 (m-10) cc_final: 0.8413 (m-80) REVERT: A 171 LEU cc_start: 0.9619 (mp) cc_final: 0.9303 (pp) REVERT: A 757 MET cc_start: 0.9496 (tpp) cc_final: 0.9056 (tpp) REVERT: B 569 MET cc_start: 0.9471 (mpp) cc_final: 0.9118 (mmp) REVERT: B 757 MET cc_start: 0.9453 (tpp) cc_final: 0.7953 (mtt) REVERT: B 939 MET cc_start: 0.9642 (mpp) cc_final: 0.8994 (mtp) REVERT: C 824 TYR cc_start: 0.9544 (m-10) cc_final: 0.9195 (m-80) REVERT: C 943 MET cc_start: 0.9744 (ttp) cc_final: 0.9533 (ttp) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.1493 time to fit residues: 22.9187 Evaluate side-chains 74 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 11 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 294 optimal weight: 0.9990 chunk 308 optimal weight: 8.9990 chunk 313 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 244 optimal weight: 30.0000 chunk 165 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN A1097 GLN B 907 GLN ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN C1208 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.028354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.020275 restraints weight = 603617.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.020409 restraints weight = 502921.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.020558 restraints weight = 429815.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.020722 restraints weight = 388497.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.020860 restraints weight = 357390.343| |-----------------------------------------------------------------------------| r_work (final): 0.2321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28401 Z= 0.136 Angle : 0.668 18.713 38743 Z= 0.327 Chirality : 0.048 0.742 4442 Planarity : 0.005 0.063 4933 Dihedral : 10.014 119.654 4734 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.14), residues: 3462 helix: 0.44 (0.19), residues: 709 sheet: -1.42 (0.18), residues: 713 loop : -1.68 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 119 TYR 0.019 0.001 TYR C 184 PHE 0.016 0.001 PHE C 967 TRP 0.013 0.001 TRP B 253 HIS 0.006 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00288 (28307) covalent geometry : angle 0.62451 (38509) SS BOND : bond 0.00352 ( 48) SS BOND : angle 1.30559 ( 96) hydrogen bonds : bond 0.03947 ( 1015) hydrogen bonds : angle 6.55012 ( 2736) link_ALPHA1-3 : bond 0.01258 ( 3) link_ALPHA1-3 : angle 3.85639 ( 9) link_ALPHA1-6 : bond 0.00683 ( 2) link_ALPHA1-6 : angle 1.53707 ( 6) link_BETA1-4 : bond 0.00656 ( 13) link_BETA1-4 : angle 2.37663 ( 39) link_NAG-ASN : bond 0.00658 ( 28) link_NAG-ASN : angle 4.53921 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.753 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: A 147 PHE cc_start: 0.8697 (m-10) cc_final: 0.8379 (m-80) REVERT: A 171 LEU cc_start: 0.9597 (mp) cc_final: 0.9346 (pp) REVERT: A 757 MET cc_start: 0.9488 (tpp) cc_final: 0.9068 (tpp) REVERT: B 278 MET cc_start: 0.9137 (mmp) cc_final: 0.8934 (mmp) REVERT: B 569 MET cc_start: 0.9419 (mpp) cc_final: 0.9132 (mmp) REVERT: B 757 MET cc_start: 0.9444 (tpp) cc_final: 0.8112 (mtt) REVERT: B 939 MET cc_start: 0.9622 (mpp) cc_final: 0.8977 (mtp) REVERT: C 278 MET cc_start: 0.8910 (mmm) cc_final: 0.8655 (tpp) REVERT: C 824 TYR cc_start: 0.9499 (m-10) cc_final: 0.9095 (m-80) REVERT: C 939 MET cc_start: 0.8810 (tpt) cc_final: 0.8430 (tpt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1595 time to fit residues: 24.6215 Evaluate side-chains 76 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 182 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 256 optimal weight: 30.0000 chunk 285 optimal weight: 40.0000 chunk 328 optimal weight: 5.9990 chunk 48 optimal weight: 40.0000 chunk 172 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN A 637 ASN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 475 ASN ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 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 = 0.2752 r_free = 0.2752 target = 0.026528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.018851 restraints weight = 636885.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.019132 restraints weight = 521120.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.019300 restraints weight = 453204.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.019480 restraints weight = 412152.