Starting phenix.real_space_refine on Fri Mar 6 01:09:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nd5_12276/03_2026/7nd5_12276.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nd5_12276/03_2026/7nd5_12276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nd5_12276/03_2026/7nd5_12276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nd5_12276/03_2026/7nd5_12276.map" model { file = "/net/cci-nas-00/data/ceres_data/7nd5_12276/03_2026/7nd5_12276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nd5_12276/03_2026/7nd5_12276.cif" } resolution = 3.4 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= 0.002 sd= 0.019 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 118 5.16 5 C 17012 2.51 5 N 4374 2.21 5 O 5206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26710 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 7628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7628 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 49, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 9, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 7571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7571 Classifications: {'peptide': 989} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 49, 'TRANS': 939} Chain breaks: 9 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 5, 'GLU:plan': 10, 'GLN:plan1': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 7582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7582 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 8, 'GLN:plan1': 3, 'GLU:plan': 10, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "H" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1597 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1646 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 215, 1642 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 215, 1642 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1673 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: 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: "F" 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: "G" 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: "M" 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: "N" 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: "O" 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: "P" 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.27, per 1000 atoms: 0.23 Number of scatterers: 26710 At special positions: 0 Unit cell: (123.82, 136.12, 245.18, 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 118 16.00 O 5206 8.00 N 4374 7.00 C 17012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1134 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 1.2 seconds 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6370 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 54 sheets defined 25.6% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.989A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.203A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 852 through 856 removed outlier: 3.661A pdb=" N ASN A 856 " --> pdb=" O GLN A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.766A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.505A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.707A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.428A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.001A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.530A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.661A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.561A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.337A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.700A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.598A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.959A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.659A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.235A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.546A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.738A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.057A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.097A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 205 through 208 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.709A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 185 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.753A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.648A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.548A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.661A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.729A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.996A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB2, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.103A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.586A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 29 removed outlier: 6.031A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.617A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.406A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.610A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.604A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC9, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.893A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.567A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.995A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.913A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.835A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 309 through 319 removed outlier: 5.948A pdb=" N LYS C 310 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLY C 601 " --> pdb=" O LYS C 310 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.508A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.192A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.105A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.797A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.340A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.068A pdb=" N TYR H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.112A pdb=" N VAL H 106 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.926A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.926A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 155 through 158 removed outlier: 4.282A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.907A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.779A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 155 through 157 removed outlier: 4.343A pdb=" N TRP L 150 " --> pdb=" O GLN L 157 " (cutoff:3.500A) 1180 hydrogen bonds defined for protein. 