Starting phenix.real_space_refine on Mon Jul 6 01:13:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kmk_22925/07_2026/7kmk_22925.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kmk_22925/07_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_22925/07_2026/7kmk_22925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kmk_22925/07_2026/7kmk_22925.map" model { file = "/net/cci-nas-00/data/ceres_data/7kmk_22925/07_2026/7kmk_22925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kmk_22925/07_2026/7kmk_22925.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7kmk_22925/07_2026/7kmk_22925.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kmk_22925/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 9 Time building chain proxies: 5.74, per 1000 atoms: 0.18 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: 2.51 Conformation dependent library (CDL) restraints added in 1.1 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: 1.12 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: 7.88 Time building geometry restraints manager: 3.39 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 - 17.95: 18021 17.95 - 35.91: 459 35.91 - 53.86: 154 53.86 - 71.82: 71 71.82 - 89.77: 22 Dihedral angle restraints: 18727 sinusoidal: 7251 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 18724 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: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 28.450 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 10.526 89.773 11197 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/Z covalent geometry : bond 0.01920 / 1.00 (31953) covalent geometry : angle 1.83489 / 1.24 (43480) SS BOND : bond 0.02076 / 1.38 ( 52) SS BOND : angle 2.40402 / 1.63 ( 104) hydrogen bonds : bond 0.15563 / 10.50 ( 1272) hydrogen bonds : angle 8.81412 / 6.18 ( 3510) link_BETA1-4 : bond 0.00737 / 0.36 ( 11) link_BETA1-4 : angle 1.53143 / 1.04 ( 33) link_NAG-ASN : bond 0.00262 / 0.15 ( 34) link_NAG-ASN : angle 1.34405 / 0.97 ( 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 : 1.148 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: 0.2255 time to fit residues: 163.1283 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 : 1.200 ------------------------------------------------------------------------------- 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... ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B1002 GLN B1011 GLN B1054 GLN B1119 ASN C 121 ASN C 125 ASN C 498 GLN ** C 954 GLN ** 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 I 186 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.049169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.040594 restraints weight = 394005.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.041635 restraints weight = 200968.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.042288 restraints weight = 126481.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.042690 restraints weight = 92601.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.042947 restraints weight = 75751.015| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 32050 Z= 0.264 Angle : 0.801 11.480 43719 Z= 0.420 Chirality : 0.049 0.614 5069 Planarity : 0.005 0.070 5557 Dihedral : 5.374 26.677 4231 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.51 % Favored : 98.46 % Rotamer: Outliers : 0.12 % Allowed : 1.37 % Favored : 98.52 % 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: 0.64 (0.13), residues: 3896 helix: 0.65 (0.19), residues: 680 sheet: 0.44 (0.15), residues: 1072 loop : 0.50 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1039 TYR 0.028 0.003 TYR C 421 PHE 0.030 0.002 PHE A 377 TRP 0.019 0.002 TRP B 104 HIS 0.008 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.26 (31953) covalent geometry : angle 0.78259 / 0.42 (43480) SS BOND : bond 0.00453 / 0.30 ( 52) SS BOND : angle 1.21418 / 0.86 ( 104) hydrogen bonds : bond 0.05540 / 3.67 ( 1272) hydrogen bonds : angle 7.34786 / 5.16 ( 3510) link_BETA1-4 : bond 0.00696 / 0.41 ( 11) link_BETA1-4 : angle 1.84546 / 1.30 ( 33) link_NAG-ASN : bond 0.01014 / 0.67 ( 34) link_NAG-ASN : angle 3.40295 / 2.47 ( 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 256 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 252 time to evaluate : 1.378 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 211 ASN cc_start: 0.7996 (m-40) cc_final: 0.7616 (p0) REVERT: A 598 ILE cc_start: 0.9871 (mp) cc_final: 0.9609 (mm) REVERT: A 855 PHE cc_start: 0.8210 (p90) cc_final: 0.7966 (t80) REVERT: A 927 PHE cc_start: 0.9440 (t80) cc_final: 0.9239 (t80) REVERT: A 933 LYS cc_start: 0.9744 (mttt) cc_final: 0.9462 (mmtp) REVERT: A 1038 LYS cc_start: 0.9006 (mmpt) cc_final: 0.8701 (mmmt) REVERT: A 1041 ASP cc_start: 0.9057 (t0) cc_final: 0.8837 (t0) REVERT: A 1063 LEU cc_start: 0.9499 (mt) cc_final: 0.9253 (mt) REVERT: A 1065 VAL cc_start: 0.9328 (t) cc_final: 0.8867 (t) REVERT: B 170 TYR cc_start: 0.9366 (t80) cc_final: 0.8829 (t80) REVERT: B 710 ASN cc_start: 0.9011 (m-40) cc_final: 0.8614 (m-40) REVERT: B 751 ASN cc_start: 0.9161 (m110) cc_final: 0.8934 (m110) REVERT: B 755 GLN cc_start: 0.9295 (mt0) cc_final: 0.8871 (mt0) REVERT: B 927 PHE cc_start: 0.9491 (t80) cc_final: 0.8966 (t80) REVERT: B 1040 VAL cc_start: 0.8774 (t) cc_final: 0.8363 (t) REVERT: B 1052 PHE cc_start: 0.9574 (m-10) cc_final: 0.9272 (m-10) REVERT: B 