Starting phenix.real_space_refine on Fri Mar 6 14:25:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kmk_22925/03_2026/7kmk_22925.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kmk_22925/03_2026/7kmk_22925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kmk_22925/03_2026/7kmk_22925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kmk_22925/03_2026/7kmk_22925.map" model { file = "/net/cci-nas-00/data/ceres_data/7kmk_22925/03_2026/7kmk_22925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kmk_22925/03_2026/7kmk_22925.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.060 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 142 5.16 5 C 19841 2.51 5 N 5148 2.21 5 O 6120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 198 residue(s): 0.03s 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: 31251 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8039 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 54, 'TRANS': 973} Chain breaks: 7 Chain: "B" Number of atoms: 8018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8018 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 54, 'TRANS': 970} Chain breaks: 7 Chain: "C" Number of atoms: 8018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8018 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 54, 'TRANS': 970} Chain breaks: 7 Chain: "L" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1635 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "M" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "I" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1635 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 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: "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: 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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.75, per 1000 atoms: 0.22 Number of scatterers: 31251 At special positions: 0 Unit cell: (147.29, 144.2, 223.51, 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 142 16.00 O 6120 8.00 N 5148 7.00 C 19841 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 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=2.04 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 15 " - pdb=" SG CYS B 136 " distance=2.10 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=2.06 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.08 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=2.08 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 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=2.10 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.09 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.05 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.02 Simple disulfide: pdb=" SG CYS L 154 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 234 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.02 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.02 Simple disulfide: pdb=" SG CYS M 154 " - pdb=" SG CYS M 214 " distance=2.03 Simple disulfide: pdb=" SG CYS M 234 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " 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 E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 343 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN B 331 " " NAG G 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1074 " " NAG N 1 " - " ASN C 122 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.3 seconds 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7374 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 68 sheets defined 21.1% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.776A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.688A 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 removed outlier: 3.716A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.571A pdb=" N GLY A 744 " --> pdb=" O MET A 740 " (cutoff:3.500A) 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 801 through 805 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.614A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) 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 removed outlier: 4.268A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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 981 Processing helix chain 'A' and resid 985 through 1032 Processing helix chain 'B' and resid 155 through 159 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 removed outlier: 3.611A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.592A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.811A 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: 3.683A 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 744 removed outlier: 3.767A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) 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 760 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 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: 3.985A 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 removed outlier: 3.907A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 344 Processing helix chain 'C' and resid 364 through 372 Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.837A pdb=" N GLY C 744 " --> pdb=" O MET C 740 " (cutoff:3.500A) 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 760 through 783 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 889 removed outlier: 3.982A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.303A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'L' and resid 143 through 147 Processing helix chain 'L' and resid 203 through 207 Processing helix chain 'H' and resid 69 through 72 Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 202 through 206 Processing helix chain 'H' and resid 216 through 219 Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'M' and resid 143 through 147 Processing helix chain 'M' and resid 203 through 207 Processing helix chain 'I' and resid 69 through 72 Processing helix chain 'I' and resid 95 through 99 Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 216 through 219 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.820A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.792A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.194A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 230 removed outlier: 7.032A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.409A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.750A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.564A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.784A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 676 through 677 Processing sheet with id=AB6, first strand: chain 'A' and resid 703 through 704 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 removed outlier: 5.679A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.950A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 29 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.374A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.300A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 224 through 230 removed outlier: 