3156 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.11 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8474 1.34 - 1.46: 6642 1.46 - 1.58: 12033 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 27296 Sorted by residual: bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.48e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.39e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.17e+00 bond pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 1.808 1.751 0.057 3.30e-02 9.18e+02 3.01e+00 ... (remaining 27291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 36621 1.96 - 3.92: 546 3.92 - 5.88: 37 5.88 - 7.84: 5 7.84 - 9.81: 2 Bond angle restraints: 37211 Sorted by residual: angle pdb=" N THR A 124 " pdb=" CA THR A 124 " pdb=" C THR A 124 " ideal model delta sigma weight residual 114.75 110.04 4.71 1.26e+00 6.30e-01 1.40e+01 angle pdb=" CA CYS C 738 " pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " ideal model delta sigma weight residual 114.40 107.19 7.21 2.30e+00 1.89e-01 9.84e+00 angle pdb=" CA LEU A 517 " pdb=" CB LEU A 517 " pdb=" CG LEU A 517 " ideal model delta sigma weight residual 116.30 126.11 -9.81 3.50e+00 8.16e-02 7.85e+00 angle pdb=" C CYS C 738 " pdb=" CA CYS C 738 " pdb=" CB CYS C 738 " ideal model delta sigma weight residual 110.79 106.27 4.52 1.66e+00 3.63e-01 7.43e+00 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 113.95 -3.25 1.22e+00 6.72e-01 7.11e+00 ... (remaining 37206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 15848 17.50 - 35.01: 752 35.01 - 52.51: 168 52.51 - 70.01: 44 70.01 - 87.51: 27 Dihedral angle restraints: 16839 sinusoidal: 6940 harmonic: 9899 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -159.50 73.50 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -158.42 72.42 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -158.21 72.21 1 1.00e+01 1.00e-02 6.67e+01 ... (remaining 16836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2969 0.038 - 0.075: 970 0.075 - 0.113: 398 0.113 - 0.150: 99 0.150 - 0.188: 10 Chirality restraints: 4446 Sorted by residual: chirality pdb=" CG LEU A 916 " pdb=" CB LEU A 916 " pdb=" CD1 LEU A 916 " pdb=" CD2 LEU A 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 4443 not shown) Planarity restraints: 4771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 122 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.15e+00 pdb=" C ASN B 122 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN B 122 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA B 123 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 122 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C ASN A 122 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN A 122 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 123 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 122 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.07e+00 pdb=" C ASN C 122 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN C 122 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA C 123 " 0.014 2.00e-02 2.50e+03 ... (remaining 4768 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 831 2.71 - 3.26: 26186 3.26 - 3.81: 42308 3.81 - 4.35: 53193 4.35 - 4.90: 91204 Nonbonded interactions: 213722 Sorted by model distance: nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.167 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.217 3.040 nonbonded pdb=" OD2 ASP H 98 " pdb=" OH TYR L 98 " model vdw 2.256 3.040 nonbonded pdb=" O ILE C 742 " pdb=" NH1 ARG C1000 " model vdw 2.262 3.120 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.263 3.040 ... (remaining 213717 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 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 52 or (resid 53 and ( \ name N or name CA or name C or name O or name CB )) or resid 54 through 66 or re \ sid 82 through 87 or (resid 88 and (name N or name CA or name C or name O or nam \ e CB )) or resid 89 through 95 or (resid 96 through 97 and (name N or name CA or \ name C or name O or name CB )) or resid 98 through 109 or (resid 110 and (name \ N or name CA or name C or name O or name CB )) or resid 111 or (resid 112 throug \ h 113 and (name N or name CA or name C or name O or name CB )) or resid 116 thro \ ugh 124 or (resid 125 and (name N or name CA or name C or name O or name CB )) o \ r resid 126 through 131 or (resid 132 and (name N or name CA or name C or name O \ or name CB )) or resid 133 or (resid 134 through 138 and (name N or name CA or \ name C or name O or name CB )) or resid 139 through 140 or resid 166 through 168 \ or (resid 169 and (name N or name CA or name C or name O or name CB )) or resid \ 170 through 171 or (resid 172 through 188 and (name N or name CA or name C or n \ ame O or name CB )) or resid 189 through 196 or resid 200 through 209 or (resid \ 210 and (name N or name CA or name C or name O or name CB )) or (resid 215 and ( \ name N or name CA or name C or name O or name CB )) or resid 216 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 219 \ through 223 or (resid 224 and (name N or name CA or name C or name O or name CB \ )) or resid 225 through 263 or resid 265 through 308 or (resid 309 and (name N \ or name CA or name C or name O or name CB )) or resid 310 through 323 or (resid \ 324 and (name N or name CA or name C or name O or name CB )) or resid 325 throug \ h 332 or (resid 333 and (name N or name CA or name C or name O or name CB )) or \ resid 334 through 457 or (resid 458 and (name N or name CA or name C or name O o \ r name CB )) or resid 459 through 528 or (resid 529 and (name N or name CA or na \ me C or name O or name CB )) or resid 530 through 536 or (resid 537 and (name N \ or name CA or name C or name O or name CB )) or resid 538 through 747 or (resid \ 748 and (name N or name CA or name C or name O or name CB )) or resid 749 throug \ h 793 or (resid 794 and (name N or name CA or name C or name O or name CB )) or \ resid 795 or (resid 796 and (name N or name CA or name C or name O or name CB )) \ or resid 797 through 827 or (resid 854 through 855 and (name N or name CA or na \ me C or name O or name CB )) or resid 856 through 867 or (resid 868 and (name N \ or name CA or name C or name O or name CB )) or resid 869 through 939 or (resid \ 940 and (name N or name CA or name C or name O or name CB )) or resid 941 throug \ h 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or \ resid 986 through 987 or (resid 988 through 989 and (name N or name CA or name C \ or name O or name CB )) or resid 990 through 1141 or (resid 1142 and (name N or \ name CA or name C or name O or name CB )) or resid 1143 through 1144 or (resid \ 1145 through 1146 and (name N or name CA or name C or name O or name CB )) or re \ sid 1147 through 1308)) selection = (chain 'B' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 109 or (resid 110 and (name N or name CA or name C or name O or n \ ame CB )) or resid 111 or (resid 112 through 113 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or \ name CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 39 through 140 or resid 166 through 190 or (resid 191 and (name N or name CA or \ name C or name O or name CB )) or resid 192 through 195 or (resid 196 and (name \ N or name CA or name C or name O or name CB )) or resid 200 through 205 or (resi \ d 206 and (name N or name CA or name C or name O or name CB )) or resid 207 thro \ ugh 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) o \ r resid 238 through 241 or (resid 242 through 263 and (name N or name CA or name \ C or name O or name CB )) or resid 265 through 280 or (resid 281 and (name N or \ name CA or name C or name O or name CB )) or resid 282 through 297 or (resid 29 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 299 through \ 323 or (resid 324 and (name N or name CA or name C or name O or name CB )) or re \ sid 325 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 457 or (resid 458 and (name N or name CA or name \ C or name O or name CB )) or resid 459 through 567 or (resid 568 and (name N or \ name CA or name C or name O or name CB )) or resid 569 through 570 or (resid 57 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 572 through \ 579 or (resid 580 and (name N or name CA or name C or name O or name CB )) or re \ sid 581 or (resid 582 through 583 and (name N or name CA or name C or name O or \ name CB )) or resid 584 through 613 or (resid 614 and (name N or name CA or name \ C or name O or name CB )) or resid 615 through 618 or (resid 619 and (name N or \ name CA or name C or name O or name CB )) or resid 620 through 676 or resid 690 \ through 744 or (resid 745 and (name N or name CA or name C or name O or name CB \ )) or resid 746 through 827 or (resid 854 through 855 and (name N or name CA or \ name C or name O or name CB )) or resid 856 through 867 or (resid 868 and (name \ N or name CA or name C or name O or name CB )) or resid 869 through 939 or (res \ id 940 and (name N or name CA or name C or name O or name CB )) or resid 941 thr \ ough 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) \ or resid 986 through 987 or (resid 988 through 989 and (name N or name CA or nam \ e C or name O or name CB )) or resid 990 through 1143 or (resid 1144 through 114 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 1147 through \ 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 through 113 or resid 116 through 134 or (resid 135 through 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 140 or resid 1 \ 66 through 172 or (resid 188 and (name N or name CA or name C or name O or name \ CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or name C or \ name O or name CB )) or resid 200 through 205 or (resid 206 and (name N or name \ CA or name C or name O or name CB )) or resid 207 through 209 or (resid 210 and \ (name N or name CA or name C or name O or name CB )) or resid 215 through 217 o \ r (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 19 through 223 or (resid 224 and (name N or name CA or name C or name O or name \ CB )) or resid 225 through 236 or (resid 237 and (name N or name CA or name C or \ name O or name CB )) or resid 238 through 297 or (resid 298 and (name N or name \ CA or name C or name O or name CB )) or resid 299 through 308 or (resid 309 and \ (name N or name CA or name C or name O or name CB )) or resid 310 through 332 o \ r (resid 333 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 34 through 388 or (resid 389 and (name N or name CA or name C or name O or name \ CB )) or resid 390 through 527 or (resid 528 through 529 and (name N or name CA \ or name C or name O or name CB )) or resid 530 through 536 or (resid 537 and (na \ me N or name CA or name C or name O or name CB )) or resid 538 through 553 or (r \ esid 554 and (name N or name CA or name C or name O or name CB )) or resid 555 t \ hrough 557 or (resid 558 and (name N or name CA or name C or name O or name CB ) \ ) or resid 559 through 567 or (resid 568 and (name N or name CA or name C or nam \ e O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name CA \ or name C or name O or name CB )) or resid 572 through 579 or (resid 580 and (na \ me N or name CA or name C or name O or name CB )) or resid 581 or (resid 582 thr \ ough 583 and (name N or name CA or name C or name O or name CB )) or resid 584 t \ hrough 618 or (resid 619 and (name N or name CA or name C or name O or name CB ) \ ) or resid 620 through 645 or (resid 646 through 647 and (name N or name CA or n \ ame C or name O or name CB )) or resid 648 through 795 or (resid 796 and (name N \ or name CA or name C or name O or name CB )) or resid 797 through 1141 or (resi \ d 1142 and (name N or name CA or