1065 VAL cc_start: 0.9618 (t) cc_final: 0.9019 (t) REVERT: B 1108 ASN cc_start: 0.8309 (m-40) cc_final: 0.7726 (m-40) REVERT: B 1113 GLN cc_start: 0.9305 (mm-40) cc_final: 0.9027 (mp10) REVERT: C 118 LEU cc_start: 0.9695 (tp) cc_final: 0.9377 (mt) REVERT: C 266 TYR cc_start: 0.8099 (t80) cc_final: 0.7749 (t80) REVERT: C 304 LYS cc_start: 0.9717 (mttt) cc_final: 0.9507 (tmtt) REVERT: C 365 TYR cc_start: 0.6740 (t80) cc_final: 0.6049 (t80) REVERT: C 740 MET cc_start: 0.8976 (mtp) cc_final: 0.8711 (ttm) REVERT: C 927 PHE cc_start: 0.9243 (t80) cc_final: 0.8792 (t80) REVERT: C 1101 HIS cc_start: 0.9270 (m90) cc_final: 0.8999 (m90) REVERT: C 1108 ASN cc_start: 0.8508 (m-40) cc_final: 0.8076 (m-40) REVERT: L 172 ASN cc_start: 0.9607 (m-40) cc_final: 0.9115 (t0) REVERT: H 115 MET cc_start: 0.8688 (tpp) cc_final: 0.8467 (mmt) REVERT: M 162 ARG cc_start: 0.9535 (tpt90) cc_final: 0.9099 (mmp80) REVERT: I 39 MET cc_start: 0.9276 (mmp) cc_final: 0.9044 (tpt) outliers start: 4 outliers final: 1 residues processed: 256 average time/residue: 0.2137 time to fit residues: 85.1233 Evaluate side-chains 165 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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: 3.9990 chunk 113 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 293 optimal weight: 0.8980 chunk 227 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 295 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 308 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 895 GLN B1023 ASN B1119 ASN C 52 GLN 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** ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.048675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.040134 restraints weight = 397426.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.041178 restraints weight = 200493.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.041841 restraints weight = 125210.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.042227 restraints weight = 90997.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.042487 restraints weight = 74491.460| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 32050 Z= 0.173 Angle : 0.653 11.324 43719 Z= 0.343 Chirality : 0.046 0.411 5069 Planarity : 0.004 0.067 5557 Dihedral : 5.117 26.062 4231 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.06 % Allowed : 1.89 % Favored : 98.05 % 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: 0.49 (0.13), residues: 3896 helix: 0.81 (0.19), residues: 686 sheet: 0.35 (0.15), residues: 1058 loop : 0.29 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 357 TYR 0.021 0.002 TYR C 421 PHE 0.022 0.002 PHE A 201 TRP 0.015 0.002 TRP I 118 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (31953) covalent geometry : angle 0.63602 / 0.34 (43480) SS BOND : bond 0.00255 / 0.17 ( 52) SS BOND : angle 0.91132 / 0.62 ( 104) hydrogen bonds : bond 0.04714 / 3.16 ( 1272) hydrogen bonds : angle 6.84790 / 4.81 ( 3510) link_BETA1-4 : bond 0.00484 / 0.25 ( 11) link_BETA1-4 : angle 1.36028 / 0.94 ( 33) link_NAG-ASN : bond 0.00597 / 0.35 ( 34) link_NAG-ASN : angle 2.94466 / 2.14 ( 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 219 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 1.227 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: A 855 PHE cc_start: 0.8222 (p90) cc_final: 0.7893 (t80) REVERT: A 900 MET cc_start: 0.8705 (tpt) cc_final: 0.8363 (tpp) REVERT: A 1038 LYS cc_start: 0.8997 (mmpt) cc_final: 0.8723 (mmmt) REVERT: A 1063 LEU cc_start: 0.9536 (mt) cc_final: 0.9332 (mt) REVERT: A 1065 VAL cc_start: 0.9306 (t) cc_final: 0.8964 (t) REVERT: A 1118 ASP cc_start: 0.8876 (t70) cc_final: 0.8509 (p0) REVERT: B 170 TYR cc_start: 0.9412 (t80) cc_final: 0.8909 (t80) REVERT: B 177 MET cc_start: 0.8000 (mmt) cc_final: 0.7470 (pmm) REVERT: B 201 PHE cc_start: 0.9275 (m-10) cc_final: 0.9002 (m-10) REVERT: B 710 ASN cc_start: 0.8887 (m-40) cc_final: 0.8547 (m110) REVERT: B 718 PHE cc_start: 0.9454 (p90) cc_final: 0.8802 (p90) REVERT: B 751 ASN cc_start: 0.9201 (m110) cc_final: 0.8917 (m110) REVERT: B 869 MET cc_start: 0.9555 (mtp) cc_final: 0.9280 (mtp) REVERT: B 927 PHE cc_start: 0.9449 (t80) cc_final: 0.8905 (t80) REVERT: B 1017 GLU cc_start: 0.9289 (tm-30) cc_final: 0.9058 (tm-30) REVERT: B 1052 PHE cc_start: 0.9542 (m-10) cc_final: 0.9204 (m-10) REVERT: B 1065 VAL cc_start: 0.9663 (t) cc_final: 0.9124 (t) REVERT: B 1108 ASN cc_start: 0.8305 (m-40) cc_final: 0.7757 (m-40) REVERT: C 118 LEU cc_start: 0.9682 (tp) cc_final: 0.9341 (mp) REVERT: C 201 PHE cc_start: 0.8654 (m-80) cc_final: 0.8151 (m-80) REVERT: C 266 TYR cc_start: 0.7958 (t80) cc_final: 0.7673 (t80) REVERT: C 304 LYS cc_start: 0.9706 (mttt) cc_final: 0.9480 (tmtt) REVERT: C 365 TYR cc_start: 0.6731 (t80) cc_final: 0.6033 (t80) REVERT: C 927 PHE cc_start: 0.9249 (t80) cc_final: 0.8877 (t80) REVERT: C 1038 LYS cc_start: 0.8777 (mmpt) cc_final: 0.8406 (mmmt) REVERT: C 1101 HIS cc_start: 0.9244 (m90) cc_final: 0.9002 (m90) REVERT: L 172 ASN cc_start: 0.9606 (m-40) cc_final: 0.9098 (t0) REVERT: M 4 MET cc_start: 0.9039 (tpt) cc_final: 0.7657 (ttm) REVERT: I 115 MET cc_start: 0.7646 (tpt) cc_final: 0.7326 (tpt) outliers start: 2 outliers final: 1 residues processed: 218 average time/residue: 0.2030 time to fit residues: 70.6527 Evaluate side-chains 164 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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: 0.9980 chunk 173 optimal weight: 1.9990 chunk 230 optimal weight: 30.0000 chunk 258 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 341 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 251 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 336 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN A 935 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** 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** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 66 HIS C 895 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 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** ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.045956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.037487 restraints weight = 404944.