Starting phenix.real_space_refine on Fri Feb 6 19:35:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4l_48897/02_2026/9n4l_48897.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4l_48897/02_2026/9n4l_48897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n4l_48897/02_2026/9n4l_48897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4l_48897/02_2026/9n4l_48897.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n4l_48897/02_2026/9n4l_48897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4l_48897/02_2026/9n4l_48897.map" } resolution = 4.24 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= -0.015 sd= 1.298 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 160 5.16 5 C 17378 2.51 5 N 4484 2.21 5 O 5161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27183 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Chain: "B" Number of atoms: 6677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 33, 'TRANS': 808} Chain: "C" Number of atoms: 6677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 33, 'TRANS': 808} Chain: "D" Number of atoms: 6577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 6577 Classifications: {'peptide': 828} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 795} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.32, per 1000 atoms: 0.23 Number of scatterers: 27183 At special positions: 0 Unit cell: (136.94, 151.7, 209.1, 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 160 16.00 O 5161 8.00 N 4484 7.00 C 17378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.05 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.04 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.05 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.05 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.05 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 5 " " BMA K 3 " - " MAN K 5 " BETA1-3 " NAG F 2 " - " BMA F 3 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A1001 " - " ASN A 67 " " NAG A1002 " - " ASN A 73 " " NAG A1003 " - " ASN A 412 " " NAG A1004 " - " ASN A 546 " " NAG A1005 " - " ASN A 751 " " NAG B1001 " - " ASN B 67 " " NAG B1002 " - " ASN B 73 " " NAG B1003 " - " ASN B 751 " " NAG C1001 " - " ASN C 275 " " NAG C1002 " - " ASN C 412 " " NAG C1003 " - " ASN C 751 " " NAG D1001 " - " ASN D 73 " " NAG D1002 " - " ASN D 275 " " NAG D1003 " - " ASN D 412 " " NAG D1004 " - " ASN D 546 " " NAG D1005 " - " ASN D 751 " " NAG E 1 " - " ASN A 275 " " NAG F 1 " - " ASN A 378 " " NAG G 1 " - " ASN B 275 " " NAG H 1 " - " ASN B 378 " " NAG I 1 " - " ASN B 412 " " NAG J 1 " - " ASN B 546 " " NAG K 1 " - " ASN C 378 " " NAG L 1 " - " ASN C 546 " " NAG M 1 " - " ASN D 378 " Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.3 seconds 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6262 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 34 sheets defined 42.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 51 through 68 removed outlier: 3.705A pdb=" N ARG A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 4.189A pdb=" N CYS A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 removed outlier: 3.563A pdb=" N VAL A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.758A pdb=" N ARG A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 185' Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.027A pdb=" N ARG A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.760A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 removed outlier: 3.650A pdb=" N ALA A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 245' Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.688A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 300 " --> pdb=" O TRP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.638A pdb=" N LEU A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.523A pdb=" N PHE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 474 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 553 through 557 removed outlier: 4.194A pdb=" N LEU A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.611A pdb=" N TYR A 566 " --> pdb=" O ASP A 562 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 569 " --> pdb=" O MET A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.575A pdb=" N GLY A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 660 removed outlier: 4.254A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 637 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.668A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.666A pdb=" N LYS A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.653A pdb=" N MET A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 738 through 747 removed outlier: 3.511A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 784 removed outlier: 4.302A pdb=" N ALA A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 794 through 799 removed outlier: 4.038A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP A 799 " --> pdb=" O LYS A 795 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 794 through 799' Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 821 through 851 removed outlier: 3.892A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 863 removed outlier: 3.651A pdb=" N GLU A 863 " --> pdb=" O SER A 