name C or name O or name CB )) or resid 1143 or \ (resid 1144 through 1146 and (name N or name CA or name C or name O or name CB \ )) or resid 1147 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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=0.29 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 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: 0.480 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.370 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 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 : 0.003 0.057 27388 Z= 0.149 Angle : 0.572 9.805 37444 Z= 0.291 Chirality : 0.045 0.188 4446 Planarity : 0.004 0.040 4733 Dihedral : 11.502 87.514 10340 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 0.32 % Allowed : 4.21 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.49 (0.14), residues: 3347 helix: 1.10 (0.21), residues: 671 sheet: -0.30 (0.16), residues: 883 loop : -0.86 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1019 TYR 0.019 0.001 TYR A 904 PHE 0.013 0.001 PHE A 318 TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00304 (27296) covalent geometry : angle 0.56245 (37211) SS BOND : bond 0.00234 ( 43) SS BOND : angle 1.09522 ( 86) hydrogen bonds : bond 0.12450 ( 1160) hydrogen bonds : angle 7.09484 ( 3156) link_BETA1-4 : bond 0.00493 ( 11) link_BETA1-4 : angle 1.27230 ( 33) link_NAG-ASN : bond 0.00232 ( 38) link_NAG-ASN : angle 1.63095 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 433 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7308 (m-90) cc_final: 0.6698 (m-10) REVERT: A 433 VAL cc_start: 0.8209 (t) cc_final: 0.7624 (p) REVERT: B 64 TRP cc_start: 0.7846 (t60) cc_final: 0.7513 (t60) REVERT: B 65 PHE cc_start: 0.7410 (m-80) cc_final: 0.7092 (m-80) REVERT: B 515 PHE cc_start: 0.7875 (m-80) cc_final: 0.7530 (m-80) REVERT: C 49 HIS cc_start: 0.7308 (t70) cc_final: 0.7032 (t70) REVERT: C 454 ARG cc_start: 0.6943 (ttm-80) cc_final: 0.6663 (mtp180) REVERT: C 581 THR cc_start: 0.7352 (m) cc_final: 0.7135 (t) REVERT: C 1027 THR cc_start: 0.8768 (m) cc_final: 0.8559 (p) REVERT: L 4 MET cc_start: -0.1497 (mmm) cc_final: -0.1857 (tpt) outliers start: 9 outliers final: 3 residues processed: 441 average time/residue: 0.1681 time to fit residues: 117.2355 Evaluate side-chains 222 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 219 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 907 ASN A 913 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 919 ASN B1054 GLN C 613 GLN C 644 GLN C 913 GLN C 926 GLN C 955 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 168 HIS L 139 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.173916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.120753 restraints weight = 92030.491| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 4.91 r_work: 0.3409 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 27388 Z= 0.318 Angle : 0.768 13.884 37444 Z= 0.397 Chirality : 0.052 0.275 4446 Planarity : 0.006 0.114 4733 Dihedral : 6.628 56.841 4664 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.25 % Allowed : 9.76 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.52 (0.14), residues: 3347 helix: 0.71 (0.19), residues: 675 sheet: 0.01 (0.17), residues: 906 loop : -0.93 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1014 TYR 0.031 0.002 TYR C1067 PHE 0.030 0.003 PHE A1121 TRP 0.023 0.002 TRP B1102 HIS 0.012 0.002 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00744 (27296) covalent geometry : angle 0.75204 (37211) SS BOND : bond 0.00528 ( 43) SS BOND : angle 1.52943 ( 86) hydrogen bonds : bond 0.05358 ( 1160) hydrogen bonds : angle 6.17505 ( 3156) link_BETA1-4 : bond 0.00445 ( 11) link_BETA1-4 : angle 1.22948 ( 33) link_NAG-ASN : bond 0.00637 ( 38) link_NAG-ASN : angle 2.64881 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 232 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.6988 (m-10) cc_final: 0.6751 (m-10) REVERT: A 66 HIS cc_start: 0.5009 (p90) cc_final: 0.4688 (p-80) REVERT: A 362 VAL cc_start: 0.7119 (t) cc_final: 0.6854 (m) REVERT: A 433 VAL cc_start: 0.7791 (t) cc_final: 0.7544 (p) REVERT: A 599 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8275 (m) REVERT: B 64 TRP cc_start: 0.7877 (t60) cc_final: 0.7661 (t60) REVERT: B 65 PHE cc_start: 0.7783 (m-80) cc_final: 0.7285 (m-80) REVERT: B 92 PHE cc_start: 0.7876 (t80) cc_final: 0.6922 (t80) REVERT: B 192 PHE cc_start: 0.9037 (m-80) cc_final: 0.8363 (m-80) REVERT: B 242 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8351 (mp) REVERT: C 49 HIS cc_start: 0.7394 (t70) cc_final: 0.7173 (t70) REVERT: C 205 SER cc_start: 0.7971 (OUTLIER) cc_final: 0.7535 (m) REVERT: C 275 PHE cc_start: 0.7185 (m-80) cc_final: 0.6631 (m-10) REVERT: C 424 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7564 (ttmt) REVERT: C 454 ARG cc_start: 0.7383 (ttm-80) cc_final: 0.6696 (mtp180) REVERT: C 508 TYR cc_start: 0.7198 (m-80) cc_final: 0.6403 (m-80) REVERT: C 731 MET cc_start: 0.8221 (mtm) cc_final: 0.7932 (mtm) REVERT: C 882 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8470 (mp) REVERT: L 4 MET cc_start: 0.3328 (mmm) cc_final: 0.1965 (tpt) outliers start: 64 outliers final: 40 residues processed: 278 average time/residue: 0.1640 time to fit residues: 74.9404 Evaluate side-chains 224 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 179 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 201 optimal weight: 0.0060 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 196 optimal weight: 0.0770 chunk 244 optimal weight: 0.5980 chunk 263 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 171 optimal weight: 0.7980 chunk 292 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.176603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.128169 restraints weight = 69142.065| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 4.01 r_work: 0.3539 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27388 Z= 0.113 Angle : 0.560 11.065 37444 Z= 0.290 Chirality : 0.044 0.208 4446 Planarity : 0.004 0.050 4733 Dihedral : 5.641 56.428 4662 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.51 % Allowed : 