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.038442 restraints weight = 202910.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.039070 restraints weight = 127966.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.039438 restraints weight = 93804.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.039673 restraints weight = 77203.820| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 32050 Z= 0.223 Angle : 0.678 10.655 43719 Z= 0.353 Chirality : 0.045 0.359 5069 Planarity : 0.005 0.070 5557 Dihedral : 5.110 24.158 4231 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.09 % Allowed : 1.92 % Favored : 97.99 % 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 (0.13), residues: 3896 helix: 0.76 (0.19), residues: 697 sheet: -0.00 (0.15), residues: 1080 loop : 0.18 (0.14), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 95 TYR 0.055 0.002 TYR B 91 PHE 0.026 0.002 PHE A 377 TRP 0.010 0.002 TRP A 104 HIS 0.008 0.002 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 (31953) covalent geometry : angle 0.66335 / 0.35 (43480) SS BOND : bond 0.00320 / 0.21 ( 52) SS BOND : angle 0.97354 / 0.70 ( 104) hydrogen bonds : bond 0.04560 / 3.04 ( 1272) hydrogen bonds : angle 6.72734 / 4.70 ( 3510) link_BETA1-4 : bond 0.00572 / 0.35 ( 11) link_BETA1-4 : angle 1.63609 / 1.14 ( 33) link_NAG-ASN : bond 0.00718 / 0.47 ( 34) link_NAG-ASN : angle 2.73095 / 1.96 ( 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 199 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 196 time to evaluate : 1.244 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: A 104 TRP cc_start: 0.8985 (m-90) cc_final: 0.8766 (m-90) REVERT: A 855 PHE cc_start: 0.8248 (p90) cc_final: 0.7740 (t80) REVERT: A 927 PHE cc_start: 0.9356 (t80) cc_final: 0.9114 (t80) REVERT: A 929 SER cc_start: 0.9487 (t) cc_final: 0.9056 (p) REVERT: A 933 LYS cc_start: 0.9720 (mttt) cc_final: 0.9497 (mttm) REVERT: A 1038 LYS cc_start: 0.9043 (mmpt) cc_final: 0.8720 (mmmt) REVERT: A 1118 ASP cc_start: 0.8997 (t70) cc_final: 0.8655 (p0) REVERT: B 170 TYR cc_start: 0.9490 (t80) cc_final: 0.9038 (t80) REVERT: B 201 PHE cc_start: 0.9398 (m-10) cc_final: 0.9126 (m-10) REVERT: B 710 ASN cc_start: 0.8971 (m-40) cc_final: 0.8647 (m110) REVERT: B 718 PHE cc_start: 0.9624 (p90) cc_final: 0.8931 (p90) REVERT: B 751 ASN cc_start: 0.9286 (m110) cc_final: 0.9000 (m110) REVERT: B 773 GLU cc_start: 0.9487 (mt-10) cc_final: 0.9124 (tp30) REVERT: B 869 MET cc_start: 0.9473 (mtp) cc_final: 0.9243 (mtp) REVERT: B 927 PHE cc_start: 0.9444 (t80) cc_final: 0.8916 (t80) REVERT: B 1017 GLU cc_start: 0.9245 (tm-30) cc_final: 0.9044 (tm-30) REVERT: B 1050 MET cc_start: 0.8798 (pmm) cc_final: 0.8538 (pmm) REVERT: C 118 LEU cc_start: 0.9674 (tp) cc_final: 0.9312 (mp) REVERT: C 201 PHE cc_start: 0.8759 (m-80) cc_final: 0.8329 (m-80) REVERT: C 365 TYR cc_start: 0.6814 (t80) cc_final: 0.6095 (t80) REVERT: C 782 PHE cc_start: 0.9670 (m-80) cc_final: 0.9296 (m-80) REVERT: C 927 PHE cc_start: 0.9309 (t80) cc_final: 0.8776 (t80) REVERT: C 1038 LYS cc_start: 0.8917 (mmpt) cc_final: 0.8618 (mmmt) REVERT: C 1101 HIS cc_start: 0.9147 (m90) cc_final: 0.8871 (m90) REVERT: C 1108 ASN cc_start: 0.8664 (m-40) cc_final: 0.8405 (m-40) REVERT: L 172 ASN cc_start: 0.9638 (m-40) cc_final: 0.9111 (t0) REVERT: M 162 ARG cc_start: 0.9461 (tpt90) cc_final: 0.8922 (mmp80) REVERT: M 172 ASN cc_start: 0.9165 (m-40) cc_final: 0.8929 (m-40) REVERT: I 39 MET cc_start: 0.9433 (mmp) cc_final: 0.8975 (tpt) outliers start: 3 outliers final: 1 residues processed: 198 average time/residue: 0.1910 time to fit residues: 60.8615 Evaluate side-chains 154 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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: 8.9990 chunk 211 optimal weight: 8.9990 chunk 285 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 189 optimal weight: 0.6980 chunk 218 optimal weight: 20.0000 chunk 210 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 703 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 66 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.044581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.036104 restraints weight = 411023.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.037069 restraints weight = 205726.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.037672 restraints weight = 128446.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.038039 restraints weight = 94714.