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 68 removed outlier: 3.705A pdb=" N ARG B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 4.190A pdb=" N CYS B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 126 removed outlier: 3.563A pdb=" N VAL B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.758A pdb=" N ARG B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 185' Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 190 through 195 removed outlier: 4.027A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.759A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 245 removed outlier: 3.650A pdb=" N ALA B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 240 through 245' Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 300 removed outlier: 3.688A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 300 " --> pdb=" O TRP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.639A pdb=" N LEU B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 removed outlier: 3.524A pdb=" N PHE B 359 " --> pdb=" O PHE B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 432 removed outlier: 3.991A pdb=" N ARG B 431 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 473 Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.558A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.838A pdb=" N TRP B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 575 " --> pdb=" O CYS B 571 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 585 " --> pdb=" O ILE B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 618 removed outlier: 3.543A pdb=" N PHE B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 659 removed outlier: 4.344A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 645 " --> pdb=" O TRP B 641 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 648 " --> pdb=" O THR B 644 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 650 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 696 removed outlier: 4.070A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 711 removed outlier: 3.592A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 Processing helix chain 'B' and resid 739 through 748 removed outlier: 3.732A pdb=" N GLU B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 748 " --> pdb=" O PHE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 786 removed outlier: 3.562A pdb=" N LEU B 783 " --> pdb=" O THR B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 796 Processing helix chain 'B' and resid 816 through 821 Processing helix chain 'B' and resid 821 through 850 removed outlier: 3.866A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 870 removed outlier: 3.770A pdb=" N ALA B 860 " --> pdb=" O SER B 856 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS B 870 " --> pdb=" O ARG B 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 68 removed outlier: 3.704A pdb=" N ARG C 66 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 4.190A pdb=" N CYS C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 126 removed outlier: 3.564A pdb=" N VAL C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 167 Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.758A pdb=" N ARG C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C 185 " --> pdb=" O GLY C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 185' Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 195 removed outlier: 4.027A pdb=" N ARG C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.760A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 removed outlier: 3.650A pdb=" N ALA C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 240 through 245' Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 286 through 300 removed outlier: 3.688A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU C 299 " --> pdb=" O LYS C 295 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG C 300 " --> pdb=" O TRP C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.639A pdb=" N LEU C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 364 removed outlier: 3.522A pdb=" N PHE C 359 " --> pdb=" O PHE C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 473 Processing helix chain 'C' and resid 502 through 507 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.558A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 4.195A pdb=" N LEU C 556 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 585 removed outlier: 3.611A pdb=" N TYR C 566 " --> pdb=" O ASP C 562 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU C 569 " --> pdb=" O MET C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.575A pdb=" N GLY C 615 " --> pdb=" O SER C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 662 removed outlier: 4.255A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY C 637 " --> pdb=" O THR C 633 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 696 removed outlier: 4.070A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 711 removed outlier: 3.593A pdb=" N LYS C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 Processing helix chain 'C' and resid 739 through 748 removed outlier: 3.732A pdb=" N GLU C 743 " --> pdb=" O SER C 739 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 748 " --> pdb=" O PHE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 