11.20 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.07 (0.14), residues: 3347 helix: 1.76 (0.20), residues: 669 sheet: 0.27 (0.17), residues: 878 loop : -0.72 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 509 TYR 0.026 0.001 TYR H 33 PHE 0.021 0.001 PHE A 168 TRP 0.019 0.001 TRP A 353 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00240 (27296) covalent geometry : angle 0.54693 (37211) SS BOND : bond 0.00280 ( 43) SS BOND : angle 1.15669 ( 86) hydrogen bonds : bond 0.04016 ( 1160) hydrogen bonds : angle 5.57747 ( 3156) link_BETA1-4 : bond 0.00401 ( 11) link_BETA1-4 : angle 1.03129 ( 33) link_NAG-ASN : bond 0.00418 ( 38) link_NAG-ASN : angle 2.01592 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 VAL cc_start: 0.7812 (t) cc_final: 0.7543 (p) REVERT: A 599 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8259 (m) REVERT: B 52 GLN cc_start: 0.7334 (pm20) cc_final: 0.7075 (pp30) REVERT: B 64 TRP cc_start: 0.7926 (t60) cc_final: 0.7591 (t60) REVERT: B 65 PHE cc_start: 0.7878 (m-80) cc_final: 0.7421 (m-80) REVERT: B 92 PHE cc_start: 0.7781 (t80) cc_final: 0.6727 (t80) REVERT: B 192 PHE cc_start: 0.8944 (m-80) cc_final: 0.8169 (m-80) REVERT: C 49 HIS cc_start: 0.7265 (t70) cc_final: 0.7064 (t70) REVERT: C 275 PHE cc_start: 0.6858 (m-80) cc_final: 0.6252 (m-10) REVERT: C 294 ASP cc_start: 0.8073 (p0) cc_final: 0.7094 (m-30) REVERT: C 424 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7683 (ttmt) REVERT: C 492 LEU cc_start: 0.8703 (mt) cc_final: 0.8180 (tp) REVERT: C 508 TYR cc_start: 0.7152 (m-80) cc_final: 0.6442 (m-80) REVERT: C 731 MET cc_start: 0.7908 (mtm) cc_final: 0.7632 (mtm) REVERT: C 882 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8439 (mp) REVERT: C 977 LEU cc_start: 0.7019 (tp) cc_final: 0.6777 (tt) REVERT: L 4 MET cc_start: 0.2307 (mmm) cc_final: 0.0751 (tpt) outliers start: 43 outliers final: 20 residues processed: 243 average time/residue: 0.1562 time to fit residues: 62.7376 Evaluate side-chains 200 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 332 optimal weight: 50.0000 chunk 273 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 130 optimal weight: 0.0370 chunk 328 optimal weight: 50.0000 chunk 135 optimal weight: 50.0000 chunk 156 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 chunk 84 optimal weight: 4.9990 chunk 127 optimal weight: 40.0000 chunk 259 optimal weight: 3.9990 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.175482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.123239 restraints weight = 65048.300| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.58 r_work: 0.3526 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27388 Z= 0.140 Angle : 0.563 14.656 37444 Z= 0.287 Chirality : 0.044 0.282 4446 Planarity : 0.004 0.058 4733 Dihedral : 5.203 52.954 4662 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.04 % Allowed : 11.76 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.19 (0.14), residues: 3347 helix: 1.78 (0.20), residues: 677 sheet: 0.34 (0.17), residues: 875 loop : -0.61 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 454 TYR 0.031 0.001 TYR C 369 PHE 0.026 0.001 PHE C 194 TRP 0.020 0.002 TRP A 353 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00322 (27296) covalent geometry : angle 0.54984 (37211) SS BOND : bond 0.00355 ( 43) SS BOND : angle 1.13174 ( 86) hydrogen bonds : bond 0.03972 ( 1160) hydrogen bonds : angle 5.45726 ( 3156) link_BETA1-4 : bond 0.00279 ( 11) link_BETA1-4 : angle 1.11194 ( 33) link_NAG-ASN : bond 0.00349 ( 38) link_NAG-ASN : angle 2.01912 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 189 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7267 (t70) cc_final: 0.7041 (p90) REVERT: A 66 HIS cc_start: 0.5806 (m90) cc_final: 0.4969 (p-80) REVERT: A 91 TYR cc_start: 0.6525 (t80) cc_final: 0.6323 (t80) REVERT: A 433 VAL cc_start: 0.7853 (t) cc_final: 0.7647 (p) REVERT: A 453 TYR cc_start: 0.7505 (p90) cc_final: 0.7086 (p90) REVERT: A 599 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8256 (m) REVERT: B 52 GLN cc_start: 0.7394 (pm20) cc_final: 0.7136 (pp30) REVERT: B 64 TRP cc_start: 0.7874 (t60) cc_final: 0.7478 (t60) REVERT: B 65 PHE cc_start: 0.7862 (m-80) cc_final: 0.7427 (m-80) REVERT: B 92 PHE cc_start: 0.7576 (t80) cc_final: 0.6451 (t80) REVERT: B 192 PHE cc_start: 0.8898 (m-80) cc_final: 0.8093 (m-80) REVERT: B 303 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7828 (tp) REVERT: C 275 PHE cc_start: 0.6904 (m-80) cc_final: 0.6521 (m-80) REVERT: C 347 PHE cc_start: 0.5924 (m-80) cc_final: 0.4876 (t80) REVERT: C 508 TYR cc_start: 0.7337 (m-80) cc_final: 0.6726 (m-80) REVERT: C 731 MET cc_start: 0.7866 (mtm) cc_final: 0.7613 (mtm) REVERT: C 882 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8386 (mp) REVERT: L 4 MET cc_start: 0.2799 (mmm) cc_final: 0.1568 (tpt) outliers start: 58 outliers final: 38 residues processed: 231 average time/residue: 0.1546 time to fit residues: 59.2275 Evaluate side-chains 219 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 268 optimal weight: 0.9990 chunk 203 optimal weight: 40.0000 chunk 230 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 210 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 chunk 195 optimal weight: 0.8980 chunk 318 optimal weight: 20.0000 chunk 206 optimal weight: 5.9990 chunk 328 optimal weight: 40.0000 chunk 254 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 935 GLN C 955 ASN C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.184134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.133062 restraints weight = 82750.551| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 4.62 r_work: 0.3407 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 27388 Z= 0.226 Angle : 0.617 12.314 37444 Z= 0.317 Chirality : 0.046 0.181 4446 Planarity : 0.004 0.056 4733 Dihedral : 5.218 50.850 4662 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.28 % Allowed : 12.46 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.02 (0.14), residues: 3347 helix: 1.32 (0.20), residues: 680 sheet: 0.34 (0.17), residues: 884 loop : -0.70 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 