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.019540 restraints weight = 385022.675| |-----------------------------------------------------------------------------| r_work (final): 0.2299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28401 Z= 0.201 Angle : 0.698 18.467 38743 Z= 0.347 Chirality : 0.048 0.749 4442 Planarity : 0.005 0.065 4933 Dihedral : 9.416 118.670 4734 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.14), residues: 3462 helix: 0.46 (0.19), residues: 704 sheet: -1.54 (0.18), residues: 726 loop : -1.68 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 62 TYR 0.016 0.002 TYR C1142 PHE 0.020 0.002 PHE C 266 TRP 0.009 0.001 TRP C 310 HIS 0.005 0.001 HIS C1122 Details of bonding type rmsd covalent geometry : bond 0.00407 (28307) covalent geometry : angle 0.65436 (38509) SS BOND : bond 0.00422 ( 48) SS BOND : angle 1.42794 ( 96) hydrogen bonds : bond 0.04334 ( 1015) hydrogen bonds : angle 6.74637 ( 2736) link_ALPHA1-3 : bond 0.01000 ( 3) link_ALPHA1-3 : angle 4.06411 ( 9) link_ALPHA1-6 : bond 0.00724 ( 2) link_ALPHA1-6 : angle 1.82896 ( 6) link_BETA1-4 : bond 0.00738 ( 13) link_BETA1-4 : angle 2.45277 ( 39) link_NAG-ASN : bond 0.00685 ( 28) link_NAG-ASN : angle 4.64365 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.708 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: A 147 PHE cc_start: 0.8649 (m-10) cc_final: 0.8301 (m-80) REVERT: A 171 LEU cc_start: 0.9601 (mp) cc_final: 0.9311 (pp) REVERT: A 757 MET cc_start: 0.9485 (tpp) cc_final: 0.9141 (tpp) REVERT: A 939 MET cc_start: 0.9590 (mpp) cc_final: 0.9081 (mtp) REVERT: A 943 MET cc_start: 0.9382 (mtp) cc_final: 0.9121 (mtp) REVERT: B 569 MET cc_start: 0.9408 (mpp) cc_final: 0.9108 (mmp) REVERT: B 757 MET cc_start: 0.9459 (tpp) cc_final: 0.8217 (mtt) REVERT: C 939 MET cc_start: 0.8692 (tpt) cc_final: 0.7977 (tpt) outliers start: 2 outliers final: 1 residues processed: 87 average time/residue: 0.1513 time to fit residues: 22.3853 Evaluate side-chains 74 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 303 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 50.0000 chunk 325 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 230 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 45 optimal weight: 50.0000 chunk 126 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 98 GLN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.027462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.019120 restraints weight = 618811.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.019364 restraints weight = 509583.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.019602 restraints weight = 443018.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.019829 restraints weight = 403161.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.019870 restraints weight = 375412.264| |-----------------------------------------------------------------------------| r_work (final): 0.2303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28401 Z= 0.157 Angle : 0.669 18.218 38743 Z= 0.329 Chirality : 0.047 0.712 4442 Planarity : 0.005 0.064 4933 Dihedral : 9.185 116.400 4734 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.14), residues: 3462 helix: 0.59 (0.19), residues: 703 sheet: -1.52 (0.18), residues: 710 loop : -1.62 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 822 TYR 0.014 0.001 TYR C1142 PHE 0.013 0.001 PHE C 266 TRP 0.014 0.001 TRP C 253 HIS 0.003 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00329 (28307) covalent geometry : angle 0.62756 (38509) SS BOND : bond 0.00347 ( 48) SS BOND : angle 1.39209 ( 96) hydrogen bonds : bond 0.03968 ( 1015) hydrogen bonds : angle 6.59543 ( 2736) link_ALPHA1-3 : bond 0.00985 ( 3) link_ALPHA1-3 : angle 3.92499 ( 9) link_ALPHA1-6 : bond 0.00675 ( 2) link_ALPHA1-6 : angle 1.48358 ( 6) link_BETA1-4 : bond 0.00710 ( 13) link_BETA1-4 : angle 2.27482 ( 39) link_NAG-ASN : bond 0.00631 ( 28) link_NAG-ASN : angle 4.37839 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.053 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: A 147 PHE cc_start: 0.8597 (m-80) cc_final: 0.8251 (m-80) REVERT: A 171 LEU cc_start: 0.9576 (mp) cc_final: 0.9304 (pp) REVERT: A 757 MET cc_start: 0.9476 (tpp) cc_final: 0.9108 (tpp) REVERT: A 939 MET cc_start: 0.9636 (mpp) cc_final: 0.9120 (mtp) REVERT: A 943 MET cc_start: 0.9401 (mtp) cc_final: 0.9128 (mtp) REVERT: B 569 MET cc_start: 0.9385 (mpp) cc_final: 