786 removed outlier: 3.562A pdb=" N LEU C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 796 Processing helix chain 'C' and resid 816 through 821 Processing helix chain 'C' and resid 821 through 851 removed outlier: 3.892A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 869 removed outlier: 3.712A pdb=" N LEU C 869 " --> pdb=" O LEU C 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 68 removed outlier: 3.704A pdb=" N ARG D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG D 68 " --> pdb=" O ILE D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.189A pdb=" N CYS D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.564A pdb=" N VAL D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 167 Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.758A pdb=" N ARG D 184 " --> pdb=" O THR D 180 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 180 through 185' Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 190 through 195 removed outlier: 4.028A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.760A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 245 removed outlier: 3.649A pdb=" N ALA D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 240 through 245' Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 286 through 300 removed outlier: 3.689A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG D 300 " --> pdb=" O TRP D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.638A pdb=" N LEU D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 3.523A pdb=" N PHE D 359 " --> pdb=" O PHE D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.941A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 522 through 527 removed outlier: 4.022A pdb=" N VAL D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 527 " --> pdb=" O ARG D 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 522 through 527' Processing helix chain 'D' and resid 560 through 585 removed outlier: 3.838A pdb=" N TRP D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER D 585 " --> pdb=" O ILE D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 618 removed outlier: 3.544A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 662 removed outlier: 4.343A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 645 " --> pdb=" O TRP D 641 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE D 648 " --> pdb=" O THR D 644 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER D 650 " --> pdb=" O ILE D 646 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 677 removed outlier: 3.729A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 697 removed outlier: 3.515A pdb=" N LYS D 695 " --> pdb=" O MET D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.653A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 739 through 747 removed outlier: 3.667A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 782 Processing helix chain 'D' and resid 789 through 800 removed outlier: 3.579A pdb=" N GLU D 796 " --> pdb=" O HIS D 792 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS D 797 " --> pdb=" O MET D 793 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TRP D 798 " --> pdb=" O MET D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 821 Processing helix chain 'D' and resid 821 through 850 removed outlier: 3.865A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 855 through 870 removed outlier: 4.192A pdb=" N SER D 859 " --> pdb=" O ARG D 855 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N MET D 867 " --> pdb=" O GLU D 863 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS D 870 " --> pdb=" O ARG D 866 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 43 removed outlier: 3.963A pdb=" N GLY A 40 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 176 Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 227 removed outlier: 6.370A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 392 through 395 Processing sheet with id=AA5, first strand: chain 'A' and resid 434 through 437 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA7, first strand: chain 'A' and resid 534 through 536 removed outlier: 4.255A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 542 removed outlier: 3.771A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 682 removed outlier: 7.350A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 684 through 685 removed outlier: 6.108A pdb=" N ALA A 684 " --> pdb=" O VAL A 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 39 through 43 removed outlier: 3.963A pdb=" N GLY B 40 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 175 through 176 Processing sheet with id=AB4, first strand: chain 'B' and resid 225 through 227 removed outlier: 6.370A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 392 through 395 Processing sheet with id=AB6, first strand: chain 'B' and resid 434 through 435 Processing sheet with id=AB7, first strand: chain 'B' and resid 444 through 445 Processing sheet with id=AB8, first strand: chain 'B' and resid 534 through 535 removed outlier: 3.571A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 735 through 738 Processing sheet with id=AC1, first strand: chain 'C' and resid 39 through 43 removed outlier: 3.962A pdb=" N GLY C 40 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 