403 TYR 0.024 0.002 TYR C1067 PHE 0.022 0.002 PHE A 168 TRP 0.024 0.002 TRP A 353 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00529 (27296) covalent geometry : angle 0.60380 (37211) SS BOND : bond 0.00441 ( 43) SS BOND : angle 1.22061 ( 86) hydrogen bonds : bond 0.04560 ( 1160) hydrogen bonds : angle 5.65353 ( 3156) link_BETA1-4 : bond 0.00320 ( 11) link_BETA1-4 : angle 1.22752 ( 33) link_NAG-ASN : bond 0.00428 ( 38) link_NAG-ASN : angle 2.13315 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5901 (m90) cc_final: 0.5143 (p-80) REVERT: A 91 TYR cc_start: 0.6794 (t80) cc_final: 0.6590 (t80) REVERT: A 204 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6151 (m-80) REVERT: A 433 VAL cc_start: 0.7863 (t) cc_final: 0.7592 (p) REVERT: A 599 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8259 (m) REVERT: B 64 TRP cc_start: 0.7811 (t60) cc_final: 0.7347 (t60) REVERT: B 65 PHE cc_start: 0.8057 (m-80) cc_final: 0.7647 (m-80) REVERT: B 92 PHE cc_start: 0.7834 (t80) cc_final: 0.6785 (t80) REVERT: B 192 PHE cc_start: 0.9024 (m-80) cc_final: 0.8197 (m-80) REVERT: B 303 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.7889 (tp) REVERT: C 420 ASP cc_start: 0.8739 (t0) cc_final: 0.8393 (t70) REVERT: C 468 ILE cc_start: 0.8933 (pt) cc_final: 0.8696 (mm) REVERT: C 506 GLN cc_start: 0.7716 (mt0) cc_final: 0.6601 (mt0) REVERT: C 508 TYR cc_start: 0.7561 (m-80) cc_final: 0.6850 (m-80) REVERT: C 882 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8515 (mp) REVERT: C 955 ASN cc_start: 0.8099 (m110) cc_final: 0.7834 (m-40) REVERT: L 4 MET cc_start: 0.3067 (mmm) cc_final: 0.1901 (tpt) outliers start: 65 outliers final: 53 residues processed: 238 average time/residue: 0.1554 time to fit residues: 61.2217 Evaluate side-chains 233 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 176 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 245 optimal weight: 9.9990 chunk 278 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 309 optimal weight: 50.0000 chunk 235 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 chunk 270 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 955 ASN C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.173600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.121941 restraints weight = 76304.168| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.96 r_work: 0.3460 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27388 Z= 0.170 Angle : 0.569 10.736 37444 Z= 0.292 Chirality : 0.044 0.178 4446 Planarity : 0.004 0.058 4733 Dihedral : 5.006 49.707 4662 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.49 % Allowed : 12.95 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.08 (0.14), residues: 3347 helix: 1.46 (0.20), residues: 681 sheet: 0.37 (0.17), residues: 856 loop : -0.64 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.023 0.001 TYR C 904 PHE 0.028 0.002 PHE C 490 TRP 0.022 0.002 TRP A 353 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00393 (27296) covalent geometry : angle 0.55719 (37211) SS BOND : bond 0.00367 ( 43) SS BOND : angle 1.11523 ( 86) hydrogen bonds : bond 0.04182 ( 1160) hydrogen bonds : angle 5.49896 ( 3156) link_BETA1-4 : bond 0.00298 ( 11) link_BETA1-4 : angle 1.10656 ( 33) link_NAG-ASN : bond 0.00405 ( 38) link_NAG-ASN : angle 1.97358 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 180 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5858 (m90) cc_final: 0.5121 (p-80) REVERT: A 91 TYR cc_start: 0.6608 (t80) cc_final: 0.6405 (t80) REVERT: A 204 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.6106 (m-80) REVERT: A 433 VAL cc_start: 0.7793 (t) cc_final: 0.7516 (p) REVERT: A 599 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8247 (m) REVERT: B 64 TRP cc_start: 0.7638 (t60) cc_final: 0.7182 (t60) REVERT: B 65 PHE cc_start: 0.7984 (m-80) cc_final: 0.7601 (m-80) REVERT: B 92 PHE cc_start: 0.7793 (t80) cc_final: 0.6654 (t80) REVERT: B 192 PHE cc_start: 0.9029 (m-80) cc_final: 0.8171 (m-80) REVERT: B 269 TYR cc_start: 0.8366 (m-80) cc_final: 0.8114 (m-80) REVERT: B 303 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.7889 (tp) REVERT: B 357 ARG cc_start: 0.0578 (OUTLIER) cc_final: -0.1226 (ttp-170) REVERT: C 420 ASP cc_start: 0.8762 (t0) cc_final: 0.8385 (t70) REVERT: C 506 GLN cc_start: 0.7751 (mt0) cc_final: 0.6628 (mt0) REVERT: C 508 TYR cc_start: 0.7654 (m-80) cc_final: 0.6938 (m-80) REVERT: C 882 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8432 (mp) REVERT: L 4 MET cc_start: 0.1330 (mmm) cc_final: 0.0556 (tpt) outliers start: 71 outliers final: 53 residues processed: 237 average time/residue: 0.1547 time to fit residues: 61.0090 Evaluate side-chains 234 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 176 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 70 optimal weight: 0.8980 chunk 272 optimal weight: 0.4980 chunk 262 optimal weight: 0.8980 chunk 321 optimal weight: 40.0000 chunk 287 optimal weight: 1.9990 chunk 292 optimal weight: 0.9990 chunk 135 optimal weight: 50.0000 chunk 318 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.174803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.123993 restraints weight = 68361.848| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.74 r_work: 0.3495 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27388 Z= 0.113 Angle : 0.534 10.276 37444 Z= 0.274 Chirality : 0.043 0.178 4446 Planarity : 0.004 0.057 4733 Dihedral : 4.710 48.950 4662 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.11 % Allowed : 13.76 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.29 (0.14), residues: 3347 helix: 1.81 (0.20), residues: 681 sheet: 0.48 (0.17), residues: 855 loop : -0.56 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.025 0.001 TYR C 904 PHE 0.027 0.001 PHE A 168 TRP 0.025 0.001 TRP A 353 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00250 (27296) covalent geometry : angle 0.52244 (37211) SS BOND : bond 0.00286 ( 43) SS BOND : angle 1.00944 ( 86) hydrogen bonds : bond 0.03766 ( 1160) hydrogen bonds : angle 5.29438 ( 3156) link_BETA1-4 : bond 0.00430 ( 11) link_BETA1-4 : angle 1.07366 ( 