0.9108 (mmp) REVERT: B 757 MET cc_start: 0.9419 (tpp) cc_final: 0.8145 (mtt) REVERT: B 939 MET cc_start: 0.9480 (pmm) cc_final: 0.9252 (pmm) REVERT: C 939 MET cc_start: 0.8620 (tpt) cc_final: 0.8395 (tpt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1834 time to fit residues: 25.4808 Evaluate side-chains 75 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 294 optimal weight: 30.0000 chunk 292 optimal weight: 3.9990 chunk 188 optimal weight: 30.0000 chunk 324 optimal weight: 7.9990 chunk 317 optimal weight: 20.0000 chunk 231 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 18 optimal weight: 50.0000 chunk 190 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 11 optimal weight: 0.2980 overall best weight: 6.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.025398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2208 r_free = 0.2208 target = 0.016079 restraints weight = 643141.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2230 r_free = 0.2230 target = 0.016423 restraints weight = 501395.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2246 r_free = 0.2246 target = 0.016710 restraints weight = 426299.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2256 r_free = 0.2256 target = 0.016840 restraints weight = 379440.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2263 r_free = 0.2263 target = 0.016959 restraints weight = 351289.778| |-----------------------------------------------------------------------------| r_work (final): 0.2329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28401 Z= 0.161 Angle : 0.664 17.759 38743 Z= 0.328 Chirality : 0.047 0.760 4442 Planarity : 0.004 0.057 4933 Dihedral : 8.993 116.072 4734 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.14), residues: 3462 helix: 0.67 (0.20), residues: 704 sheet: -1.47 (0.18), residues: 730 loop : -1.60 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 334 TYR 0.016 0.001 TYR C 184 PHE 0.017 0.002 PHE B 281 TRP 0.012 0.001 TRP C 253 HIS 0.006 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00336 (28307) covalent geometry : angle 0.62379 (38509) SS BOND : bond 0.00369 ( 48) SS BOND : angle 1.36604 ( 96) hydrogen bonds : bond 0.03976 ( 1015) hydrogen bonds : angle 6.57634 ( 2736) link_ALPHA1-3 : bond 0.00991 ( 3) link_ALPHA1-3 : angle 3.85096 ( 9) link_ALPHA1-6 : bond 0.00669 ( 2) link_ALPHA1-6 : angle 1.48577 ( 6) link_BETA1-4 : bond 0.00705 ( 13) link_BETA1-4 : angle 2.25827 ( 39) link_NAG-ASN : bond 0.00614 ( 28) link_NAG-ASN : angle 4.30648 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.919 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: A 147 PHE cc_start: 0.8796 (m-80) cc_final: 0.8524 (m-80) REVERT: A 939 MET cc_start: 0.8989 (mpp) cc_final: 0.8668 (mtp) REVERT: B 569 MET cc_start: 0.9199 (mpp) cc_final: 0.8918 (mmp) REVERT: B 757 MET cc_start: 0.7833 (tpp) cc_final: 0.6577 (mtt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1587 time to fit residues: 21.9499 Evaluate side-chains 71 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 67 optimal weight: 0.9980 chunk 244 optimal weight: 50.0000 chunk 202 optimal weight: 6.9990 chunk 253 optimal weight: 20.0000 chunk 339 optimal weight: 9.9990 chunk 47 optimal weight: 40.0000 chunk 266 optimal weight: 40.0000 chunk 250 optimal weight: 1.9990 chunk 246 optimal weight: 30.0000 chunk 284 optimal weight: 4.9990 chunk 265 optimal weight: 30.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.027293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.019068 restraints weight = 621734.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.019353 restraints weight = 506844.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.019546 restraints weight = 436096.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.019728 restraints weight = 398213.