175 through 176 Processing sheet with id=AC3, first strand: chain 'C' and resid 225 through 227 removed outlier: 6.370A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 392 through 395 Processing sheet with id=AC5, first strand: chain 'C' and resid 434 through 435 Processing sheet with id=AC6, first strand: chain 'C' and resid 444 through 445 Processing sheet with id=AC7, first strand: chain 'C' and resid 534 through 535 removed outlier: 3.571A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 735 through 738 Processing sheet with id=AC9, first strand: chain 'D' and resid 39 through 43 removed outlier: 3.963A pdb=" N GLY D 40 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 175 through 176 Processing sheet with id=AD2, first strand: chain 'D' and resid 225 through 227 removed outlier: 6.370A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 392 through 395 Processing sheet with id=AD4, first strand: chain 'D' and resid 435 through 437 Processing sheet with id=AD5, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD6, first strand: chain 'D' and resid 737 through 738 removed outlier: 3.821A pdb=" N MET D 737 " --> pdb=" O SER D 539 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 684 through 685 removed outlier: 6.023A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 857 hydrogen bonds defined for protein. 2499 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: 4.61 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8433 1.34 - 1.46: 5854 1.46 - 1.58: 13216 1.58 - 1.70: 6 1.70 - 1.81: 272 Bond restraints: 27781 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.535 -0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C1 NAG D1005 " pdb=" O5 NAG D1005 " ideal model delta sigma weight residual 1.406 1.526 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C1 NAG A1005 " pdb=" O5 NAG A1005 " ideal model delta sigma weight residual 1.406 1.524 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" C1 NAG A1004 " pdb=" O5 NAG A1004 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C ASN C 557 " pdb=" N PRO C 558 " ideal model delta sigma weight residual 1.337 1.378 -0.042 9.80e-03 1.04e+04 1.80e+01 ... (remaining 27776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 37113 4.23 - 8.46: 448 8.46 - 12.69: 36 12.69 - 16.92: 3 16.92 - 21.15: 2 Bond angle restraints: 37602 Sorted by residual: angle pdb=" N VAL B 716 " pdb=" CA VAL B 716 " pdb=" C VAL B 716 " ideal model delta sigma weight residual 113.42 102.52 10.90 1.17e+00 7.31e-01 8.68e+01 angle pdb=" N VAL C 716 " pdb=" CA VAL C 716 " pdb=" C VAL C 716 " ideal model delta sigma weight residual 113.42 102.52 10.90 1.17e+00 7.31e-01 8.68e+01 angle pdb=" N VAL C 552 " pdb=" CA VAL C 552 " pdb=" C VAL C 552 " ideal model delta sigma weight residual 113.71 106.49 7.22 9.50e-01 1.11e+00 5.78e+01 angle pdb=" C LYS C 810 " pdb=" N GLU C 811 " pdb=" CA GLU C 811 " ideal model delta sigma weight residual 121.54 133.73 -12.19 1.91e+00 2.74e-01 4.08e+01 angle pdb=" CA LEU D 453 " pdb=" CB LEU D 453 " pdb=" CG LEU D 453 " ideal model delta sigma weight residual 116.30 137.45 -21.15 3.50e+00 8.16e-02 3.65e+01 ... (remaining 37597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.96: 16348 24.96 - 49.93: 576 49.93 - 74.89: 123 74.89 - 99.86: 77 99.86 - 124.82: 58 Dihedral angle restraints: 17182 sinusoidal: 7451 harmonic: 9731 Sorted by residual: dihedral pdb=" CA GLU B 441 " pdb=" C GLU B 441 " pdb=" N PRO B 442 " pdb=" CA PRO B 442 " ideal model delta harmonic sigma weight residual 180.00 72.28 107.72 0 5.00e+00 4.00e-02 4.64e+02 dihedral pdb=" CA GLU C 441 " pdb=" C GLU C 441 " pdb=" N PRO C 442 " pdb=" CA PRO C 442 " ideal model delta harmonic sigma weight residual 180.00 72.31 107.69 0 5.00e+00 4.00e-02 4.64e+02 dihedral pdb=" CA LEU A 85 " pdb=" C LEU A 85 " pdb=" N TYR A 86 " pdb=" CA TYR A 86 " ideal model delta harmonic sigma weight residual -180.00 -132.04 -47.96 0 5.00e+00 4.00e-02 9.20e+01 ... (remaining 17179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.244: 4282 0.244 - 0.487: 26 0.487 - 0.731: 1 0.731 - 0.975: 0 0.975 - 1.218: 2 Chirality restraints: 4311 Sorted by residual: chirality pdb=" C1 NAG A1002 " pdb=" ND2 ASN A 73 " pdb=" C2 NAG A1002 " pdb=" O5 NAG A1002 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.71e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 378 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.39 -1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" C1 NAG C1003 " pdb=" ND2 ASN C 751 " pdb=" C2 NAG C1003 " pdb=" O5 NAG C1003 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.58e+00 ... (remaining 4308 not shown) Planarity restraints: 4740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 415 " 0.034 2.00e-02 2.50e+03 6.63e-02 4.39e+01 pdb=" C GLU C 415 " -0.115 2.00e-02 2.50e+03 pdb=" O GLU C 415 " 0.042 2.00e-02 2.50e+03 pdb=" N SER C 416 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 73 " 0.002 2.00e-02 2.50e+03 4.22e-02 2.22e+01 pdb=" CG ASN A 73 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 73 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN A 73 " -0.063 2.00e-02 2.50e+03 pdb=" C1 NAG A1002 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 378 " 0.037 