4.026A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.496A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.511A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.541A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.710A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.553A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.553A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B1104 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLU B1111 " --> pdb=" O VAL B1104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.568A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 29 through 30 removed outlier: 9.009A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.500A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.251A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.369A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.767A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 355 through 358 removed outlier: 3.534A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE8, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 653 through 660 removed outlier: 6.905A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.992A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.808A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AF5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.017A pdb=" N VAL L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR L 55 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 134 through 138 removed outlier: 5.361A pdb=" N TYR L 193 " --> pdb=" O ASN L 158 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 173 through 174 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'H' and resid 11 through 13 removed outlier: 7.135A pdb=" N TYR H 37 " --> pdb=" O TYR H 57 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR H 57 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET H 39 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.462A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.462A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 166 through 169 Processing sheet with id=AG5, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.576A pdb=" N LEU M 11 " --> pdb=" O GLU M 125 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL M 39 " --> pdb=" O TYR M 55 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYR M 55 " --> pdb=" O VAL M 39 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 134 through 138 removed outlier: 5.541A pdb=" N TYR M 193 " --> pdb=" O ASN M 158 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 173 through 174 Processing sheet with id=AG9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AH1, first strand: chain 'I' and resid 11 through 13 removed outlier: 7.142A pdb=" N TYR I 37 " --> pdb=" O TYR I 57 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR I 57 " --> pdb=" O TYR I 37 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET I 39 " --> pdb=" O GLY I 55 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY I 55 " --> pdb=" O MET I 39 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP I 41 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 11 through 13 removed outlier: 4.098A pdb=" N TYR I 117 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.218A pdb=" N ALA I 152 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL I 199 " --> pdb=" O ALA I 152 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY I 154 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL I 197 " --> pdb=" O GLY I 154 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU I 156 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N SER I 195 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS I 158 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU I 193 " --> pdb=" O LYS I 158 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.218A pdb=" N ALA I 152 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL I 199 " --> pdb=" O ALA I 152 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY I 154 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL I 197 " --> pdb=" O GLY I 154 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU I 156 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N SER I 195 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS I 158 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU I 193 " --> pdb=" O LYS I 158 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 166 through 169 1323 hydrogen bonds defined for protein. 3510 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: 8.15 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 6693 1.32 - 1.47: 11666 1.47 - 1.62: 13407 1.62 - 1.76: 38 1.76 - 1.91: 149 Bond restraints: 31953 Sorted by residual: bond pdb=" CB ILE C 692 " pdb=" CG1 ILE C 692 " ideal model delta sigma weight residual 1.530 1.413 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" NE1 TRP C 64 " pdb=" CE2 TRP C 64 " ideal model delta sigma weight residual 1.370 1.307 0.063 1.10e-02 8.26e+03 3.33e+01 bond pdb=" C CYS A 15 " pdb=" O CYS A 15 " ideal model delta sigma weight residual 1.233 1.306 -0.073 1.30e-02 5.92e+03 3.12e+01 bond pdb=" CG GLU B1072 " pdb=" CD GLU B1072 " ideal model delta sigma weight residual 1.516 1.377 0.139 2.50e-02 1.60e+03 3.11e+01 bond pdb=" CG TYR A1138 " pdb=" CD2 TYR A1138 " ideal model delta sigma weight residual 1.389 1.498 -0.109 2.10e-02 2.27e+03 2.67e+01 ... (remaining 31948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 36841 2.42 - 4.85: 5610 4.85 - 7.27: 898 7.27 - 9.69: 120 9.69 - 12.11: 11 Bond angle restraints: 43480 Sorted by residual: angle pdb=" C GLY A 526 " pdb=" N PRO A 527 " pdb=" CA PRO A 527 " ideal model delta sigma weight residual 119.56 129.03 -9.47 1.02e+00 9.61e-01 8.63e+01 angle pdb=" C PHE L 138 " pdb=" N PRO L 139 " pdb=" CA PRO L 139 " ideal model delta sigma weight residual 119.66 126.30 -6.64 7.30e-01 1.88e+00 8.28e+01 angle pdb=" N THR B 333 " pdb=" CA THR B 333 " pdb=" C THR B 333 " ideal model delta sigma weight residual 114.31 102.89 11.42 1.29e+00 6.01e-01 7.83e+01 angle pdb=" C LEU C 560 " pdb=" N PRO C 561 " pdb=" CA PRO C 561 " ideal model delta sigma weight residual 119.56 128.06 -8.50 1.02e+00 9.61e-01 6.94e+01 angle pdb=" N VAL C 341 " pdb=" CA VAL C 341 " pdb=" C VAL C 341 " ideal model delta sigma weight residual 110.53 102.96 7.57 9.40e-01 1.13e+00 6.49e+01 ... (remaining 43475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 18998 21.29 - 42.58: 435 42.58 - 63.88: 160 63.88 - 85.17: 50 85.17 - 106.46: 25 Dihedral angle restraints: 19668 sinusoidal: 8192 harmonic: 11476 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -39.64 -46.36 1 1.00e+01 1.00e-02 2.97e+01 dihedral pdb=" C PHE A 201 " pdb=" N PHE A 201 " pdb=" CA PHE A 201 " pdb=" CB PHE A 201 " ideal model delta harmonic sigma weight residual -122.60 -136.17 13.57 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual 93.00 47.33 45.67 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 19665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3252 0.087 - 0.174: 1410 0.174 - 0.261: 350 0.261 - 0.348: 49 0.348 - 0.435: 8 Chirality restraints: 5069 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.05e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.42e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.00e+01 ... (remaining 5066 not shown) Planarity restraints: 5591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 489 " -0.103 