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.019808 restraints weight = 371555.510| |-----------------------------------------------------------------------------| r_work (final): 0.2306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28401 Z= 0.145 Angle : 0.667 17.748 38743 Z= 0.327 Chirality : 0.047 0.722 4442 Planarity : 0.004 0.062 4933 Dihedral : 8.850 115.259 4734 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.14), residues: 3462 helix: 0.78 (0.20), residues: 699 sheet: -1.42 (0.18), residues: 723 loop : -1.57 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 629 TYR 0.014 0.001 TYR C 184 PHE 0.015 0.001 PHE A 266 TRP 0.012 0.001 TRP B 253 HIS 0.007 0.001 HIS B 681 Details of bonding type rmsd covalent geometry : bond 0.00311 (28307) covalent geometry : angle 0.62735 (38509) SS BOND : bond 0.00370 ( 48) SS BOND : angle 1.61307 ( 96) hydrogen bonds : bond 0.03876 ( 1015) hydrogen bonds : angle 6.51652 ( 2736) link_ALPHA1-3 : bond 0.00966 ( 3) link_ALPHA1-3 : angle 3.68764 ( 9) link_ALPHA1-6 : bond 0.00681 ( 2) link_ALPHA1-6 : angle 1.49792 ( 6) link_BETA1-4 : bond 0.00713 ( 13) link_BETA1-4 : angle 2.21022 ( 39) link_NAG-ASN : bond 0.00638 ( 28) link_NAG-ASN : angle 4.25385 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.917 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: A 757 MET cc_start: 0.9602 (tpt) cc_final: 0.9266 (tpp) REVERT: A 939 MET cc_start: 0.9689 (mpp) cc_final: 0.9233 (mtp) REVERT: A 943 MET cc_start: 0.9414 (mtp) cc_final: 0.9152 (mtp) REVERT: B 569 MET cc_start: 0.9412 (mpp) cc_final: 0.9168 (mmp) REVERT: B 757 MET cc_start: 0.9349 (tpp) cc_final: 0.8282 (mtt) REVERT: B 939 MET cc_start: 0.9555 (pmm) cc_final: 0.9350 (pmm) REVERT: C 278 MET cc_start: 0.8964 (mmm) cc_final: 0.8516 (mmp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1751 time to fit residues: 24.1589 Evaluate side-chains 71 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 196 optimal weight: 8.9990 chunk 17 optimal weight: 0.0050 chunk 112 optimal weight: 20.0000 chunk 258 optimal weight: 30.0000 chunk 305 optimal weight: 8.9990 chunk 339 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 244 optimal weight: 50.0000 chunk 53 optimal weight: 50.0000 overall best weight: 9.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.025111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.017095 restraints weight = 648438.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.017288 restraints weight = 561077.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2354 r_free = 0.2354 target = 0.017390 restraints weight = 507983.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.017589 restraints weight = 471858.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.017637 restraints weight = 444602.738| |-----------------------------------------------------------------------------| r_work (final): 0.2349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28401 Z= 0.216 Angle : 0.717 17.633 38743 Z= 0.359 Chirality : 0.048 0.760 4442 Planarity : 0.005 0.057 4933 Dihedral : 8.879 115.446 4734 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.14), residues: 3462 helix: 0.60 (0.19), residues: 689 sheet: -1.57 (0.18), residues: 717 loop : -1.61 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 401 TYR 0.025 0.002 TYR C 184 PHE 0.030 0.002 PHE C 165 TRP 0.010 0.001 TRP C 253 HIS 0.007 0.002 HIS B1138 Details of bonding type rmsd covalent geometry : bond 0.00439 (28307) covalent geometry : angle 0.67686 (38509) SS BOND : bond 0.00484 ( 48) SS BOND : angle 1.77063 ( 96) hydrogen bonds : bond 0.04381 ( 1015) hydrogen bonds : angle 6.84983 ( 2736) link_ALPHA1-3 : bond 0.00777 ( 3) link_ALPHA1-3 : angle 4.05954 ( 9) link_ALPHA1-6 : bond 0.00596 ( 2) link_ALPHA1-6 : angle 1.58681 ( 6) link_BETA1-4 : bond 0.00763 ( 13) link_BETA1-4 : angle 2.30190 ( 39) link_NAG-ASN : bond 0.00696 ( 28) link_NAG-ASN : angle 4.39841 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.984 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: A 939 MET cc_start: 0.9498 (mpp) cc_final: 0.9228 (mtp) REVERT: A 943 MET cc_start: 0.9470 (mtp) cc_final: 0.9221 (mtp) REVERT: B 569 MET cc_start: 0.9459 (mpp) cc_final: 0.9175 (mmp) REVERT: B 757 MET cc_start: 0.9002 (tpp) cc_final: 0.8335 (mtt) REVERT: C 84 MET cc_start: 0.9418 (tmm) cc_final: 0.9062 (tmm) REVERT: C 278 MET cc_start: 0.8951 (mmm) cc_final: 0.8697 (mmp) REVERT: C 1137 MET cc_start: 0.9725 (mpp) cc_final: 0.9410 (mpp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1678 time to fit residues: 23.8388 Evaluate side-chains 74 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 55 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 307 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 176 optimal weight: 50.0000 chunk 306 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 317 optimal weight: 6.9990 chunk 271 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.026820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.018663 restraints weight = 624317.