2.00e-02 2.50e+03 3.99e-02 1.99e+01 pdb=" CG ASN B 378 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 378 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 378 " -0.063 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.047 2.00e-02 2.50e+03 ... (remaining 4737 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5142 2.77 - 3.30: 25019 3.30 - 3.83: 43889 3.83 - 4.37: 51570 4.37 - 4.90: 85940 Nonbonded interactions: 211560 Sorted by model distance: nonbonded pdb=" OG SER B 554 " pdb=" O ASN B 819 " model vdw 2.231 3.040 nonbonded pdb=" OG SER D 554 " pdb=" O ASN D 819 " model vdw 2.232 3.040 nonbonded pdb=" O ASN B 456 " pdb=" OH TYR B 478 " model vdw 2.293 3.040 nonbonded pdb=" O ASN C 456 " pdb=" OH TYR C 478 " model vdw 2.293 3.040 nonbonded pdb=" O SER B 100 " pdb=" OG SER B 344 " model vdw 2.317 3.040 ... (remaining 211555 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 33 through 415 or resid 430 through 1003)) selection = (chain 'B' and (resid 33 through 415 or resid 430 through 1003)) selection = (chain 'C' and (resid 33 through 415 or resid 430 through 1003)) selection = (chain 'D' and resid 33 through 1003) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'K' } 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: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.650 Find NCS groups from input model: 0.940 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: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 27832 Z= 0.305 Angle : 1.310 21.148 37747 Z= 0.730 Chirality : 0.064 1.218 4311 Planarity : 0.008 0.084 4715 Dihedral : 16.789 124.820 10896 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.71 % Favored : 86.90 % Rotamer: Outliers : 0.58 % Allowed : 5.21 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.47 % 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: -6.48 (0.09), residues: 3344 helix: -4.21 (0.06), residues: 1452 sheet: -5.20 (0.18), residues: 356 loop : -4.08 (0.12), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 58 TYR 0.025 0.003 TYR C 702 PHE 0.020 0.002 PHE C 228 TRP 0.030 0.003 TRP A 353 HIS 0.014 0.002 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00613 (27781) covalent geometry : angle 1.25148 (37602) SS BOND : bond 0.01153 ( 8) SS BOND : angle 1.22653 ( 16) hydrogen bonds : bond 0.29652 ( 857) hydrogen bonds : angle 9.95292 ( 2499) link_ALPHA1-3 : bond 0.01368 ( 3) link_ALPHA1-3 : angle 3.74876 ( 9) link_ALPHA1-6 : bond 0.01024 ( 3) link_ALPHA1-6 : angle 1.77547 ( 9) link_BETA1-3 : bond 0.00951 ( 1) link_BETA1-3 : angle 7.45470 ( 3) link_BETA1-4 : bond 0.01549 ( 11) link_BETA1-4 : angle 5.30478 ( 33) link_NAG-ASN : bond 0.01404 ( 25) link_NAG-ASN : angle 7.84793 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 801 time to evaluate : 1.078 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 114 SER cc_start: 0.8691 (m) cc_final: 0.8294 (t) REVERT: A 152 ASP cc_start: 0.8126 (t70) cc_final: 0.7730 (t0) REVERT: A 200 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8398 (mtpt) REVERT: A 223 GLU cc_start: 0.6186 (mt-10) cc_final: 0.5839 (mt-10) REVERT: A 249 THR cc_start: 0.8393 (p) cc_final: 0.8139 (t) REVERT: A 252 TYR cc_start: 0.7836 (m-80) cc_final: 0.7226 (m-80) REVERT: A 289 VAL cc_start: 0.8362 (t) cc_final: 0.7685 (t) REVERT: A 360 MET cc_start: 0.8080 (tpt) cc_final: 0.7832 (tpt) REVERT: A 647 ILE cc_start: 0.9407 (tp) cc_final: 0.9128 (tp) REVERT: B 71 LEU cc_start: 0.7279 (pp) cc_final: 0.6783 (mt) REVERT: B 200 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7531 (mttt) REVERT: B 254 TYR cc_start: 0.9008 (m-80) cc_final: 0.8568 (m-80) REVERT: B 388 ASP cc_start: 0.8239 (m-30) cc_final: 0.7464 (p0) REVERT: B 529 PHE cc_start: 0.8244 (m-80) cc_final: 0.8023 (m-10) REVERT: B 620 MET cc_start: 0.8448 (mmp) cc_final: 0.7779 (mmp) REVERT: B 834 SER cc_start: 0.7815 (m) cc_final: 0.7377 (t) REVERT: B 867 MET cc_start: 0.7246 (tmt) cc_final: 0.7043 (tmm) REVERT: C 195 TYR cc_start: 0.6807 (m-80) cc_final: 0.6129 (m-80) REVERT: C 365 GLU cc_start: 0.6490 (mt-10) cc_final: 0.6157 (mm-30) REVERT: C 584 PHE cc_start: 0.8231 (t80) cc_final: 0.8022 (t80) REVERT: C 620 MET cc_start: 0.8415 (mmt) cc_final: 0.7971 (mmt) REVERT: C 635 ILE cc_start: 0.7905 (mm) cc_final: 0.7682 (tp) REVERT: C 645 LEU cc_start: 0.8863 (tt) cc_final: 0.8558 (tp) REVERT: C 735 PHE cc_start: 0.7728 (t80) cc_final: 0.7197 (t80) REVERT: C 785 LEU cc_start: 0.8591 (mm) cc_final: 0.8332 (tp) REVERT: C 793 MET cc_start: 0.7695 (ttm) cc_final: 0.7456 (ttm) REVERT: C 861 MET cc_start: 0.7925 (mmp) cc_final: 0.6893 (tmm) REVERT: D 129 HIS cc_start: 0.8055 (t-90) cc_final: 0.7513 (t-90) REVERT: D 195 TYR cc_start: 0.6466 (m-80) cc_final: 0.6216 (m-10) REVERT: D 200 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7695 (mttt) REVERT: D 247 MET cc_start: 0.8357 (mtp) cc_final: 0.8146 (mtt) REVERT: D 319 ASP cc_start: 0.7364 (m-30) cc_final: 0.7003 (p0) REVERT: D 505 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.5914 (mm) outliers start: 17 outliers final: 4 residues processed: 817 average time/residue: 0.1896 time to fit residues: 238.5039 Evaluate side-chains 463 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 455 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 137 GLN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN A 819 ASN B 65 ASN B 784 GLN C 65 ASN C 136 HIS C 350 HIS C 367 HIS C 499 ASN C 721 ASN D 65 ASN D 136 HIS D 335 GLN D 508 HIS D 677 GLN D 802 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.157581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.149395 restraints weight = 47831.