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.038262 restraints weight = 78222.599| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 32050 Z= 0.225 Angle : 0.660 10.271 43719 Z= 0.345 Chirality : 0.045 0.481 5069 Planarity : 0.005 0.046 5557 Dihedral : 5.101 23.267 4231 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.03 % Allowed : 1.63 % Favored : 98.34 % 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 (0.13), residues: 3896 helix: 0.92 (0.19), residues: 703 sheet: -0.19 (0.15), residues: 1079 loop : 0.07 (0.14), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 319 TYR 0.025 0.002 TYR B 453 PHE 0.029 0.002 PHE A 782 TRP 0.010 0.002 TRP B 104 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.22 (31953) covalent geometry : angle 0.64623 / 0.34 (43480) SS BOND : bond 0.00378 / 0.24 ( 52) SS BOND : angle 1.02784 / 0.72 ( 104) hydrogen bonds : bond 0.04515 / 3.01 ( 1272) hydrogen bonds : angle 6.79255 / 4.73 ( 3510) link_BETA1-4 : bond 0.00361 / 0.20 ( 11) link_BETA1-4 : angle 1.48515 / 1.04 ( 33) link_NAG-ASN : bond 0.00795 / 0.44 ( 34) link_NAG-ASN : angle 2.62497 / 1.93 ( 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 193 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 1.217 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: A 104 TRP cc_start: 0.9058 (m-90) cc_final: 0.8830 (m-90) REVERT: A 731 MET cc_start: 0.8761 (tpp) cc_final: 0.8538 (mmm) REVERT: A 855 PHE cc_start: 0.8199 (p90) cc_final: 0.7425 (t80) REVERT: A 900 MET cc_start: 0.8807 (tpp) cc_final: 0.8339 (tpp) REVERT: A 927 PHE cc_start: 0.9365 (t80) cc_final: 0.9126 (t80) REVERT: A 929 SER cc_start: 0.9507 (t) cc_final: 0.9150 (p) REVERT: A 933 LYS cc_start: 0.9728 (mttt) cc_final: 0.9511 (ptpt) REVERT: A 1038 LYS cc_start: 0.9029 (mmpt) cc_final: 0.8783 (mmmt) REVERT: A 1063 LEU cc_start: 0.9634 (mt) cc_final: 0.9420 (mt) REVERT: A 1118 ASP cc_start: 0.9070 (t70) cc_final: 0.8705 (p0) REVERT: B 170 TYR cc_start: 0.9543 (t80) cc_final: 0.9104 (t80) REVERT: B 201 PHE cc_start: 0.9462 (m-10) cc_final: 0.9192 (m-10) REVERT: B 710 ASN cc_start: 0.9027 (m-40) cc_final: 0.8715 (m110) REVERT: B 718 PHE cc_start: 0.9682 (p90) cc_final: 0.9017 (p90) REVERT: B 751 ASN cc_start: 0.9346 (m110) cc_final: 0.9079 (m110) REVERT: B 869 MET cc_start: 0.9488 (mtp) cc_final: 0.9246 (mtp) REVERT: B 927 PHE cc_start: 0.9464 (t80) cc_final: 0.8949 (t80) REVERT: B 1004 LEU cc_start: 0.9706 (tp) cc_final: 0.9504 (tp) REVERT: C 118 LEU cc_start: 0.9677 (tp) cc_final: 0.9320 (mp) REVERT: C 153 MET cc_start: 0.6097 (pmm) cc_final: 0.4656 (ttt) REVERT: C 177 MET cc_start: 0.8924 (mmt) cc_final: 0.8596 (mmm) REVERT: C 201 PHE cc_start: 0.8784 (m-80) cc_final: 0.8419 (m-80) REVERT: C 365 TYR cc_start: 0.6845 (t80) cc_final: 0.6109 (t80) REVERT: C 718 PHE cc_start: 0.9613 (p90) cc_final: 0.8959 (p90) REVERT: C 740 MET cc_start: 0.9140 (ttm) cc_final: 0.8839 (ttm) REVERT: C 782 PHE cc_start: 0.9701 (m-80) cc_final: 0.9346 (m-80) REVERT: C 927 PHE cc_start: 0.9341 (t80) cc_final: 0.8844 (t80) REVERT: C 1038 LYS cc_start: 0.8932 (mmpt) cc_final: 0.8635 (mmmt) REVERT: C 1101 HIS cc_start: 0.9156 (m90) cc_final: 0.8869 (m90) REVERT: C 1108 ASN cc_start: 0.8753 (m-40) cc_final: 0.8520 (m-40) REVERT: L 172 ASN cc_start: 0.9668 (m-40) cc_final: 0.9168 (t0) REVERT: H 39 MET cc_start: 0.6439 (tmm) cc_final: 0.5956 (tmm) REVERT: H 115 MET cc_start: 0.6868 (tpt) cc_final: 0.6048 (tpt) REVERT: M 4 MET cc_start: 0.9019 (tpt) cc_final: 0.8725 (ttt) REVERT: M 172 ASN cc_start: 0.9218 (m-40) cc_final: 0.8999 (m-40) REVERT: I 39 MET cc_start: 0.9465 (mmp) cc_final: 0.8930 (tpt) REVERT: I 115 MET cc_start: 0.7199 (tpt) cc_final: 0.6890 (tpt) outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 0.1987 time to fit residues: 61.9528 Evaluate side-chains 141 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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: 6.9990 chunk 293 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 284 optimal weight: 0.4980 chunk 57 optimal weight: 9.9990 chunk 350 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 388 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 257 optimal weight: 0.0060 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B1119 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.046496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.038101 restraints weight = 399529.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.039072 restraints weight = 197961.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.039692 restraints weight = 123499.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.040060 restraints weight = 90570.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.040292 restraints weight = 74636.194| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32050 Z= 0.127 Angle : 0.585 11.764 43719 Z= 0.303 Chirality : 0.045 0.431 5069 Planarity : 0.004 0.045 5557 Dihedral : 4.842 21.907 4231 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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 (0.13), residues: 3896 helix: 1.15 (0.20), residues: 702 sheet: -0.17 (0.15), residues: 1069 loop : 0.08 (0.14), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 466 TYR 0.053 0.002 TYR B 91 PHE 0.017 0.001 PHE L 159 TRP 0.013 0.001 TRP M 41 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (31953) covalent geometry : angle 0.57018 / 0.30 (43480) SS BOND : bond 0.00240 / 0.16 ( 52) SS BOND : angle 0.95569 / 0.66 ( 104) hydrogen bonds : bond 