2.00e-02 2.50e+03 6.05e-02 7.33e+01 pdb=" CG TYR B 489 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 489 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR B 489 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR B 489 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR B 489 " 0.047 2.00e-02 2.50e+03 pdb=" CZ TYR B 489 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR B 489 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 707 " -0.072 2.00e-02 2.50e+03 3.89e-02 3.03e+01 pdb=" CG TYR C 707 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 707 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR C 707 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR C 707 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 707 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR C 707 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR C 707 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 453 " -0.072 2.00e-02 2.50e+03 3.88e-02 3.01e+01 pdb=" CG TYR C 453 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR C 453 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR C 453 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR C 453 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR C 453 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR C 453 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR C 453 " -0.051 2.00e-02 2.50e+03 ... (remaining 5588 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 11811 2.88 - 3.39: 29438 3.39 - 3.89: 55887 3.89 - 4.40: 64987 4.40 - 4.90: 103719 Nonbonded interactions: 265842 Sorted by model distance: nonbonded pdb=" N THR B 333 " pdb=" N ASN B 334 " model vdw 2.381 2.560 nonbonded pdb=" O ASN B 603 " pdb=" OD1 ASN B 603 " model vdw 2.397 3.040 nonbonded pdb=" N PRO B 600 " pdb=" O PRO B 600 " model vdw 2.398 2.496 nonbonded pdb=" N PRO C 600 " pdb=" O PRO C 600 " model vdw 2.422 2.496 nonbonded pdb=" N ASN C1125 " pdb=" O ASN C1125 " model vdw 2.423 2.496 ... (remaining 265837 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 14 through 676 or resid 689 through 1308)) selection = chain 'B' selection = (chain 'C' and resid 14 through 1308) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.030 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 29.640 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.019 0.139 32050 Z= 0.997 Angle : 1.835 12.113 43719 Z= 1.238 Chirality : 0.098 0.435 5069 Planarity : 0.009 0.061 5557 Dihedral : 11.497 106.460 12138 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.98 % Favored : 97.95 % Rotamer: Outliers : 0.20 % Allowed : 0.93 % Favored : 98.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.13), residues: 3896 helix: -0.20 (0.18), residues: 661 sheet: 0.67 (0.15), residues: 1050 loop : 0.61 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 80 TYR 0.103 0.010 TYR B 489 PHE 0.056 0.008 PHE C 374 TRP 0.047 0.010 TRP I 52 HIS 0.019 0.003 HIS L 218 Details of bonding type rmsd covalent geometry : bond 0.01920 (31953) covalent geometry : angle 1.83489 (43480) SS BOND : bond 0.02076 ( 52) SS BOND : angle 2.40402 ( 104) hydrogen bonds : bond 0.15563 ( 1272) hydrogen bonds : angle 8.81412 ( 3510) link_BETA1-4 : bond 0.00737 ( 11) link_BETA1-4 : angle 1.53143 ( 33) link_NAG-ASN : bond 0.00262 ( 34) link_NAG-ASN : angle 1.34405 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 465 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 211 ASN cc_start: 0.7726 (m-40) cc_final: 0.7478 (p0) REVERT: A 308 VAL cc_start: 0.8932 (t) cc_final: 0.8567 (t) REVERT: A 763 LEU cc_start: 0.9620 (mt) cc_final: 0.9354 (mp) REVERT: A 797 PHE cc_start: 0.8170 (m-10) cc_final: 0.7869 (m-10) REVERT: A 801 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8037 (m-40) REVERT: A 927 PHE cc_start: 0.9418 (t80) cc_final: 0.9012 (t80) REVERT: A 988 GLU cc_start: 0.9774 (mt-10) cc_final: 0.9567 (pt0) REVERT: A 1018 ILE cc_start: 0.9597 (mm) cc_final: 0.9132 (tp) REVERT: A 1063 LEU cc_start: 0.9563 (mt) cc_final: 0.9312 (mt) REVERT: A 1065 VAL cc_start: 0.9341 (t) cc_final: 0.7842 (t) REVERT: B 88 ASP cc_start: 0.9546 (m-30) cc_final: 0.9251 (t0) REVERT: B 104 TRP cc_start: 0.8882 (m-90) cc_final: 0.8171 (m-90) REVERT: B 170 TYR cc_start: 0.9393 (t80) cc_final: 0.9058 (t80) REVERT: B 640 SER cc_start: 0.8813 (m) cc_final: 0.8613 (p) REVERT: B 657 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8226 (p0) REVERT: B 755 GLN cc_start: 0.9111 (mt0) cc_final: 0.8636 (mt0) REVERT: B 773 GLU cc_start: 0.9506 (mm-30) cc_final: 0.9290 (mm-30) REVERT: B 779 GLN cc_start: 0.9609 (mt0) cc_final: 0.9297 (tm-30) REVERT: B 782 PHE cc_start: 0.9610 (m-80) cc_final: 0.9317 (m-80) REVERT: B 927 PHE cc_start: 0.9501 (t80) cc_final: 0.8753 (t80) REVERT: B 947 LYS cc_start: 0.9779 (mmtt) cc_final: 0.9568 (mppt) REVERT: B 1004 LEU cc_start: 0.9754 (tp) cc_final: 0.9533 (tp) REVERT: B 1049 LEU cc_start: 0.9508 (mt) cc_final: 0.9136 (mm) REVERT: B 1065 VAL cc_start: 0.9617 (t) cc_final: 0.8402 (t) REVERT: B 1108 ASN cc_start: 0.8210 (m-40) cc_final: 0.7357 (m-40) REVERT: C 118 LEU cc_start: 0.9721 (tp) cc_final: 0.9400 (mt) REVERT: C 201 PHE cc_start: 0.8939 (m-80) cc_final: 0.8368 (m-80) REVERT: C 266 TYR cc_start: 0.8089 (t80) cc_final: 0.7475 (t80) REVERT: C 365 TYR cc_start: 0.6810 (t80) cc_final: 0.6145 (t80) REVERT: C 654 GLU cc_start: 0.9491 (mt-10) cc_final: 0.9279 (mp0) REVERT: C 697 MET cc_start: 0.8070 (mtp) cc_final: 0.7821 (tpt) REVERT: C 702 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9171 (mm-30) REVERT: C 708 SER cc_start: 0.9253 (m) cc_final: 0.8936 (t) REVERT: C 714 ILE cc_start: 0.9010 (mt) cc_final: 0.8718 (mp) REVERT: C 781 VAL cc_start: 0.9646 (t) cc_final: 0.9054 (m) REVERT: C 786 LYS cc_start: 0.9429 (tttt) cc_final: 0.9149 (mtmt) REVERT: C 865 LEU cc_start: 0.9235 (tp) cc_final: 0.8834 (tt) REVERT: C 900 MET cc_start: 0.9119 (mmm) cc_final: 0.8855 (tpp) REVERT: C 927 PHE cc_start: 0.9321 (t80) cc_final: 0.8896 (t80) REVERT: C 1004 LEU cc_start: 0.9693 (mt) cc_final: 0.9483 (mp) REVERT: C 1038 LYS cc_start: 0.9609 (mttt) cc_final: 0.9383 (mmmt) REVERT: C 1047 TYR cc_start: 0.8788 (m-80) cc_final: 0.8574 (m-10) REVERT: C 1108 ASN cc_start: 0.8198 (m-40) cc_final: 0.7459 (m-40) REVERT: C 1111 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8937 (mp0) REVERT: L 162 ARG cc_start: 0.9483 (tpt90) cc_final: 0.8763 (tpp80) REVERT: L 172 ASN cc_start: 0.9812 (m-40) cc_final: 0.9464 (t0) REVERT: M 4 MET cc_start: 0.8341 (tpp) cc_final: 0.7951 (tpp) REVERT: M 203 LYS cc_start: 0.9332 (tttt) cc_final: 0.9062 (mtmm) REVERT: M 219 GLN cc_start: 0.8979 (tt0) cc_final: 0.8779 (tt0) outliers start: 7 outliers final: 1 residues processed: 472 average time/residue: 0.2190 time to fit residues: 157.6994 Evaluate side-chains 239 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 236 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B1002 GLN B1011 GLN B1054 GLN B1119 ASN C 52 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 498 GLN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 180 GLN ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 167 GLN ** M 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.048762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.040170 restraints weight = 393312.