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.146615 restraints weight = 93151.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.144906 restraints weight = 91842.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144356 restraints weight = 97574.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.144163 restraints weight = 72949.408| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27832 Z= 0.178 Angle : 0.860 17.203 37747 Z= 0.423 Chirality : 0.049 0.502 4311 Planarity : 0.006 0.074 4715 Dihedral : 17.494 109.686 4510 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.05 % Favored : 87.65 % Rotamer: Outliers : 0.07 % Allowed : 4.21 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.31 % 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: -4.81 (0.12), residues: 3344 helix: -2.35 (0.11), residues: 1420 sheet: -4.72 (0.21), residues: 373 loop : -3.60 (0.13), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 349 TYR 0.037 0.002 TYR B 566 PHE 0.020 0.002 PHE D 708 TRP 0.028 0.002 TRP B 613 HIS 0.007 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00393 (27781) covalent geometry : angle 0.82271 (37602) SS BOND : bond 0.00389 ( 8) SS BOND : angle 1.41926 ( 16) hydrogen bonds : bond 0.05247 ( 857) hydrogen bonds : angle 5.79307 ( 2499) link_ALPHA1-3 : bond 0.01274 ( 3) link_ALPHA1-3 : angle 2.77792 ( 9) link_ALPHA1-6 : bond 0.00850 ( 3) link_ALPHA1-6 : angle 2.32932 ( 9) link_BETA1-3 : bond 0.01336 ( 1) link_BETA1-3 : angle 5.65212 ( 3) link_BETA1-4 : bond 0.00725 ( 11) link_BETA1-4 : angle 3.20239 ( 33) link_NAG-ASN : bond 0.01098 ( 25) link_NAG-ASN : angle 5.02200 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 581 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 SER cc_start: 0.8643 (m) cc_final: 0.8070 (t) REVERT: A 223 GLU cc_start: 0.6088 (mt-10) cc_final: 0.5605 (mt-10) REVERT: A 360 MET cc_start: 0.8281 (tpt) cc_final: 0.7960 (tpt) REVERT: A 389 LEU cc_start: 0.8534 (mm) cc_final: 0.8103 (mt) REVERT: B 43 GLU cc_start: 0.7603 (tp30) cc_final: 0.7340 (tm-30) REVERT: B 388 ASP cc_start: 0.8445 (m-30) cc_final: 0.7751 (p0) REVERT: B 389 LEU cc_start: 0.8168 (mm) cc_final: 0.7931 (mm) REVERT: B 529 PHE cc_start: 0.8240 (m-80) cc_final: 0.7977 (m-10) REVERT: B 834 SER cc_start: 0.7041 (m) cc_final: 0.6692 (t) REVERT: C 284 THR cc_start: 0.8108 (m) cc_final: 0.7849 (m) REVERT: C 389 LEU cc_start: 0.8538 (mm) cc_final: 0.8134 (mt) REVERT: C 861 MET cc_start: 0.6801 (mmp) cc_final: 0.6421 (tmm) outliers start: 2 outliers final: 0 residues processed: 583 average time/residue: 0.1735 time to fit residues: 163.3498 Evaluate side-chains 400 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 34 optimal weight: 3.9990 chunk 265 optimal weight: 0.8980 chunk 283 optimal weight: 0.0570 chunk 217 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 136 HIS A 604 ASN A 621 GLN A 819 ASN B 136 HIS B 186 GLN B 335 GLN B 499 ASN C 34 HIS C 98 GLN C 367 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS D 747 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.156185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.147419 restraints weight = 48034.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143256 restraints weight = 102365.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.141885 restraints weight = 95876.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.141128 restraints weight = 96019.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.141485 restraints weight = 72820.266| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27832 Z= 0.170 Angle : 0.794 12.737 37747 Z= 0.385 Chirality : 0.047 0.367 4311 Planarity : 0.005 0.069 4715 Dihedral : 15.769 112.530 4510 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.29 % Favored : 87.44 % Rotamer: Outliers : 0.10 % Allowed : 3.90 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.28 % 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: -3.95 (0.13), residues: 3344 helix: -1.31 (0.12), residues: 1444 sheet: -4.51 (0.22), residues: 339 loop : -3.50 (0.13), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 133 TYR 0.023 0.002 TYR B 86 PHE 0.023 0.002 PHE D 824 TRP 0.027 0.002 TRP B 613 HIS 0.008 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00391 (27781) covalent geometry : angle 0.76429 (37602) SS BOND : bond 0.00804 ( 8) SS BOND : angle 1.10181 ( 16) hydrogen bonds : bond 0.04399 ( 857) hydrogen bonds : angle 5.18132 ( 2499) link_ALPHA1-3 : bond 0.01292 ( 3) link_ALPHA1-3 : angle 2.79996 ( 9) link_ALPHA1-6 : bond 0.01236 ( 3) link_ALPHA1-6 : angle 2.26377 ( 9) link_BETA1-3 : bond 0.02055 ( 1) link_BETA1-3 : angle 6.03264 ( 3) link_BETA1-4 : bond 0.00754 ( 11) link_BETA1-4 : angle 3.16302 ( 33) link_NAG-ASN : bond 0.00734 ( 25) link_NAG-ASN : angle 4.12063 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 554 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.7404 (mp) cc_final: 