33) link_NAG-ASN : bond 0.00272 ( 38) link_NAG-ASN : angle 1.84963 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 187 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5864 (m90) cc_final: 0.5138 (p-80) REVERT: A 91 TYR cc_start: 0.6623 (t80) cc_final: 0.6391 (t80) REVERT: A 204 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.6122 (m-80) REVERT: A 433 VAL cc_start: 0.7805 (t) cc_final: 0.7537 (p) REVERT: A 599 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8202 (m) REVERT: A 1139 ASP cc_start: 0.7984 (t0) cc_final: 0.7778 (t0) REVERT: B 64 TRP cc_start: 0.7595 (t60) cc_final: 0.7125 (t60) REVERT: B 65 PHE cc_start: 0.8083 (m-80) cc_final: 0.7687 (m-80) REVERT: B 92 PHE cc_start: 0.7791 (t80) cc_final: 0.6640 (t80) REVERT: B 192 PHE cc_start: 0.9014 (m-80) cc_final: 0.8161 (m-80) REVERT: B 269 TYR cc_start: 0.8378 (m-80) cc_final: 0.8154 (m-80) REVERT: B 303 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.7809 (tp) REVERT: B 357 ARG cc_start: 0.0665 (OUTLIER) cc_final: -0.1202 (ttp-170) REVERT: C 275 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6558 (m-80) REVERT: C 294 ASP cc_start: 0.8322 (p0) cc_final: 0.6987 (m-30) REVERT: C 347 PHE cc_start: 0.5911 (OUTLIER) cc_final: 0.4970 (t80) REVERT: C 388 ASN cc_start: 0.8272 (t0) cc_final: 0.7653 (p0) REVERT: C 420 ASP cc_start: 0.8754 (t0) cc_final: 0.8377 (t70) REVERT: C 508 TYR cc_start: 0.7695 (m-80) cc_final: 0.7096 (m-80) REVERT: C 882 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8402 (mp) REVERT: C 1005 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8165 (mm-40) REVERT: L 4 MET cc_start: 0.1404 (mmm) cc_final: 0.0576 (tpt) outliers start: 60 outliers final: 43 residues processed: 235 average time/residue: 0.1537 time to fit residues: 60.5055 Evaluate side-chains 230 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 321 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 129 optimal weight: 30.0000 chunk 276 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.180822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.125185 restraints weight = 80841.447| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 4.31 r_work: 0.3396 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 27388 Z= 0.240 Angle : 0.622 9.640 37444 Z= 0.319 Chirality : 0.046 0.178 4446 Planarity : 0.004 0.068 4733 Dihedral : 5.029 50.744 4662 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.53 % Allowed : 13.79 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -0.00 (0.14), residues: 3347 helix: 1.29 (0.20), residues: 679 sheet: 0.38 (0.17), residues: 861 loop : -0.68 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 44 TYR 0.025 0.001 TYR C 904 PHE 0.025 0.002 PHE C 559 TRP 0.027 0.002 TRP A 353 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00564 (27296) covalent geometry : angle 0.60930 (37211) SS BOND : bond 0.00428 ( 43) SS BOND : angle 1.21696 ( 86) hydrogen bonds : bond 0.04588 ( 1160) hydrogen bonds : angle 5.60149 ( 3156) link_BETA1-4 : bond 0.00360 ( 11) link_BETA1-4 : angle 1.26483 ( 33) link_NAG-ASN : bond 0.00454 ( 38) link_NAG-ASN : angle 2.08938 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 183 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5780 (m90) cc_final: 0.5140 (p-80) REVERT: A 91 TYR cc_start: 0.6747 (t80) cc_final: 0.6531 (t80) REVERT: A 189 LEU cc_start: 0.8477 (tt) cc_final: 0.8212 (tp) REVERT: A 204 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6215 (m-80) REVERT: A 433 VAL cc_start: 0.7684 (t) cc_final: 0.7438 (p) REVERT: A 599 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8210 (m) REVERT: A 1139 ASP cc_start: 0.8264 (t0) cc_final: 0.8058 (t0) REVERT: B 92 PHE cc_start: 0.7821 (t80) cc_final: 0.6722 (t80) REVERT: B 192 PHE cc_start: 0.8942 (m-80) cc_final: 0.8106 (m-80) REVERT: B 303 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.7910 (tp) REVERT: B 357 ARG cc_start: 0.0241 (OUTLIER) cc_final: -0.1366 (ttp-170) REVERT: C 508 TYR cc_start: 0.7851 (m-80) cc_final: 0.7228 (m-80) REVERT: C 878 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7905 (mt) REVERT: C 882 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8490 (mp) REVERT: L 4 MET cc_start: 0.5628 (mmm) cc_final: 0.4242 (tpt) outliers start: 72 outliers final: 59 residues processed: 244 average time/residue: 0.1566 time to fit residues: 63.6231 Evaluate side-chains 240 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 175 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 211 optimal weight: 0.7980 chunk 177 optimal weight: 0.9980 chunk 217 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 315 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 127 optimal weight: 0.0050 chunk 146 optimal weight: 9.9990 chunk 156 optimal weight: 0.7980 chunk 210 optimal weight: 40.0000 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.174568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.123121 restraints weight = 75754.175| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 4.04 r_work: 0.3481 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27388 Z= 0.111 Angle : 0.543 9.660 37444 Z= 0.279 Chirality : 0.044 0.278 4446 Planarity : 0.004 0.059 4733 Dihedral : 4.668 49.570 4662 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.93 % Allowed : 14.64 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.27 (0.14), residues: 3347 helix: 1.70 (0.20), residues: 686 sheet: 0.49 (0.17), residues: 851 loop : -0.55 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 815 TYR 0.025 0.001 TYR C 904 PHE 0.035 0.001 PHE C 275 TRP 0.030 0.002 TRP A 353 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00247 (27296) covalent geometry : angle 0.53324 (37211) SS BOND : bond 0.00234 ( 43) SS BOND : angle 1.01705 ( 86) hydrogen bonds : bond 0.03782 ( 1160) hydrogen bonds : angle 5.27998 ( 3156) link_BETA1-4 : bond 0.00392 ( 11) link_BETA1-4 : angle 1.04375 ( 33) link_NAG-ASN : bond 0.00283 ( 38) link_NAG-ASN : angle 1.76110 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5825 (m90) cc_final: 0.5180 (p-80) REVERT: A 91 TYR cc_start: 0.6478 (t80) cc_final: 0.6248 (t80) REVERT: A 204 