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.041197 restraints weight = 201131.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.041858 restraints weight = 126887.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.042253 restraints weight = 92545.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.042495 restraints weight = 75721.103| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 32050 Z= 0.265 Angle : 0.809 11.026 43719 Z= 0.421 Chirality : 0.049 0.549 5069 Planarity : 0.005 0.067 5557 Dihedral : 7.839 86.969 5172 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.59 % Favored : 98.38 % Rotamer: Outliers : 0.12 % Allowed : 1.57 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.13), residues: 3896 helix: 0.47 (0.19), residues: 687 sheet: 0.41 (0.15), residues: 1051 loop : 0.47 (0.14), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1039 TYR 0.028 0.002 TYR C 421 PHE 0.034 0.003 PHE A 377 TRP 0.018 0.002 TRP B 104 HIS 0.010 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00553 (31953) covalent geometry : angle 0.79139 (43480) SS BOND : bond 0.00501 ( 52) SS BOND : angle 1.26592 ( 104) hydrogen bonds : bond 0.05416 ( 1272) hydrogen bonds : angle 7.35933 ( 3510) link_BETA1-4 : bond 0.00577 ( 11) link_BETA1-4 : angle 2.46549 ( 33) link_NAG-ASN : bond 0.01043 ( 34) link_NAG-ASN : angle 3.18247 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 254 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 211 ASN cc_start: 0.8077 (m-40) cc_final: 0.7651 (p0) REVERT: A 598 ILE cc_start: 0.9884 (mp) cc_final: 0.9635 (mm) REVERT: A 855 PHE cc_start: 0.8269 (p90) cc_final: 0.7957 (t80) REVERT: A 927 PHE cc_start: 0.9489 (t80) cc_final: 0.9266 (t80) REVERT: A 933 LYS cc_start: 0.9755 (mttt) cc_final: 0.9471 (mmtp) REVERT: A 1038 LYS cc_start: 0.9018 (mmpt) cc_final: 0.8730 (mmmt) REVERT: A 1063 LEU cc_start: 0.9492 (mt) cc_final: 0.9256 (mt) REVERT: A 1065 VAL cc_start: 0.9378 (t) cc_final: 0.8967 (t) REVERT: B 170 TYR cc_start: 0.9339 (t80) cc_final: 0.8793 (t80) REVERT: B 710 ASN cc_start: 0.9049 (m-40) cc_final: 0.8662 (m-40) REVERT: B 718 PHE cc_start: 0.9431 (p90) cc_final: 0.9223 (p90) REVERT: B 751 ASN cc_start: 0.9206 (m110) cc_final: 0.8945 (m110) REVERT: B 927 PHE cc_start: 0.9513 (t80) cc_final: 0.8981 (t80) REVERT: B 1040 VAL cc_start: 0.8784 (t) cc_final: 0.8334 (t) REVERT: B 1050 MET cc_start: 0.8555 (pmm) cc_final: 0.8348 (pmm) REVERT: B 1052 PHE cc_start: 0.9605 (m-10) cc_final: 0.9274 (m-10) REVERT: B 1065 VAL cc_start: 0.9674 (t) cc_final: 0.9130 (t) REVERT: B 1108 ASN cc_start: 0.8448 (m-40) cc_final: 0.7920 (m-40) REVERT: B 1113 GLN cc_start: 0.9268 (mm-40) cc_final: 0.9010 (mp10) REVERT: C 118 LEU cc_start: 0.9725 (tp) cc_final: 0.9404 (mt) REVERT: C 266 TYR cc_start: 0.8163 (t80) cc_final: 0.7808 (t80) REVERT: C 365 TYR cc_start: 0.6640 (t80) cc_final: 0.5899 (t80) REVERT: C 714 ILE cc_start: 0.8951 (mt) cc_final: 0.8735 (mp) REVERT: C 740 MET cc_start: 0.9008 (mtp) cc_final: 0.8775 (ttm) REVERT: C 927 PHE cc_start: 0.9283 (t80) cc_final: 0.8834 (t80) REVERT: C 1101 HIS cc_start: 0.9329 (m90) cc_final: 0.9064 (m90) REVERT: C 1108 ASN cc_start: 0.8500 (m-40) cc_final: 0.8064 (m-40) REVERT: L 172 ASN cc_start: 0.9650 (m-40) cc_final: 0.9165 (t0) REVERT: H 115 MET cc_start: 0.8828 (tpp) cc_final: 0.8621 (mmt) REVERT: I 39 MET cc_start: 0.9334 (mmp) cc_final: 0.9048 (tpt) outliers start: 4 outliers final: 1 residues processed: 258 average time/residue: 0.2130 time to fit residues: 85.3638 Evaluate side-chains 166 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 289 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 295 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 308 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B1023 ASN B1119 ASN C 66 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 GLN ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.048582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.040053 restraints weight = 394801.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.041087 restraints weight = 199267.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.041734 restraints weight = 124350.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.042119 restraints weight = 90424.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.042373 restraints weight = 74146.736| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 32050 Z= 0.163 Angle : 0.643 11.361 43719 Z= 0.336 Chirality : 0.046 0.444 5069 Planarity : 0.004 0.062 5557 Dihedral : 6.771 79.324 5172 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.13), residues: 3896 helix: 0.90 (0.20), residues: 681 sheet: 0.28 (0.15), residues: 1066 loop : 0.32 (0.14), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 357 TYR 0.020 0.002 TYR C 421 PHE 0.022 0.002 PHE A 201 TRP 0.014 0.001 TRP I 118 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00349 (31953) covalent geometry : angle 0.62443 (43480) SS BOND : bond 0.00294 ( 52) SS BOND : angle 0.87826 ( 104) hydrogen bonds : bond 0.04592 ( 1272) hydrogen bonds : angle 6.75283 ( 3510) link_BETA1-4 : bond 0.00521 ( 11) link_BETA1-4 : angle 1.94646 ( 33) link_NAG-ASN : bond 0.00629 ( 34) link_NAG-ASN : angle 3.00028 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 598 ILE cc_start: 0.9873 (mp) cc_final: 0.9491 (tt) REVERT: A 855 PHE cc_start: 0.8253 (p90) cc_final: 0.7864 (t80) REVERT: A 900 MET cc_start: 0.8707 (tpt) cc_final: 0.8326 (tpp) REVERT: A 1038 LYS cc_start: 0.9007 (mmpt) cc_final: 0.8714 (mmmt) REVERT: A 1063 LEU cc_start: 0.9537 (mt) cc_final: 0.9331 (mt) REVERT: A 1065 VAL cc_start: 0.9310 (t) cc_final: 0.8966 (t) REVERT: A 1110 TYR cc_start: 0.9347 (t80) cc_final: 0.8917 (t80) REVERT: A 1118 ASP cc_start: 0.8866 (t70) cc_final: 0.8523 (p0) REVERT: B 170 TYR cc_start: 0.9423 (t80) cc_final: 0.8926 (t80) REVERT: B 177 MET cc_start: 0.8022 (mmt) cc_final: 0.7524 (pmm) REVERT: B 201 PHE cc_start: 0.9279 (m-10) cc_final: 0.9010 (m-10) REVERT: B 710 ASN cc_start: 0.8923 (m-40) cc_final: 0.8601 (m110) REVERT: B 718 PHE cc_start: 0.9450 (p90) cc_final: 0.8803 (p90) REVERT: B 751 ASN cc_start: 0.9213 (m110) cc_final: 0.8910 (m110) REVERT: B 773 GLU cc_start: 0.9551 (mm-30) cc_final: 0.9020 (tp30) REVERT: B 869 MET cc_start: 0.9562 (mtp) cc_final: 0.9301 (mtp) REVERT: B 927 PHE cc_start: 0.9422 (t80) cc_final: 0.8877 (t80) REVERT: B 1052 PHE cc_start: 0.9534 (m-10) cc_final: 0.9248 (m-10) REVERT: B 1065 VAL cc_start: 0.9667 (t) cc_final: 0.9021 (t) REVERT: B 1108 ASN cc_start: 0.8338 (m-40) cc_final: 0.7812 (m-40) REVERT: C 118 LEU cc_start: 0.9672 (tp) cc_final: 0.9324 (mp) REVERT: C 201 PHE cc_start: 0.8686 (m-80) cc_final: 0.8214 (m-80) REVERT: C 365 TYR cc_start: 0.6776 (t80) cc_final: 0.6091 (t80) REVERT: C 782 PHE cc_start: 0.9611 (m-80) cc_final: 0.9335 (m-80) REVERT: C 797 PHE cc_start: 0.8873 (m-80) cc_final: 0.8085 (m-10) REVERT: C 927 PHE cc_start: 0.9211 (t80) cc_final: 0.8992 (t80) REVERT: C 1038 LYS cc_start: 0.8783 (mmpt) cc_final: 0.8440 (mmmt) REVERT: C 1101 HIS cc_start: 0.9251 (m90) cc_final: 0.8989 (m90) REVERT: L 172 ASN cc_start: 0.9603 (m-40) cc_final: 0.9081 (t0) REVERT: M 4 MET cc_start: 0.9063 (tpt) cc_final: 0.8209 (mmm) REVERT: I 115 MET cc_start: 0.7533 (tpt) cc_final: 0.7201 (tpt) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2034 time to fit residues: 70.2756 Evaluate side-chains 160 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 103 optimal weight: 0.0470 chunk 173 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 chunk 258 optimal weight: 8.9990 chunk 226 optimal weight: 6.9990 chunk 341 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 336 optimal weight: 7.