0.03943 / 2.64 ( 1272) hydrogen bonds : angle 6.40306 / 4.46 ( 3510) link_BETA1-4 : bond 0.00403 / 0.22 ( 11) link_BETA1-4 : angle 1.14100 / 0.79 ( 33) link_NAG-ASN : bond 0.00555 / 0.31 ( 34) link_NAG-ASN : angle 2.64051 / 1.88 ( 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 203 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.095 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: 0.8861 (m-90) cc_final: 0.8644 (m-90) REVERT: A 855 PHE cc_start: 0.8157 (p90) cc_final: 0.7454 (t80) REVERT: A 900 MET cc_start: 0.8684 (tpp) cc_final: 0.8248 (tpp) REVERT: A 927 PHE cc_start: 0.9402 (t80) cc_final: 0.9140 (t80) REVERT: A 929 SER cc_start: 0.9463 (t) cc_final: 0.9126 (p) REVERT: A 933 LYS cc_start: 0.9716 (mttt) cc_final: 0.9434 (ptpp) REVERT: A 1038 LYS cc_start: 0.9049 (mmpt) cc_final: 0.8789 (mmmt) REVERT: A 1063 LEU cc_start: 0.9601 (mt) cc_final: 0.9356 (mt) REVERT: A 1118 ASP cc_start: 0.9035 (t70) cc_final: 0.8650 (p0) REVERT: B 170 TYR cc_start: 0.9497 (t80) cc_final: 0.9085 (t80) REVERT: B 201 PHE cc_start: 0.9530 (m-10) cc_final: 0.9235 (m-10) REVERT: B 710 ASN cc_start: 0.9066 (m-40) cc_final: 0.8722 (m110) REVERT: B 718 PHE cc_start: 0.9641 (p90) cc_final: 0.8934 (p90) REVERT: B 751 ASN cc_start: 0.9339 (m110) cc_final: 0.9058 (m-40) REVERT: B 869 MET cc_start: 0.9499 (mtp) cc_final: 0.9230 (mtp) REVERT: B 927 PHE cc_start: 0.9441 (t80) cc_final: 0.8722 (t80) REVERT: B 1004 LEU cc_start: 0.9658 (tp) cc_final: 0.9447 (tp) REVERT: B 1010 GLN cc_start: 0.9552 (mt0) cc_final: 0.9347 (mm-40) REVERT: C 118 LEU cc_start: 0.9673 (tp) cc_final: 0.9282 (mp) REVERT: C 153 MET cc_start: 0.6107 (pmm) cc_final: 0.4688 (ttt) REVERT: C 201 PHE cc_start: 0.8808 (m-80) cc_final: 0.8474 (m-80) REVERT: C 365 TYR cc_start: 0.6855 (t80) cc_final: 0.6155 (t80) REVERT: C 718 PHE cc_start: 0.9537 (p90) cc_final: 0.8882 (p90) REVERT: C 740 MET cc_start: 0.9228 (ttm) cc_final: 0.8986 (ttm) REVERT: C 782 PHE cc_start: 0.9690 (m-80) cc_final: 0.9203 (m-80) REVERT: C 927 PHE cc_start: 0.9289 (t80) cc_final: 0.8830 (t80) REVERT: C 1038 LYS cc_start: 0.8941 (mmpt) cc_final: 0.8573 (mmmt) REVERT: C 1101 HIS cc_start: 0.9191 (m90) cc_final: 0.8902 (m90) REVERT: C 1108 ASN cc_start: 0.8591 (m-40) cc_final: 0.8220 (m-40) REVERT: L 172 ASN cc_start: 0.9664 (m-40) cc_final: 0.9146 (t0) REVERT: H 39 MET cc_start: 0.6285 (tmm) cc_final: 0.5755 (tmm) REVERT: H 115 MET cc_start: 0.6948 (tpt) cc_final: 0.6211 (tpt) REVERT: M 4 MET cc_start: 0.8852 (tpt) cc_final: 0.8054 (ttm) REVERT: M 172 ASN cc_start: 0.9155 (m-40) cc_final: 0.8923 (m-40) REVERT: I 39 MET cc_start: 0.9485 (mmp) cc_final: 0.8942 (tpt) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2038 time to fit residues: 67.1578 Evaluate side-chains 153 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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: 30.0000 chunk 192 optimal weight: 0.7980 chunk 338 optimal weight: 8.9990 chunk 385 optimal weight: 30.0000 chunk 314 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 250 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN B 919 ASN ** 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** ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 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 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 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.042684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.034247 restraints weight = 419326.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.035157 restraints weight = 210157.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.035729 restraints weight = 132328.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.036073 restraints weight = 98613.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.036291 restraints weight = 81977.883| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 32050 Z= 0.276 Angle : 0.721 10.948 43719 Z= 0.378 Chirality : 0.045 0.336 5069 Planarity : 0.005 0.047 5557 Dihedral : 5.145 23.669 4231 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.38 % Rotamer: Outliers : 0.06 % Allowed : 1.28 % Favored : 98.66 % 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: 0.62 (0.19), residues: 702 sheet: -0.38 (0.15), residues: 1085 loop : -0.07 (0.14), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 231 TYR 0.035 0.002 TYR B 37 PHE 0.018 0.002 PHE C1103 TRP 0.015 0.002 TRP B 64 HIS 0.008 0.002 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.28 (31953) covalent geometry : angle 0.70741 / 0.38 (43480) SS BOND : bond 0.00504 / 0.34 ( 52) SS BOND : angle 1.21903 / 0.84 ( 104) hydrogen bonds : bond 0.04670 / 3.08 ( 1272) hydrogen bonds : angle 6.92163 / 4.81 ( 3510) link_BETA1-4 : bond 0.00293 / 0.15 ( 11) link_BETA1-4 : angle 1.71934 / 1.22 ( 33) link_NAG-ASN : bond 0.00617 / 0.41 ( 34) link_NAG-ASN : angle 2.69182 / 1.95 ( 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 178 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 1.282 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: 0.9094 (m-90) cc_final: 0.8812 (m-90) REVERT: A 718 PHE cc_start: 0.9405 (p90) cc_final: 0.9062 (p90) REVERT: A 731 MET cc_start: 0.9124 (tpp) cc_final: 0.8723 (tpp) REVERT: A 855 PHE cc_start: 0.8233 (p90) cc_final: 0.7357 (t80) REVERT: A 900 MET cc_start: 0.8857 (tpp) cc_final: 0.8365 (tpp) REVERT: A 927 PHE cc_start: 0.9449 (t80) cc_final: 0.9195 (t80) REVERT: A 933 LYS cc_start: 0.9736 (mttt) cc_final: 0.9436 (ptpp) REVERT: A 1038 LYS cc_start: 0.9031 (mmpt) cc_final: 0.8811 (mmmt) REVERT: A 1063 LEU cc_start: 0.9641 (mt) cc_final: 0.9432 (mt) REVERT: A 1118 ASP cc_start: 0.9160 (t70) cc_final: 0.8883 (p0) REVERT: B 201 PHE cc_start: 0.9537 (m-10) cc_final: 0.9278 (m-10) REVERT: B 710 ASN cc_start: 0.9031 (m-40) cc_final: 0.8701 (m110) REVERT: B 721 SER cc_start: 0.9385 (t) cc_final: 0.9146 (p) REVERT: B 751 ASN cc_start: 0.9413 (m110) cc_final: 0.9166 (m110) REVERT: B 927 PHE cc_start: 0.9492 (t80) cc_final: 0.9017 (t80) REVERT: B 1050 MET cc_start: 0.8888 (pmm) cc_final: 0.8670 (pmm) REVERT: C 118 LEU cc_start: 0.9677 (tp) cc_final: 0.9336 (mm) REVERT: C 365 TYR cc_start: 0.6750 (t80) cc_final: 0.5963 (t80) REVERT: C 718 PHE cc_start: 0.9703 (p90) cc_final: 0.9066 (p90) REVERT: C 740 MET cc_start: 0.9206 (ttm) cc_final: 0.8982 (ttm) REVERT: C 782 PHE cc_start: 0.9700 (m-80) cc_final: 0.9415 (m-80) REVERT: C 927 PHE cc_start: 0.9322 (t80) cc_final: 0.8815 (t80) REVERT: C 1038 LYS cc_start: 0.8909 (mmpt) cc_final: 0.8580 (mmmt) REVERT: C 1101 HIS cc_start: 0.9244 (m90) cc_final: 0.8999 (m90) REVERT: L 172 ASN cc_start: 0.9722 (m-40) cc_final: 0.9248 (t0) REVERT: H 39 MET cc_start: 0.6472 (tmm) cc_final: 0.6040 (tmm) REVERT: H 115 MET cc_start: 0.7567 (tpt) cc_final: 0.6802 (tpt) REVERT: M 172 ASN cc_start: 0.9270 (m-40) cc_final: 0.9067 (m-40) REVERT: I 39 MET cc_start: 0.9515 (mmp) cc_final: 0.8974 (tpt) outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.2008 time to fit residues: 58.7811 Evaluate side-chains 131 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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: 0.8980 chunk 321 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 159 optimal weight: 0.0970 chunk 22 optimal weight: 0.8980 chunk 224 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 266 optimal weight: 20.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.045497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.037136 restraints weight = 405822.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.038064 restraints weight = 198793.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.038676 restraints weight = 124428.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.039036 restraints weight = 91052.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.039257 restraints weight = 75196.462| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32050 Z= 0.128 Angle : 0.597 9.224 43719 Z= 0.308 Chirality : 0.047 0.523 5069 Planarity : 0.004 0.051 5557 Dihedral : 4.912 23.322 4231 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: 0.04 (0.14), residues: 3896 helix: 1.06 (0.20), residues: 698 sheet: -0.31 (0.15), residues: 1081 loop : -0.02 (0.14), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1019 TYR 0.038 0.002 TYR B 91 PHE 0.017 0.001 PHE B1109 TRP 0.013 0.001 TRP B 886 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (31953) covalent geometry : angle 0.58437 / 0.31 (43480) SS BOND : bond 0.00244 / 0.16 ( 52) SS BOND : angle 1.02393 / 0.71 ( 104) hydrogen bonds : bond 0.03861 / 2.56 ( 1272) hydrogen bonds : angle 6.46678 / 4.51 ( 3510) link_BETA1-4 : bond 0.00333 / 0.18 ( 11) link_BETA1-4 : angle 1.09067 / 0.75 ( 33) link_NAG-ASN : bond 0.00568 / 0.32 ( 34) link_NAG-ASN : angle 2.35907 / 1.77 ( 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 186 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 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: A 104 TRP cc_start: 0.8876 (m-90) cc_final: 0.8648 (m-90) REVERT: A 731 MET cc_start: 0.9165 (tpp) cc_final: 0.8528 (tpp) REVERT: A 855 PHE cc_start: 0.8061 (p90) cc_final: 0.7359 (t80) REVERT: A 900 MET cc_start: 0.8664 (tpp) cc_final: 0.8149 (tpp) REVERT: A 927 PHE cc_start: 0.9397 (t80) cc_final: 0.9132 (t80) REVERT: A 1038 LYS cc_start: 0.9024 (mmpt) cc_final: 0.8796 (mmmt) REVERT: A 1063 LEU cc_start: 0.9619 (mt) cc_final: 0.9360 (mt) REVERT: B 170 TYR cc_start: 0.9531 (t80) cc_final: 0.9133 (t80) REVERT: B 194 PHE cc_start: 0.8283 (m-10) cc_final: 0.7480 (m-10) REVERT: B 201 PHE cc_start: 0.9496 (m-10) cc_final: 0.9229 (m-10) REVERT: B 710 ASN cc_start: 0.9107 (m-40) cc_final: 0.8777 (m110) REVERT: B 718 PHE cc_start: 0.9620 (p90) cc_final: 0.8872 (p90) REVERT: B 751 ASN cc_start: 0.9353 (m110) cc_final: 0.9096 (m110) REVERT: B 869 MET cc_start: 0.9568 (mtp) cc_final: 0.9327 (mtp) REVERT: B 927 PHE cc_start: 0.9438 (t80) cc_final: 0.8776 (t80) REVERT: B 1017 GLU cc_start: 0.9249 (tm-30) cc_final: 0.9042 (tm-30) REVERT: B 1050 MET cc_start: 0.8772 (pmm) cc_final: 0.8565 (pmm) REVERT: C 118 LEU cc_start: 0.9674 (tp) cc_final: 0.9283 (mp) REVERT: C 266 TYR cc_start: 0.8014 (t80) cc_final: 0.7751 (t80) REVERT: C 365 TYR cc_start: 0.6804 (t80) cc_final: 0.6105 (t80) REVERT: C 718 PHE cc_start: 0.9645 (p90) cc_final: 0.8982 (p90) REVERT: C 740 MET cc_start: 0.9208 (ttm) cc_final: 0.8926 (ttm) REVERT: C 782 PHE cc_start: 0.9702 (m-80) cc_final: 0.9209 (m-80) REVERT: C 927 PHE cc_start: 0.9316 (t80) cc_final: 0.8810 (t80) REVERT: C 1038 LYS cc_start: 0.8934 (mmpt) cc_final: 0.8608 (mmmt) REVERT: C 1101 HIS cc_start: 0.9220 (m90) cc_final: 0.8966 (m90) REVERT: L 172 ASN cc_start: 0.9691 (m-40) cc_final: 0.9203 (t0) REVERT: H 39 MET cc_start: 0.6432 (tmm) cc_final: 