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.018922 restraints weight = 506671.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.019199 restraints weight = 435166.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.019289 restraints weight = 395593.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.019432 restraints weight = 371795.308| |-----------------------------------------------------------------------------| r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28401 Z= 0.150 Angle : 0.692 17.464 38743 Z= 0.341 Chirality : 0.048 0.728 4442 Planarity : 0.005 0.113 4933 Dihedral : 8.820 115.690 4734 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.14), residues: 3462 helix: 0.65 (0.20), residues: 711 sheet: -1.49 (0.18), residues: 707 loop : -1.57 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 401 TYR 0.046 0.002 TYR A 184 PHE 0.033 0.002 PHE C 165 TRP 0.024 0.001 TRP B 253 HIS 0.004 0.001 HIS B1122 Details of bonding type rmsd covalent geometry : bond 0.00324 (28307) covalent geometry : angle 0.65330 (38509) SS BOND : bond 0.00491 ( 48) SS BOND : angle 1.67299 ( 96) hydrogen bonds : bond 0.03887 ( 1015) hydrogen bonds : angle 6.66405 ( 2736) link_ALPHA1-3 : bond 0.00849 ( 3) link_ALPHA1-3 : angle 3.62809 ( 9) link_ALPHA1-6 : bond 0.00650 ( 2) link_ALPHA1-6 : angle 1.56451 ( 6) link_BETA1-4 : bond 0.00720 ( 13) link_BETA1-4 : angle 2.16947 ( 39) link_NAG-ASN : bond 0.00635 ( 28) link_NAG-ASN : angle 4.28076 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.075 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: A 943 MET cc_start: 0.9432 (mtp) cc_final: 0.9186 (mtp) REVERT: A 1008 MET cc_start: 0.9662 (ppp) cc_final: 0.9382 (ttt) REVERT: B 569 MET cc_start: 0.9429 (mpp) cc_final: 0.9228 (mmp) REVERT: B 757 MET cc_start: 0.8951 (tpp) cc_final: 0.8275 (mtt) REVERT: C 84 MET cc_start: 0.9388 (tmm) cc_final: 0.9046 (tmm) REVERT: C 939 MET cc_start: 0.8108 (tpt) cc_final: 0.7853 (tpt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1508 time to fit residues: 21.7449 Evaluate side-chains 74 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 62 optimal weight: 8.9990 chunk 297 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 193 optimal weight: 8.9990 chunk 33 optimal weight: 30.0000 chunk 45 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 257 optimal weight: 0.2980 chunk 317 optimal weight: 40.0000 chunk 122 optimal weight: 30.0000 chunk 311 optimal weight: 20.0000 overall best weight: 6.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 GLN ** B1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.026454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.018557 restraints weight = 632658.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.018696 restraints weight = 520274.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.018889 restraints weight = 450793.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.018993 restraints weight = 407851.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.019100 restraints weight = 377139.869| |-----------------------------------------------------------------------------| r_work (final): 0.2362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28401 Z= 0.177 Angle : 0.692 17.206 38743 Z= 0.345 Chirality : 0.048 0.731 4442 Planarity : 0.005 0.087 4933 Dihedral : 8.723 114.596 4734 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.14), residues: 3462 helix: 0.71 (0.20), residues: 699 sheet: -1.55 (0.18), residues: 724 loop : -1.54 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 401 TYR 0.021 0.002 TYR C 184 PHE 0.036 0.002 PHE C 165 TRP 0.018 0.001 TRP B 253 HIS 0.006 0.001 HIS B 681 Details of bonding type rmsd covalent geometry : bond 0.00368 (28307) covalent geometry : angle 0.65370 (38509) SS BOND : bond 0.00427 ( 48) SS BOND : angle 1.62319 ( 96) hydrogen bonds : bond 0.04054 ( 1015) hydrogen bonds : angle 6.74041 ( 2736) link_ALPHA1-3 : bond 0.00870 ( 3) link_ALPHA1-3 : angle 3.78494 ( 9) link_ALPHA1-6 : bond 0.00618 ( 2) link_ALPHA1-6 : angle 1.57389 ( 6) link_BETA1-4 : bond 0.00752 ( 13) link_BETA1-4 : angle 2.22894 ( 39) link_NAG-ASN : bond 0.00633 ( 28) link_NAG-ASN : angle 4.25330 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3593.24 seconds wall clock time: 64 minutes 18.13 seconds (3858.13 seconds total)