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 125 ASN A 703 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 87 ASN B 207 HIS ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 895 GLN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 209 HIS ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.045432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.036955 restraints weight = 406931.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.037894 restraints weight = 204324.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.038499 restraints weight = 128827.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.038862 restraints weight = 94710.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.039096 restraints weight = 78103.930| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 32050 Z= 0.234 Angle : 0.693 12.018 43719 Z= 0.359 Chirality : 0.045 0.396 5069 Planarity : 0.005 0.061 5557 Dihedral : 6.499 76.014 5172 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.09 % Allowed : 1.89 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.13), residues: 3896 helix: 0.78 (0.19), residues: 698 sheet: -0.00 (0.15), residues: 1075 loop : 0.14 (0.14), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 357 TYR 0.059 0.002 TYR B 91 PHE 0.025 0.002 PHE L 159 TRP 0.012 0.002 TRP A 104 HIS 0.009 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00484 (31953) covalent geometry : angle 0.67696 (43480) SS BOND : bond 0.00354 ( 52) SS BOND : angle 0.99168 ( 104) hydrogen bonds : bond 0.04609 ( 1272) hydrogen bonds : angle 6.75190 ( 3510) link_BETA1-4 : bond 0.00752 ( 11) link_BETA1-4 : angle 2.31291 ( 33) link_NAG-ASN : bond 0.00578 ( 34) link_NAG-ASN : angle 2.77512 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 193 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9016 (m-90) cc_final: 0.8790 (m-90) REVERT: A 598 ILE cc_start: 0.9867 (mp) cc_final: 0.9332 (tt) REVERT: A 776 LYS cc_start: 0.9750 (mtmm) cc_final: 0.9538 (ptpt) REVERT: A 855 PHE cc_start: 0.8230 (p90) cc_final: 0.7666 (t80) REVERT: A 927 PHE cc_start: 0.9360 (t80) cc_final: 0.9125 (t80) REVERT: A 933 LYS cc_start: 0.9718 (mttt) cc_final: 0.9476 (pttm) REVERT: A 1038 LYS cc_start: 0.9086 (mmpt) cc_final: 0.8838 (mmmt) REVERT: A 1118 ASP cc_start: 0.9002 (t70) cc_final: 0.8664 (p0) REVERT: B 201 PHE cc_start: 0.9394 (m-10) cc_final: 0.9116 (m-10) REVERT: B 710 ASN cc_start: 0.9001 (m-40) cc_final: 0.8700 (m110) REVERT: B 718 PHE cc_start: 0.9638 (p90) cc_final: 0.8973 (p90) REVERT: B 751 ASN cc_start: 0.9279 (m110) cc_final: 0.8996 (m110) REVERT: B 869 MET cc_start: 0.9483 (mtp) cc_final: 0.9257 (mtp) REVERT: B 900 MET cc_start: 0.9482 (pmm) cc_final: 0.9277 (pmm) REVERT: B 927 PHE cc_start: 0.9443 (t80) cc_final: 0.8930 (t80) REVERT: B 1050 MET cc_start: 0.8960 (pmm) cc_final: 0.8716 (pmm) REVERT: C 118 LEU cc_start: 0.9670 (tp) cc_final: 0.9320 (mp) REVERT: C 365 TYR cc_start: 0.6846 (t80) cc_final: 0.6126 (t80) REVERT: C 718 PHE cc_start: 0.9549 (p90) cc_final: 0.8918 (p90) REVERT: C 740 MET cc_start: 0.9107 (ttm) cc_final: 0.8901 (ttm) REVERT: C 782 PHE cc_start: 0.9661 (m-80) cc_final: 0.9353 (m-80) REVERT: C 927 PHE cc_start: 0.9249 (t80) cc_final: 0.8698 (t80) REVERT: C 1038 LYS cc_start: 0.8902 (mmpt) cc_final: 0.8633 (mmmt) REVERT: C 1101 HIS cc_start: 0.9164 (m90) cc_final: 0.8890 (m90) REVERT: C 1108 ASN cc_start: 0.8635 (m-40) cc_final: 0.8361 (m-40) REVERT: L 172 ASN cc_start: 0.9649 (m-40) cc_final: 0.9149 (t0) REVERT: M 162 ARG cc_start: 0.9455 (tpt90) cc_final: 0.8923 (mmp80) REVERT: M 172 ASN cc_start: 0.9173 (m-40) cc_final: 0.8946 (m-40) REVERT: I 39 MET cc_start: 0.9447 (mmp) cc_final: 0.9002 (tpt) outliers start: 3 outliers final: 0 residues processed: 196 average time/residue: 0.1955 time to fit residues: 62.0853 Evaluate side-chains 146 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 123 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 285 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 189 optimal weight: 0.6980 chunk 218 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.044899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.036381 restraints weight = 409210.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.037354 restraints weight = 205520.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.037955 restraints weight = 127984.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.038312 restraints weight = 94270.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.038543 restraints weight = 77961.203| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 32050 Z= 0.204 Angle : 0.633 11.862 43719 Z= 0.331 Chirality : 0.045 0.369 5069 Planarity : 0.004 0.045 5557 Dihedral : 6.279 70.703 5172 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.13), residues: 3896 helix: 0.98 (0.19), residues: 702 sheet: -0.16 (0.15), residues: 1088 loop : 0.10 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 95 TYR 0.025 0.002 TYR B 453 PHE 0.026 0.002 PHE A 800 TRP 0.011 0.002 TRP H 41 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00423 (31953) covalent geometry : angle 0.61764 (43480) SS BOND : bond 0.00308 ( 52) SS BOND : angle 0.96437 ( 104) hydrogen bonds : bond 0.04361 ( 1272) hydrogen bonds : angle 6.66940 ( 3510) link_BETA1-4 : bond 0.00484 ( 11) link_BETA1-4 : angle 1.82523 ( 33) link_NAG-ASN : bond 0.00633 ( 34) link_NAG-ASN : angle 2.67339 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9016 (m-90) cc_final: 0.8799 (m-90) REVERT: A 598 ILE cc_start: 0.9872 (mp) cc_final: 0.9385 (tt) REVERT: A 855 PHE cc_start: 0.8195 (p90) cc_final: 0.7419 (t80) REVERT: A 869 MET cc_start: 0.9653 (mtp) cc_final: 0.9439 (mtp) REVERT: A 900 MET cc_start: 0.8782 (tpp) cc_final: 0.8315 (tpp) REVERT: A 927 PHE cc_start: 0.9343 (t80) cc_final: 0.9075 (t80) REVERT: A 1038 LYS cc_start: 0.9050 (mmpt) cc_final: 0.8764 (mmmt) REVERT: A 1063 LEU cc_start: 0.9638 (mt) cc_final: 0.9422 (mt) REVERT: A 1118 ASP cc_start: 0.9054 (t70) cc_final: 0.8703 (p0) REVERT: B 170 TYR cc_start: 0.9540 (t80) cc_final: 0.9102 (t80) REVERT: B 201 PHE cc_start: 0.9465 (m-10) cc_final: 0.9197 (m-10) REVERT: B 710 ASN cc_start: 0.9048 (m-40) cc_final: 0.8742 (m-40) REVERT: B 718 PHE cc_start: 0.9672 (p90) cc_final: 0.9001 (p90) REVERT: B 751 ASN cc_start: 0.9332 (m110) cc_final: 0.9058 (m110) REVERT: B 773 GLU cc_start: 0.9548 (mm-30) cc_final: 0.8913 (tp30) REVERT: B 869 MET cc_start: 0.9494 (mtp) cc_final: 0.9254 (mtp) REVERT: B 927 PHE cc_start: 0.9457 (t80) cc_final: 0.8951 (t80) REVERT: C 118 LEU cc_start: 0.9666 (tp) cc_final: 0.9304 (mp) REVERT: C 201 PHE cc_start: 0.8783 (m-80) cc_final: 0.8427 (m-80) REVERT: C 365 TYR cc_start: 0.6845 (t80) cc_final: 0.6108 (t80) REVERT: C 718 PHE cc_start: 0.9635 (p90) cc_final: 0.9163 (p90) REVERT: C 782 PHE cc_start: 0.9673 (m-80) cc_final: 0.9359 (m-80) REVERT: C 927 PHE