0.7098 (mp) REVERT: A 114 SER cc_start: 0.8536 (m) cc_final: 0.8204 (t) REVERT: A 360 MET cc_start: 0.8339 (tpt) cc_final: 0.7970 (tpt) REVERT: B 43 GLU cc_start: 0.7762 (tp30) cc_final: 0.7508 (tm-30) REVERT: B 114 SER cc_start: 0.8661 (m) cc_final: 0.8433 (t) REVERT: B 223 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7067 (mt-10) REVERT: B 260 ASP cc_start: 0.7470 (m-30) cc_final: 0.7002 (m-30) REVERT: B 360 MET cc_start: 0.8672 (tpt) cc_final: 0.8190 (tpp) REVERT: B 388 ASP cc_start: 0.8422 (m-30) cc_final: 0.7788 (p0) REVERT: B 626 LEU cc_start: 0.8215 (mm) cc_final: 0.7993 (mm) REVERT: B 737 MET cc_start: 0.6401 (ttp) cc_final: 0.6007 (ttt) REVERT: B 834 SER cc_start: 0.7258 (m) cc_final: 0.6923 (t) REVERT: B 861 MET cc_start: 0.7892 (pmm) cc_final: 0.7519 (pmm) REVERT: C 265 ASP cc_start: 0.7876 (t0) cc_final: 0.7661 (t0) REVERT: C 284 THR cc_start: 0.8233 (m) cc_final: 0.7990 (m) REVERT: C 389 LEU cc_start: 0.8735 (mm) cc_final: 0.8212 (mt) REVERT: C 861 MET cc_start: 0.6684 (mmp) cc_final: 0.6413 (tmm) outliers start: 3 outliers final: 1 residues processed: 557 average time/residue: 0.1758 time to fit residues: 158.6226 Evaluate side-chains 405 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 404 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 64 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 329 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS A 604 ASN A 677 GLN A 819 ASN B 111 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS B 350 HIS ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS C 610 ASN D 491 GLN D 591 ASN D 721 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.153978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.145267 restraints weight = 47632.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141275 restraints weight = 106183.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.139918 restraints weight = 87399.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138751 restraints weight = 94158.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.139212 restraints weight = 66916.564| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27832 Z= 0.200 Angle : 0.804 12.808 37747 Z= 0.389 Chirality : 0.049 0.668 4311 Planarity : 0.005 0.068 4715 Dihedral : 14.914 111.653 4510 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.01 % Favored : 86.72 % Rotamer: Outliers : 0.10 % Allowed : 3.49 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.28 % 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: -3.54 (0.13), residues: 3344 helix: -0.82 (0.13), residues: 1452 sheet: -4.33 (0.23), residues: 364 loop : -3.42 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 133 TYR 0.025 0.002 TYR C 764 PHE 0.021 0.002 PHE A 459 TRP 0.033 0.002 TRP B 613 HIS 0.011 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00470 (27781) covalent geometry : angle 0.77672 (37602) SS BOND : bond 0.00264 ( 8) SS BOND : angle 1.18200 ( 16) hydrogen bonds : bond 0.03991 ( 857) hydrogen bonds : angle 4.96664 ( 2499) link_ALPHA1-3 : bond 0.01686 ( 3) link_ALPHA1-3 : angle 2.67655 ( 9) link_ALPHA1-6 : bond 0.01237 ( 3) link_ALPHA1-6 : angle 2.55701 ( 9) link_BETA1-3 : bond 0.01525 ( 1) link_BETA1-3 : angle 6.16819 ( 3) link_BETA1-4 : bond 0.00742 ( 11) link_BETA1-4 : angle 3.15279 ( 33) link_NAG-ASN : bond 0.00812 ( 25) link_NAG-ASN : angle 3.90296 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 510 time to evaluate : 1.142 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: A 114 SER cc_start: 0.8622 (m) cc_final: 0.8272 (t) REVERT: A 360 MET cc_start: 0.8224 (tpt) cc_final: 0.7956 (tpt) REVERT: A 620 MET cc_start: 0.9212 (mmt) cc_final: 0.8849 (mmt) REVERT: B 114 SER cc_start: 0.8566 (m) cc_final: 0.8321 (t) REVERT: B 337 PHE cc_start: 0.7539 (t80) cc_final: 0.7011 (t80) REVERT: B 388 ASP cc_start: 0.8508 (m-30) cc_final: 0.7662 (p0) REVERT: B 539 SER cc_start: 0.8554 (m) cc_final: 0.8310 (p) REVERT: B 542 TYR cc_start: 0.7279 (t80) cc_final: 0.6990 (t80) REVERT: B 647 ILE cc_start: 0.8760 (mm) cc_final: 0.8252 (mm) REVERT: B 728 VAL cc_start: 0.8261 (m) cc_final: 0.8023 (m) REVERT: B 737 MET cc_start: 0.6371 (ttp) cc_final: 0.6044 (ttt) REVERT: B 834 SER cc_start: 0.7405 (m) cc_final: 0.7079 (t) REVERT: B 861 MET cc_start: 0.7798 (pmm) cc_final: 0.7438 (pmm) REVERT: C 265 ASP cc_start: 0.7611 (t0) cc_final: 0.7342 (t0) REVERT: C 284 THR cc_start: 0.8332 (m) cc_final: 0.8048 (m) REVERT: C 631 LEU cc_start: 0.8069 (tt) cc_final: 0.7839 (tt) REVERT: C 764 TYR cc_start: 0.6960 (m-80) cc_final: 0.6695 (m-80) REVERT: C 861 MET cc_start: 0.6683 (mmp) cc_final: 0.6431 (tmm) REVERT: D 132 THR cc_start: 0.8898 (p) cc_final: 0.8651 (p) REVERT: D 194 ARG cc_start: 0.7484 (ptt180) cc_final: 0.7107 (mtm180) outliers start: 3 outliers final: 2 residues processed: 513 average time/residue: 0.1792 time to fit residues: 149.8262 Evaluate side-chains 391 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 389 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 35 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 203 optimal weight: 0.0470 chunk 250 optimal weight: 1.9990 chunk 283 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 254 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 222 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN A 819 ASN B 111 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN C 98 GLN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 ASN D 593 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.156333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.146851 restraints weight = 47274.