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.6116 (m-80) REVERT: A 433 VAL cc_start: 0.7885 (t) cc_final: 0.7623 (p) REVERT: A 437 ASN cc_start: 0.9164 (m-40) cc_final: 0.8424 (t0) REVERT: A 453 TYR cc_start: 0.7445 (p90) cc_final: 0.6926 (p90) REVERT: A 455 LEU cc_start: 0.9068 (tp) cc_final: 0.8700 (tp) REVERT: A 599 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8165 (m) REVERT: A 902 MET cc_start: 0.8512 (mmm) cc_final: 0.7975 (mmm) REVERT: A 1139 ASP cc_start: 0.8165 (t0) cc_final: 0.7939 (t0) REVERT: B 92 PHE cc_start: 0.7715 (t80) cc_final: 0.6594 (t80) REVERT: B 192 PHE cc_start: 0.8985 (m-80) cc_final: 0.8112 (m-80) REVERT: B 269 TYR cc_start: 0.8339 (m-80) cc_final: 0.7572 (m-80) REVERT: B 303 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.7826 (tp) REVERT: B 357 ARG cc_start: 0.0683 (OUTLIER) cc_final: -0.1266 (ttp-170) REVERT: C 294 ASP cc_start: 0.8341 (p0) cc_final: 0.7030 (m-30) REVERT: C 388 ASN cc_start: 0.8258 (t0) cc_final: 0.7645 (p0) REVERT: C 420 ASP cc_start: 0.8811 (t0) cc_final: 0.8411 (t0) REVERT: C 508 TYR cc_start: 0.7894 (m-80) cc_final: 0.7303 (m-80) REVERT: C 882 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8426 (mp) REVERT: C 1005 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8180 (mm-40) REVERT: L 4 MET cc_start: 0.1931 (mmm) cc_final: 0.1021 (tpt) outliers start: 55 outliers final: 43 residues processed: 232 average time/residue: 0.1571 time to fit residues: 60.7098 Evaluate side-chains 227 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 231 optimal weight: 6.9990 chunk 273 optimal weight: 0.6980 chunk 315 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 333 optimal weight: 1.9990 chunk 258 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 146 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.177582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.124070 restraints weight = 86099.652| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 4.66 r_work: 0.3430 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27388 Z= 0.153 Angle : 0.567 11.207 37444 Z= 0.290 Chirality : 0.044 0.262 4446 Planarity : 0.004 0.059 4733 Dihedral : 4.644 49.299 4662 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.07 % Allowed : 14.46 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: 0.27 (0.14), residues: 3347 helix: 1.68 (0.20), residues: 680 sheet: 0.52 (0.17), residues: 845 loop : -0.54 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 815 TYR 0.027 0.001 TYR C 904 PHE 0.044 0.002 PHE C 275 TRP 0.030 0.002 TRP A 353 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00355 (27296) covalent geometry : angle 0.55656 (37211) SS BOND : bond 0.00319 ( 43) SS BOND : angle 1.05868 ( 86) hydrogen bonds : bond 0.03970 ( 1160) hydrogen bonds : angle 5.31297 ( 3156) link_BETA1-4 : bond 0.00334 ( 11) link_BETA1-4 : angle 1.10841 ( 33) link_NAG-ASN : bond 0.00302 ( 38) link_NAG-ASN : angle 1.81227 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5918 (m90) cc_final: 0.5297 (p-80) REVERT: A 91 TYR cc_start: 0.6714 (t80) cc_final: 0.6509 (t80) REVERT: A 204 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6171 (m-80) REVERT: A 414 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7932 (tp40) REVERT: A 433 VAL cc_start: 0.7915 (t) cc_final: 0.7665 (p) REVERT: A 437 ASN cc_start: 0.9134 (m-40) cc_final: 0.8390 (t0) REVERT: A 453 TYR cc_start: 0.7329 (p90) cc_final: 0.6625 (p90) REVERT: A 599 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8136 (m) REVERT: A 1139 ASP cc_start: 0.8199 (t0) cc_final: 0.7972 (t0) REVERT: B 192 PHE cc_start: 0.9023 (m-80) cc_final: 0.8815 (m-80) REVERT: B 269 TYR cc_start: 0.8392 (m-80) cc_final: 0.7592 (m-80) REVERT: B 357 ARG cc_start: 0.0699 (OUTLIER) cc_final: -0.1237 (ttp-170) REVERT: C 388 ASN cc_start: 0.8387 (t0) cc_final: 0.7719 (p0) REVERT: C 420 ASP cc_start: 0.8830 (t0) cc_final: 0.8438 (t0) REVERT: C 506 GLN cc_start: 0.7701 (mt0) cc_final: 0.6616 (mt0) REVERT: C 508 TYR cc_start: 0.7984 (m-80) cc_final: 0.7340 (m-80) REVERT: C 554 GLU cc_start: 0.7861 (tp30) cc_final: 0.7467 (mm-30) REVERT: C 882 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8421 (mp) REVERT: C 1005 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8220 (mm-40) REVERT: H 100 MET cc_start: 0.2914 (pmm) cc_final: 0.2586 (pmm) REVERT: L 4 MET cc_start: 0.3131 (mmm) cc_final: 0.2012 (tpt) outliers start: 59 outliers final: 52 residues processed: 228 average time/residue: 0.1526 time to fit residues: 58.3371 Evaluate side-chains 230 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 174 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 89 optimal weight: 1.9990 chunk 306 optimal weight: 2.9990 chunk 132 optimal weight: 0.0770 chunk 108 optimal weight: 1.9990 chunk 307 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 250 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.185810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.133312 restraints weight = 67006.094| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.72 r_work: 0.3466 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27388 Z= 0.154 Angle : 0.563 10.083 37444 Z= 0.289 Chirality : 0.044 0.258 4446 Planarity : 0.004 0.058 4733 Dihedral : 4.634 49.159 4662 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.18 % Allowed : 14.71 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: 0.28 (0.14), residues: 3347 helix: 1.67 (0.20), residues: 679 sheet: 0.51 (0.17), residues: 846 loop : -0.53 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 815 TYR 0.031 0.001 TYR A 453 PHE 0.023 0.001 PHE C 490 TRP 0.029 0.002 TRP A 353 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00357 (27296) covalent geometry : angle 0.55362 (37211) SS BOND : bond 0.00317 ( 43) SS BOND : angle 1.04844 ( 86) hydrogen bonds : bond 0.03950 ( 1160) hydrogen bonds : angle 5.28840 ( 3156) link_BETA1-4 : bond 0.00362 ( 11) link_BETA1-4 : angle 1.06207 ( 33) link_NAG-ASN : bond 0.00300 ( 38) link_NAG-ASN : angle 1.75871 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8725.46 seconds wall clock time: 149 minutes 27.60 seconds (8967.60 seconds total)