cc_start: 0.9239 (t80) cc_final: 0.8778 (t80) REVERT: C 1038 LYS cc_start: 0.8868 (mmpt) cc_final: 0.8601 (mmmt) REVERT: C 1101 HIS cc_start: 0.9166 (m90) cc_final: 0.8880 (m90) REVERT: L 172 ASN cc_start: 0.9687 (m-40) cc_final: 0.9190 (t0) REVERT: H 39 MET cc_start: 0.6388 (tmm) cc_final: 0.5909 (tmm) REVERT: H 115 MET cc_start: 0.6740 (tpt) cc_final: 0.6204 (tpp) REVERT: M 172 ASN cc_start: 0.9195 (m-40) cc_final: 0.8971 (m-40) REVERT: I 39 MET cc_start: 0.9494 (mmp) cc_final: 0.8943 (tpt) REVERT: I 115 MET cc_start: 0.7294 (tpt) cc_final: 0.6906 (tpt) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2032 time to fit residues: 61.6828 Evaluate side-chains 142 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 132 optimal weight: 4.9990 chunk 293 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 284 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 350 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 388 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 257 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.044874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.036479 restraints weight = 404557.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.037401 restraints weight = 200888.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.038000 restraints weight = 125868.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.038354 restraints weight = 92616.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.038560 restraints weight = 76987.111| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 32050 Z= 0.172 Angle : 0.614 11.877 43719 Z= 0.317 Chirality : 0.045 0.389 5069 Planarity : 0.004 0.063 5557 Dihedral : 6.048 66.073 5172 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.13), residues: 3896 helix: 1.11 (0.20), residues: 702 sheet: -0.27 (0.15), residues: 1088 loop : 0.03 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 466 TYR 0.052 0.002 TYR B 91 PHE 0.023 0.001 PHE A 782 TRP 0.022 0.002 TRP M 41 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00362 (31953) covalent geometry : angle 0.59511 (43480) SS BOND : bond 0.00330 ( 52) SS BOND : angle 1.03038 ( 104) hydrogen bonds : bond 0.04143 ( 1272) hydrogen bonds : angle 6.53855 ( 3510) link_BETA1-4 : bond 0.00426 ( 11) link_BETA1-4 : angle 1.84600 ( 33) link_NAG-ASN : bond 0.00586 ( 34) link_NAG-ASN : angle 2.86828 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.9057 (m-90) cc_final: 0.8825 (m-90) REVERT: A 855 PHE cc_start: 0.8259 (p90) cc_final: 0.7377 (t80) REVERT: A 900 MET cc_start: 0.8783 (tpp) cc_final: 0.8354 (tpp) REVERT: A 927 PHE cc_start: 0.9388 (t80) cc_final: 0.9074 (t80) REVERT: A 933 LYS cc_start: 0.9732 (mttt) cc_final: 0.9437 (mttm) REVERT: A 1063 LEU cc_start: 0.9639 (mt) cc_final: 0.9428 (mt) REVERT: A 1118 ASP cc_start: 0.9077 (t70) cc_final: 0.8722 (p0) REVERT: B 170 TYR cc_start: 0.9551 (t80) cc_final: 0.9105 (t80) REVERT: B 194 PHE cc_start: 0.8580 (m-80) cc_final: 0.8297 (m-80) REVERT: B 201 PHE cc_start: 0.9572 (m-10) cc_final: 0.9293 (m-10) REVERT: B 710 ASN cc_start: 0.9111 (m-40) cc_final: 0.8799 (m-40) REVERT: B 718 PHE cc_start: 0.9683 (p90) cc_final: 0.9037 (p90) REVERT: B 721 SER cc_start: 0.9374 (t) cc_final: 0.9152 (p) REVERT: B 751 ASN cc_start: 0.9385 (m110) cc_final: 0.9121 (m110) REVERT: B 773 GLU cc_start: 0.9564 (mm-30) cc_final: 0.8985 (tp30) REVERT: B 927 PHE cc_start: 0.9463 (t80) cc_final: 0.8764 (t80) REVERT: C 118 LEU cc_start: 0.9692 (tp) cc_final: 0.9338 (mm) REVERT: C 201 PHE cc_start: 0.8854 (m-80) cc_final: 0.8539 (m-80) REVERT: C 365 TYR cc_start: 0.6803 (t80) cc_final: 0.6057 (t80) REVERT: C 718 PHE cc_start: 0.9692 (p90) cc_final: 0.9042 (p90) REVERT: C 740 MET cc_start: 0.9234 (ttm) cc_final: 0.8982 (ttm) REVERT: C 782 PHE cc_start: 0.9716 (m-80) cc_final: 0.9221 (m-80) REVERT: C 927 PHE cc_start: 0.9400 (t80) cc_final: 0.8856 (t80) REVERT: C 1038 LYS cc_start: 0.8924 (mmpt) cc_final: 0.8619 (mmmt) REVERT: C 1101 HIS cc_start: 0.9258 (m90) cc_final: 0.8990 (m90) REVERT: L 172 ASN cc_start: 0.9712 (m-40) cc_final: 0.9223 (t0) REVERT: H 39 MET cc_start: 0.6403 (tmm) cc_final: 0.5841 (tmm) REVERT: H 115 MET cc_start: 0.7134 (tpt) cc_final: 0.6369 (tpp) REVERT: M 172 ASN cc_start: 0.9244 (m-40) cc_final: 0.9035 (m-40) REVERT: I 39 MET cc_start: 0.9506 (mmp) cc_final: 0.8979 (tpt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2079 time to fit residues: 61.9476 Evaluate side-chains 138 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 334 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 338 optimal weight: 30.0000 chunk 385 optimal weight: 0.6980 chunk 314 optimal weight: 8.9990 chunk 175 optimal weight: 0.9980 chunk 222 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.045603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.037226 restraints weight = 402780.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.038163 restraints weight = 200031.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.038758 restraints weight = 124675.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.039124 restraints weight = 91410.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.039352 restraints weight = 75400.169| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32050 Z= 0.134 Angle : 0.586 12.019 43719 Z= 0.303 Chirality : 0.045 0.360 5069 Planarity : 0.004 0.053 5557 Dihedral : 5.807 61.697 5172 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.80 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 3896 helix: 1.18 (0.20), residues: 696 sheet: -0.26 (0.15), residues: 1104 loop : 0.05 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 905 TYR 0.033 0.001 TYR M 42 PHE 0.016 0.001 PHE A 782 TRP 0.011 0.001 TRP B 104 HIS 0.004 0.001 HIS L 108 Details of bonding type rmsd covalent geometry : bond 0.00291 (31953) covalent geometry : angle 0.57003 (43480) SS BOND : bond 0.00245 ( 52) SS BOND : angle 0.96551 ( 104) hydrogen bonds : bond 0.03890 ( 1272) hydrogen bonds : angle 6.39439 ( 3510) link_BETA1-4 : bond 0.00479 ( 11) link_BETA1-4 : angle 1.71577 ( 33) link_NAG-ASN : bond 0.00623 ( 34) link_NAG-ASN : angle 2.58117 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8885 (m-90) cc_final: 0.8667 (m-90) REVERT: A 855 PHE cc_start: 0.8109 (p90) cc_final: 0.7288 (t80) REVERT: A 900 MET cc_start: 0.8719 (tpp) cc_final: 0.8239 (tpp) REVERT: A 927 PHE cc_start: 0.9358 (t80) cc_final: 0.9034 (t80) REVERT: A 1038 LYS cc_start: 0.9012 (mmpt) cc_final: 0.8798 (mmmt) REVERT: A 1063 LEU cc_start: 0.9605 (mt) cc_final: 0.9367 (mt) REVERT: A 1118 ASP cc_start: 0.9018 (t70) cc_final: 0.8662 (p0) REVERT: B 170 TYR cc_start: 0.9525 (t80) cc_final: 0.9114 (t80) REVERT: B 201 PHE cc_start: 0.9545 (m-10) cc_final: 0.9254 (m-10) REVERT: B 710 ASN cc_start: 0.9097 (m-40) cc_final: 0.8765 (m110) REVERT: B 718 PHE cc_start: 0.9662 (p90) cc_final: 0.9004 (p90) REVERT: B 751 ASN cc_start: 0.9334 (m110) cc_final: 0.9065 (m110) REVERT: B 773 GLU cc_start: 0.9518 (mm-30) cc_final: 0.8909 (tp30) REVERT: B 775 ASP cc_start: 0.9267 (m-30) cc_final: 0.9007 (m-30) REVERT: B 869 MET cc_start: 0.9561 (mtp) cc_final: 0.9315 (mtp) REVERT: B 927 PHE cc_start: 0.9433 (t80) cc_final: 0.8751 (t80) REVERT: B 1010 GLN cc_start: 0.9570 (mt0) cc_final: 0.9364 (mm-40) REVERT: C 118 LEU