0.5906 (tmm) REVERT: H 115 MET cc_start: 0.6944 (tpt) cc_final: 0.6376 (tpt) REVERT: M 4 MET cc_start: 0.8916 (mmm) cc_final: 0.8204 (mtt) REVERT: M 172 ASN cc_start: 0.9173 (m-40) cc_final: 0.8945 (m-40) REVERT: I 39 MET cc_start: 0.9471 (mmp) cc_final: 0.8933 (tpt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1978 time to fit residues: 59.8906 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 : 0.863 ------------------------------------------------------------------------------- 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: 5.9990 chunk 182 optimal weight: 0.0270 chunk 303 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 322 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 304 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 212 optimal weight: 9.9990 chunk 264 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.045090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.036714 restraints weight = 408508.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.037675 restraints weight = 201809.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.038270 restraints weight = 125724.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.038625 restraints weight = 93122.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.038854 restraints weight = 76819.842| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32050 Z= 0.134 Angle : 0.575 9.141 43719 Z= 0.300 Chirality : 0.045 0.345 5069 Planarity : 0.004 0.052 5557 Dihedral : 4.781 23.289 4231 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % 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: 0.07 (0.14), residues: 3896 helix: 1.09 (0.20), residues: 698 sheet: -0.29 (0.15), residues: 1087 loop : -0.00 (0.14), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1019 TYR 0.038 0.002 TYR B 37 PHE 0.027 0.001 PHE B 194 TRP 0.011 0.001 TRP B 104 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (31953) covalent geometry : angle 0.56341 / 0.30 (43480) SS BOND : bond 0.00239 / 0.15 ( 52) SS BOND : angle 0.91304 / 0.64 ( 104) hydrogen bonds : bond 0.03775 / 2.51 ( 1272) hydrogen bonds : angle 6.33841 / 4.41 ( 3510) link_BETA1-4 : bond 0.00426 / 0.25 ( 11) link_BETA1-4 : angle 1.24890 / 0.88 ( 33) link_NAG-ASN : bond 0.00471 / 0.26 ( 34) link_NAG-ASN : angle 2.28009 / 1.67 ( 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 175 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.328 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 731 MET cc_start: 0.8979 (tpp) cc_final: 0.8537 (tpp) REVERT: A 855 PHE cc_start: 0.8046 (p90) cc_final: 0.7505 (t80) REVERT: A 878 LEU cc_start: 0.9593 (mt) cc_final: 0.9162 (tt) REVERT: A 927 PHE cc_start: 0.9391 (t80) cc_final: 0.9139 (t80) REVERT: A 1038 LYS cc_start: 0.9035 (mmpt) cc_final: 0.8787 (mmmt) REVERT: A 1063 LEU cc_start: 0.9621 (mt) cc_final: 0.9369 (mt) REVERT: B 170 TYR cc_start: 0.9542 (t80) cc_final: 0.9124 (t80) REVERT: B 201 PHE cc_start: 0.9474 (m-10) cc_final: 0.9201 (m-10) REVERT: B 710 ASN cc_start: 0.9131 (m-40) cc_final: 0.8806 (m110) REVERT: B 751 ASN cc_start: 0.9358 (m110) cc_final: 0.9108 (m110) REVERT: B 773 GLU cc_start: 0.9569 (mp0) cc_final: 0.9367 (pm20) REVERT: B 869 MET cc_start: 0.9572 (mtp) cc_final: 0.9337 (mtp) REVERT: B 927 PHE cc_start: 0.9431 (t80) cc_final: 0.8778 (t80) REVERT: B 1010 GLN cc_start: 0.9436 (mp10) cc_final: 0.9202 (mp10) REVERT: B 1050 MET cc_start: 0.8764 (pmm) cc_final: 0.8552 (pmm) REVERT: C 118 LEU cc_start: 0.9621 (tp) cc_final: 0.9272 (mp) REVERT: C 365 TYR cc_start: 0.6821 (t80) cc_final: 0.6091 (t80) REVERT: C 718 PHE cc_start: 0.9645 (p90) cc_final: 0.8938 (p90) REVERT: C 740 MET cc_start: 0.9241 (ttm) cc_final: 0.8967 (ttm) REVERT: C 782 PHE cc_start: 0.9690 (m-80) cc_final: 0.9218 (m-80) REVERT: C 925 ASN cc_start: 0.9318 (m110) cc_final: 0.9039 (p0) REVERT: C 927 PHE cc_start: 0.9304 (t80) cc_final: 0.8819 (t80) REVERT: C 1038 LYS cc_start: 0.8927 (mmpt) cc_final: 0.8569 (mmmt) REVERT: C 1101 HIS cc_start: 0.9231 (m90) cc_final: 0.8976 (m90) REVERT: L 172 ASN cc_start: 0.9693 (m-40) cc_final: 0.9206 (t0) REVERT: H 39 MET cc_start: 0.6279 (tmm) cc_final: 0.5701 (tmm) REVERT: H 115 MET cc_start: 0.6777 (tpt) cc_final: 0.6135 (tpt) REVERT: M 4 MET cc_start: 0.8834 (mmm) cc_final: 0.8131 (mtt) REVERT: I 39 MET cc_start: 0.9496 (mmp) cc_final: 0.8942 (tpt) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1927 time to fit residues: 55.4280 Evaluate side-chains 135 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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: 5.9990 chunk 269 optimal weight: 0.5980 chunk 3 optimal weight: 9.9990 chunk 301 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 295 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 306 optimal weight: 20.0000 chunk 216 optimal weight: 1.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.043682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.035274 restraints weight = 413110.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.036205 restraints weight = 204276.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.036792 restraints weight = 127832.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.037145 restraints weight = 94457.