cc_start: 0.9666 (tp) cc_final: 0.9272 (mp) REVERT: C 201 PHE cc_start: 0.8793 (m-80) cc_final: 0.8491 (m-80) REVERT: C 266 TYR cc_start: 0.7995 (t80) cc_final: 0.7732 (t80) REVERT: C 365 TYR cc_start: 0.6875 (t80) cc_final: 0.6199 (t80) REVERT: C 718 PHE cc_start: 0.9657 (p90) cc_final: 0.9015 (p90) REVERT: C 740 MET cc_start: 0.9208 (ttm) cc_final: 0.8992 (ttm) REVERT: C 782 PHE cc_start: 0.9679 (m-80) cc_final: 0.9192 (m-80) REVERT: C 927 PHE cc_start: 0.9268 (t80) cc_final: 0.8791 (t80) REVERT: C 1038 LYS cc_start: 0.8934 (mmpt) cc_final: 0.8632 (mmmt) REVERT: C 1101 HIS cc_start: 0.9229 (m90) cc_final: 0.8970 (m90) REVERT: L 172 ASN cc_start: 0.9690 (m-40) cc_final: 0.9194 (t0) REVERT: H 39 MET cc_start: 0.6384 (tmm) cc_final: 0.5911 (tmm) REVERT: H 115 MET cc_start: 0.6940 (tpt) cc_final: 0.6152 (tpt) REVERT: M 172 ASN cc_start: 0.9173 (m-40) cc_final: 0.8942 (m-40) REVERT: I 39 MET cc_start: 0.9489 (mmp) cc_final: 0.8940 (tpt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1960 time to fit residues: 58.5767 Evaluate side-chains 140 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 109 optimal weight: 1.9990 chunk 321 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.045224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.036856 restraints weight = 405681.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.037801 restraints weight = 200461.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.038394 restraints weight = 125195.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.038753 restraints weight = 91857.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.038976 restraints weight = 75840.150| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32050 Z= 0.140 Angle : 0.576 12.069 43719 Z= 0.299 Chirality : 0.045 0.343 5069 Planarity : 0.004 0.090 5557 Dihedral : 5.623 56.697 5172 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3896 helix: 1.18 (0.20), residues: 699 sheet: -0.25 (0.15), residues: 1123 loop : 0.02 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 346 TYR 0.032 0.001 TYR M 42 PHE 0.015 0.001 PHE A 782 TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00301 (31953) covalent geometry : angle 0.56140 (43480) SS BOND : bond 0.00245 ( 52) SS BOND : angle 0.95196 ( 104) hydrogen bonds : bond 0.03841 ( 1272) hydrogen bonds : angle 6.32753 ( 3510) link_BETA1-4 : bond 0.00458 ( 11) link_BETA1-4 : angle 1.76197 ( 33) link_NAG-ASN : bond 0.00473 ( 34) link_NAG-ASN : angle 2.46807 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 855 PHE cc_start: 0.8157 (p90) cc_final: 0.7515 (t80) REVERT: A 900 MET cc_start: 0.8684 (tpp) cc_final: 0.8148 (tpp) REVERT: A 927 PHE cc_start: 0.9368 (t80) cc_final: 0.9077 (t80) REVERT: A 1038 LYS cc_start: 0.9025 (mmpt) cc_final: 0.8799 (mmmt) REVERT: A 1063 LEU cc_start: 0.9599 (mt) cc_final: 0.9372 (mt) REVERT: A 1118 ASP cc_start: 0.9057 (t70) cc_final: 0.8718 (p0) REVERT: B 194 PHE cc_start: 0.8594 (m-80) cc_final: 0.8337 (m-80) REVERT: B 201 PHE cc_start: 0.9561 (m-10) cc_final: 0.9283 (m-10) REVERT: B 710 ASN cc_start: 0.9115 (m-40) cc_final: 0.8786 (m110) REVERT: B 718 PHE cc_start: 0.9675 (p90) cc_final: 0.8989 (p90) REVERT: B 751 ASN cc_start: 0.9332 (m110) cc_final: 0.9077 (m110) REVERT: B 775 ASP cc_start: 0.9253 (m-30) cc_final: 0.8950 (m-30) REVERT: B 869 MET cc_start: 0.9550 (mtp) cc_final: 0.9305 (mtp) REVERT: B 927 PHE cc_start: 0.9440 (t80) cc_final: 0.8783 (t80) REVERT: C 118 LEU cc_start: 0.9669 (tp) cc_final: 0.9308 (mm) REVERT: C 177 MET cc_start: 0.8974 (mmm) cc_final: 0.8343 (mmm) REVERT: C 201 PHE cc_start: 0.8802 (m-80) cc_final: 0.8507 (m-80) REVERT: C 365 TYR cc_start: 0.6813 (t80) cc_final: 0.6137 (t80) REVERT: C 718 PHE cc_start: 0.9653 (p90) cc_final: 0.8906 (p90) REVERT: C 740 MET cc_start: 0.9262 (ttm) cc_final: 0.9013 (ttp) REVERT: C 782 PHE cc_start: 0.9678 (m-80) cc_final: 0.9200 (m-80) REVERT: C 925 ASN cc_start: 0.9333 (m110) cc_final: 0.9125 (p0) REVERT: C 927 PHE cc_start: 0.9266 (t80) cc_final: 0.8777 (t80) REVERT: C 1038 LYS cc_start: 0.8932 (mmpt) cc_final: 0.8625 (mmmt) REVERT: C 1101 HIS cc_start: 0.9238 (m90) cc_final: 0.8976 (m90) REVERT: L 172 ASN cc_start: 0.9690 (m-40) cc_final: 0.9196 (t0) REVERT: H 39 MET cc_start: 0.6340 (tmm) cc_final: 0.6047 (tmm) REVERT: H 115 MET cc_start: 0.6853 (tpt) cc_final: 0.6145 (tpp) REVERT: M 172 ASN cc_start: 0.9165 (m-40) cc_final: 0.8947 (m-40) REVERT: I 39 MET cc_start: 0.9492 (mmp) cc_final: 0.8973 (tpt) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1983 time to fit residues: 57.9618 Evaluate side-chains 137 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 258 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 303 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 chunk 322 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 304 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 chunk 54 optimal weight: 0.0030 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1036 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1036 GLN B1119 ASN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.046704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.038252 restraints weight = 400369.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.039231 restraints weight = 198197.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.039842 restraints weight = 122842.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.040202 restraints weight = 89978.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.040429 restraints weight = 74263.882| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32050 Z= 0.110 Angle : 0.562 12.250 43719 Z= 0.289 Chirality : 0.045 0.353 5069 Planarity : 0.004 0.048 5557 Dihedral : 5.303 52.939 5172 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.03 % Allowed : 0.52 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3896 helix: 1.15 (0.20), residues: 697 sheet: -0.15 (0.15), residues: 1103 loop : 0.04 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 408 TYR 0.027 0.001 TYR M 42 PHE 0.019 0.001 PHE A 194 TRP 0.015 0.001 TRP I 118 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00238 (31953) covalent geometry : angle 0.54902 (43480) SS BOND : bond 0.00181 ( 52) SS BOND : angle 0.83497 ( 104) hydrogen bonds : bond 0.03598 ( 1272) hydrogen bonds : angle 6.06800 ( 3510) link_BETA1-4 : bond 0.00592 ( 11) link_BETA1-4 : angle 1.60234 ( 33) link_NAG-ASN : bond 0.00523 ( 34) link_NAG-ASN : angle 2.30409 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8737 (m-90) cc_final: 0.8519 (m-90) REVERT: A 855 PHE cc_start: 0.8005 (p90) cc_final: 0.7545 (t80) REVERT: A 927 PHE cc_start: 0.9346 (t80) cc_final: 0.9077 (t80) REVERT: A 1038 LYS cc_start: 0.9014 (mmpt) cc_final: 0.8808 (mmmt) REVERT: A 1063 LEU cc_start: 0.9562 (mt) cc_final: 0.9330 (mt) REVERT: B 170 TYR cc_start: 0.9548 (t80) cc_final: 0.9127 (t80) REVERT: B 194 PHE cc_start: 0.8630 (m-80) cc_final: 0.7048 (m-80) REVERT: B 201 PHE cc_start: 0.9538 (m-10) cc_final: 0.9262 (m-10) REVERT: B 710 ASN cc_start: 0.9098 (m-40) cc_final: 0.8733 (m110) REVERT: B 718 PHE cc_start: 0.9651 (p90) cc_final: 0.8992 (p90) REVERT: B 751 ASN cc_start: 0.9299 (m110) cc_final: 0.9043 (m110) REVERT: B 773 GLU cc_start: 0.9477 (mm-30) cc_final: 0.8732 (tp30) REVERT: B 775 ASP cc_start: 0.9288 (m-30) cc_final: 0.8951 (m-30) REVERT: B 869 MET cc_start: 0.9555 (mtp) cc_final: 0.9324 (mtp) REVERT: B 927 PHE cc_start: 0.9394 (t80) cc_final: 0.8788 (t80) REVERT: B 1010 GLN cc_start: 0.9482 (mp10) cc_final: 0.9182 (mp10) REVERT: C 118 LEU cc_start: 0.9635 (tp) cc_final: 0.9249 (mp) REVERT: C 177 MET cc_start: 0.8836 (mmm) cc_final: 0.8539 (mmm) REVERT: C 365 TYR cc_start: 0.6824 (t80) cc_final: 0.6093 (t80) REVERT: C 718 PHE cc_start: 0.9588 (p90) cc_final: 0.8893 (p90) REVERT: C 740 MET cc_start: 0.9278 (ttm) cc_final: 0.8994 (ttm) REVERT: C 782 PHE cc_start: 0.9696 (m-80) cc_final: 0.9239 (m-80) REVERT: C 797 PHE cc_start: 0.8817 (m-10) cc_final: 0.8609 (m-10) REVERT: C 925 ASN cc_start: 0.9390 (m110) cc_final: 0.9110 (p0) REVERT: C 927 PHE cc_start: 0.9265 (t80) cc_final: 0.8814 (t80) REVERT: C 1038 LYS cc_start: 0.8890 (mmpt) cc_final: 0.8488 (mmmt) REVERT: C 1101 HIS cc_start: 0.9248 (m90) cc_final: 0.9002 (m90) REVERT: C 1108 ASN cc_start: 0.8637 (m-40) cc_final: 0.8241 (p0) REVERT: L 4 MET cc_start: 0.7185 (pmm) cc_final: 0.3394 (tmm) REVERT: L 172 ASN cc_start: 0.9678 (m-40) cc_final: 0.9177 (t0) REVERT: L 181 GLU cc_start: 0.8738 (pt0) cc_final: 0.7850 (tm-30) REVERT: H 39 MET cc_start: 0.6218 (tmm) cc_final: 0.5896 (tmm) REVERT: H 115 MET cc_start: 0.6268 (tpt) cc_final: 0.5619 (tpp) REVERT: I 39 MET cc_start: 0.9472 (mmp) cc_final: 0.8907 (tpt) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.1993 time to fit residues: 63.3079 Evaluate side-chains 150 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 253 optimal weight: 2.9990 chunk 269 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 301 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 295 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 306 optimal weight: 20.0000 chunk 216 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 23 GLN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.045870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.037514 restraints weight = 403229.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.038482 restraints weight = 200389.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.039076 restraints weight = 124118.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.039439 restraints weight = 91467.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.039666 restraints weight = 75446.272| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32050 Z= 0.123 Angle : 0.562 12.153 43719 Z= 0.289 Chirality : 0.045 0.412 5069 Planarity : 0.004 0.053 5557 Dihedral : 5.238 53.213 5172 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3896 helix: 1.20 (0.20), residues: 697 sheet: -0.16 (0.15), residues: 1121 loop : 0.08 (0.14), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1091 TYR 0.041 0.001 TYR B 91 PHE 0.018 0.001 PHE A 194 TRP 0.035 0.001 TRP B 104 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00268 (31953) covalent geometry : angle 0.54647 (43480) SS BOND : bond 0.00207 ( 52) SS BOND : angle 0.86648 ( 104) hydrogen bonds : bond 0.03609 ( 1272) hydrogen bonds : angle 6.04738 ( 3510) link_BETA1-4 : bond 0.00575 ( 11) link_BETA1-4 : angle 1.84188 ( 33) link_NAG-ASN : bond 0.00461 ( 34) link_NAG-ASN : angle 2.45702 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 855 PHE cc_start: 0.8082 (p90) cc_final: 0.7641 (t80) REVERT: A 900 MET cc_start: 0.9362 (mmp) cc_final: 0.9151 (tpp) REVERT: A 927 PHE cc_start: 0.9362 (t80) cc_final: 0.9090 (t80) REVERT: A 1038 LYS cc_start: 0.9016 (mmpt) cc_final: 0.8814 (mmmt) REVERT: A 1063 LEU cc_start: 0.9587 (mt) cc_final: 0.9344 (mt) REVERT: B 201 PHE cc_start: 0.9559 (m-10) cc_final: 0.9163 (m-10) REVERT: B 710 ASN cc_start: 0.9177 (m-40) cc_final: 0.8833 (m110) REVERT: B 718 PHE cc_start: 0.9676 (p90) cc_final: 0.9028 (p90) REVERT: B 751 ASN cc_start: 0.9312 (m110) cc_final: 0.8981 (m110) REVERT: B 773 GLU cc_start: 0.9490 (mm-30) cc_final: 0.8753 (tp30) REVERT: B 775 ASP cc_start: 0.9330 (m-30) cc_final: 0.9029 (m-30) REVERT: B 869 MET cc_start: 0.9541 (mtp) cc_final: 0.9245 (mtp) REVERT: B 927 PHE cc_start: 0.9413 (t80) cc_final: 0.8799 (t80) REVERT: B 1004 LEU cc_start: 0.9637 (tp) cc_final: 0.9415 (tp) REVERT: B 1010 GLN cc_start: 0.9428 (mp10) cc_final: 0.9175 (mp10) REVERT: C 118 LEU cc_start: 0.9629 (tp) cc_final: 0.9244 (mp) REVERT: C 177 MET cc_start: 0.8863 (mmm) cc_final: 0.8428 (mmm) REVERT: C 304 LYS cc_start: 0.9455 (mmpt) cc_final: 0.9252 (tppt) REVERT: C 365 TYR cc_start: 0.6845 (t80) cc_final: 0.6151 (t80) REVERT: C 718 PHE cc_start: 0.9632 (p90) cc_final: 0.8929 (p90) REVERT: C 740 MET cc_start: 0.9297 (ttm) cc_final: 0.9023 (ttm) REVERT: C 782 PHE cc_start: 0.9657 (m-80) cc_final: 0.9196 (m-80) REVERT: C 925 ASN cc_start: 0.9402 (m110) cc_final: 0.9120 (p0) REVERT: C 927 PHE cc_start: 0.9294 (t80) cc_final: 0.8781 (t80) REVERT: C 1038 LYS cc_start: 0.8911 (mmpt) cc_final: 0.8500 (mmmt) REVERT: C 1101 HIS cc_start: 0.9254 (m90) cc_final: 0.9000 (m90) REVERT: C 1108 ASN cc_start: 0.8711 (m-40) cc_final: 0.8285 (p0) REVERT: L 4 MET cc_start: 0.7195 (pmm) cc_final: 0.3485 (tmm) REVERT: L 172 ASN cc_start: 0.9683 (m-40) cc_final: 0.9185 (t0) REVERT: L 181 GLU cc_start: 0.8752 (pt0) cc_final: 0.8048 (mm-30) REVERT: H 39 MET cc_start: 0.6203 (tmm) cc_final: 0.5882 (tmm) REVERT: H 115 MET cc_start: 0.6325 (tpt) cc_final: 0.5614 (tpp) REVERT: I 39 MET cc_start: 0.9492 (mmp) cc_final: 0.8922 (tpt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1902 time to fit residues: 55.4235 Evaluate side-chains 144 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 299 optimal weight: 9.9990 chunk 276 optimal weight: 1.9990 chunk 352 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 chunk 283 optimal weight: 0.6980 chunk 152 optimal weight: 10.0000 chunk 196 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.045755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.037415 restraints weight = 404368.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.038384 restraints weight = 201030.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.038980 restraints weight = 124777.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.039350 restraints weight = 91750.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.039566 restraints weight = 75525.141| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32050 Z= 0.117 Angle : 0.550 12.216 43719 Z= 0.283 Chirality : 0.045 0.340 5069 Planarity : 0.004 0.048 5557 Dihedral : 5.125 53.185 5172 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3896 helix: 1.23 (0.20), residues: 697 sheet: -0.15 (0.15), residues: 1112 loop : 0.09 (0.14), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1091 TYR 0.033 0.001 TYR B 91 PHE 0.025 0.001 PHE B 194 TRP 0.029 0.001 TRP B 104 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00254 (31953) covalent geometry : angle 0.53523 (43480) SS BOND : bond 0.00200 ( 52) SS BOND : angle 0.80429 ( 104) hydrogen bonds : bond 0.03545 ( 1272) hydrogen bonds : angle 5.98160 ( 3510) link_BETA1-4 : bond 0.00522 ( 11) link_BETA1-4 : angle 1.67095 ( 33) link_NAG-ASN : bond 0.00487 ( 34) link_NAG-ASN : angle 2.40388 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5397.67 seconds wall clock time: 94 minutes 30.05 seconds (5670.05 seconds total)