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.037365 restraints weight = 78314.943| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5765 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= 0.177 Angle : 0.602 8.933 43719 Z= 0.315 Chirality : 0.044 0.325 5069 Planarity : 0.004 0.055 5557 Dihedral : 4.854 20.895 4231 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.75 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.01 (0.14), residues: 3896 helix: 1.02 (0.20), residues: 699 sheet: -0.33 (0.15), residues: 1088 loop : -0.06 (0.14), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1091 TYR 0.031 0.002 TYR M 42 PHE 0.018 0.002 PHE C1103 TRP 0.019 0.002 TRP A 104 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (31953) covalent geometry : angle 0.59019 / 0.31 (43480) SS BOND : bond 0.00277 / 0.18 ( 52) SS BOND : angle 0.98972 / 0.72 ( 104) hydrogen bonds : bond 0.04027 / 2.66 ( 1272) hydrogen bonds : angle 6.44596 / 4.48 ( 3510) link_BETA1-4 : bond 0.00275 / 0.14 ( 11) link_BETA1-4 : angle 1.36506 / 0.97 ( 33) link_NAG-ASN : bond 0.00477 / 0.28 ( 34) link_NAG-ASN : angle 2.30986 / 1.69 ( 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 164 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.310 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: 0.8998 (m-90) cc_final: 0.8788 (m-90) REVERT: A 718 PHE cc_start: 0.9359 (p90) cc_final: 0.9027 (p90) REVERT: A 731 MET cc_start: 0.8998 (tpp) cc_final: 0.8635 (tpp) REVERT: A 855 PHE cc_start: 0.8236 (p90) cc_final: 0.7488 (t80) REVERT: A 878 LEU cc_start: 0.9602 (mt) cc_final: 0.9171 (tt) REVERT: A 900 MET cc_start: 0.9387 (mmp) cc_final: 0.8976 (tpp) REVERT: A 927 PHE cc_start: 0.9456 (t80) cc_final: 0.9180 (t80) REVERT: A 1038 LYS cc_start: 0.9028 (mmpt) cc_final: 0.8824 (mmmt) REVERT: A 1063 LEU cc_start: 0.9653 (mt) cc_final: 0.9424 (mt) REVERT: B 194 PHE cc_start: 0.9043 (m-80) cc_final: 0.8631 (m-10) REVERT: B 201 PHE cc_start: 0.9625 (m-10) cc_final: 0.9269 (m-10) REVERT: B 710 ASN cc_start: 0.9149 (m-40) cc_final: 0.8830 (m-40) REVERT: B 751 ASN cc_start: 0.9405 (m110) cc_final: 0.9152 (m110) REVERT: B 773 GLU cc_start: 0.9589 (mp0) cc_final: 0.9365 (pm20) REVERT: B 775 ASP cc_start: 0.9352 (m-30) cc_final: 0.9110 (m-30) REVERT: B 869 MET cc_start: 0.9572 (mtp) cc_final: 0.9320 (mtp) REVERT: B 927 PHE cc_start: 0.9495 (t80) cc_final: 0.8864 (t80) REVERT: B 1010 GLN cc_start: 0.9424 (mp10) cc_final: 0.9207 (mp10) REVERT: C 118 LEU cc_start: 0.9657 (tp) cc_final: 0.9311 (mt) REVERT: C 365 TYR cc_start: 0.6732 (t80) cc_final: 0.5933 (t80) REVERT: C 718 PHE cc_start: 0.9715 (p90) cc_final: 0.9139 (p90) REVERT: C 740 MET cc_start: 0.9264 (ttm) cc_final: 0.8994 (ttm) REVERT: C 782 PHE cc_start: 0.9721 (m-80) cc_final: 0.9225 (m-80) REVERT: C 865 LEU cc_start: 0.9323 (tp) cc_final: 0.8738 (tt) REVERT: C 925 ASN cc_start: 0.9346 (m110) cc_final: 0.9061 (p0) REVERT: C 927 PHE cc_start: 0.9407 (t80) cc_final: 0.8876 (t80) REVERT: C 1038 LYS cc_start: 0.8976 (mmpt) cc_final: 0.8636 (mmmt) REVERT: C 1101 HIS cc_start: 0.9228 (m90) cc_final: 0.9003 (m90) REVERT: L 172 ASN cc_start: 0.9719 (m-40) cc_final: 0.9246 (t0) REVERT: H 39 MET cc_start: 0.6322 (tmm) cc_final: 0.5744 (tmm) REVERT: H 115 MET cc_start: 0.6943 (tpt) cc_final: 0.6181 (tpt) REVERT: M 4 MET cc_start: 0.8951 (mmm) cc_final: 0.8321 (mtt) REVERT: I 39 MET cc_start: 0.9523 (mmp) cc_final: 0.8967 (tpt) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2086 time to fit residues: 55.7468 Evaluate side-chains 130 residues out of total 3437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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: 0.0870 chunk 81 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 299 optimal weight: 4.9990 chunk 276 optimal weight: 0.3980 chunk 352 optimal weight: 5.9990 chunk 348 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 196 optimal weight: 0.8980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.045362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.036972 restraints weight = 406179.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.037923 restraints weight = 199541.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.038520 restraints weight = 124304.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.038886 restraints weight = 91203.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.039111 restraints weight = 75326.365| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5740 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= 0.118 Angle : 0.568 9.030 43719 Z= 0.295 Chirality : 0.045 0.342 5069 Planarity : 0.004 0.056 5557 Dihedral : 4.694 20.340 4231 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 0.04 (0.14), residues: 3896 helix: 1.09 (0.20), residues: 697 sheet: -0.26 (0.15), residues: 1113 loop : -0.05 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.030 0.001 TYR A 789 PHE 0.022 0.001 PHE A 194 TRP 0.014 0.001 TRP B 104 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (31953) covalent geometry : angle 0.55761 / 0.29 (43480) SS BOND : bond 0.00198 / 0.13 ( 52) SS BOND : angle 0.88458 / 0.63 ( 104) hydrogen bonds : bond 0.03691 / 2.45 ( 1272) hydrogen bonds : angle 6.21015 / 4.33 ( 3510) link_BETA1-4 : bond 0.00419 / 0.22 ( 11) link_BETA1-4 : angle 1.12715 / 0.79 ( 33) link_NAG-ASN : bond 0.00505 / 0.28 ( 34) link_NAG-ASN : angle 2.13148 / 1.54 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5525.26 seconds wall clock time: 96 minutes 48.41 seconds (5808.41 seconds total)