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.146338 restraints weight = 104410.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.146050 restraints weight = 96272.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145680 restraints weight = 67340.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.145908 restraints weight = 56835.885| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27832 Z= 0.142 Angle : 0.760 12.707 37747 Z= 0.364 Chirality : 0.046 0.431 4311 Planarity : 0.004 0.067 4715 Dihedral : 13.937 110.903 4510 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.81 % Favored : 87.95 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.28 % 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: -3.14 (0.14), residues: 3344 helix: -0.42 (0.14), residues: 1420 sheet: -4.24 (0.23), residues: 349 loop : -3.21 (0.14), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 523 TYR 0.029 0.002 TYR C 86 PHE 0.030 0.002 PHE D 529 TRP 0.018 0.001 TRP B 613 HIS 0.007 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00322 (27781) covalent geometry : angle 0.73265 (37602) SS BOND : bond 0.00228 ( 8) SS BOND : angle 1.32461 ( 16) hydrogen bonds : bond 0.03527 ( 857) hydrogen bonds : angle 4.68358 ( 2499) link_ALPHA1-3 : bond 0.01787 ( 3) link_ALPHA1-3 : angle 2.96421 ( 9) link_ALPHA1-6 : bond 0.01095 ( 3) link_ALPHA1-6 : angle 2.68915 ( 9) link_BETA1-3 : bond 0.01829 ( 1) link_BETA1-3 : angle 5.98518 ( 3) link_BETA1-4 : bond 0.00728 ( 11) link_BETA1-4 : angle 3.07145 ( 33) link_NAG-ASN : bond 0.00760 ( 25) link_NAG-ASN : angle 3.72921 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 1.066 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: A 71 LEU cc_start: 0.7573 (mp) cc_final: 0.7250 (mp) REVERT: A 114 SER cc_start: 0.8662 (m) cc_final: 0.8358 (t) REVERT: A 223 GLU cc_start: 0.6420 (mt-10) cc_final: 0.6176 (mt-10) REVERT: A 340 MET cc_start: 0.5756 (mmm) cc_final: 0.4791 (mmm) REVERT: A 647 ILE cc_start: 0.9478 (tp) cc_final: 0.9239 (tt) REVERT: B 337 PHE cc_start: 0.7450 (t80) cc_final: 0.7178 (t80) REVERT: B 539 SER cc_start: 0.8597 (m) cc_final: 0.8376 (p) REVERT: B 620 MET cc_start: 0.8527 (tpp) cc_final: 0.8326 (mmt) REVERT: B 639 ILE cc_start: 0.8307 (tt) cc_final: 0.7736 (mm) REVERT: B 709 MET cc_start: 0.4632 (tpt) cc_final: 0.4301 (tpt) REVERT: B 737 MET cc_start: 0.6399 (ttp) cc_final: 0.6061 (ttt) REVERT: B 834 SER cc_start: 0.7343 (m) cc_final: 0.6890 (t) REVERT: C 86 TYR cc_start: 0.6169 (m-80) cc_final: 0.5818 (m-80) REVERT: C 372 THR cc_start: 0.8734 (p) cc_final: 0.8508 (p) REVERT: C 711 SER cc_start: 0.7964 (p) cc_final: 0.7578 (t) REVERT: D 132 THR cc_start: 0.8920 (p) cc_final: 0.8717 (p) REVERT: D 140 ASP cc_start: 0.8405 (p0) cc_final: 0.7467 (p0) REVERT: D 323 MET cc_start: 0.8305 (tpp) cc_final: 0.8078 (tpp) REVERT: D 516 PRO cc_start: 0.6998 (Cg_exo) cc_final: 0.6611 (Cg_endo) REVERT: D 622 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8649 (mm110) REVERT: D 626 LEU cc_start: 0.7092 (mt) cc_final: 0.6715 (mp) REVERT: D 824 PHE cc_start: 0.5627 (m-80) cc_final: 0.5424 (m-80) outliers start: 0 outliers final: 0 residues processed: 526 average time/residue: 0.1700 time to fit residues: 145.6678 Evaluate side-chains 388 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 132 optimal weight: 0.9990 chunk 234 optimal weight: 0.9990 chunk 172 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 233 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 251 optimal weight: 8.9990 chunk 245 optimal weight: 10.0000 chunk 158 optimal weight: 0.1980 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS C 622 GLN D 491 GLN D 557 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.155912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.148754 restraints weight = 47507.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.145287 restraints weight = 85490.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.143095 restraints weight = 111954.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.143125 restraints weight = 102432.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.142860 restraints weight = 73666.547| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27832 Z= 0.147 Angle : 0.770 12.653 37747 Z= 0.366 Chirality : 0.047 0.378 4311 Planarity : 0.004 0.060 4715 Dihedral : 13.324 115.542 4510 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.53 % Favored : 87.23 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.28 % 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: -2.93 (0.14), residues: 3344 helix: -0.22 (0.14), residues: 1426 sheet: -4.11 (0.23), residues: 379 loop : -3.11 (0.14), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 583 TYR 0.069 0.002 TYR B 86 PHE 0.019 0.002 PHE D 476 TRP 0.038 0.001 TRP B 613 HIS 0.006 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00341 (27781) covalent geometry : angle 0.74310 (37602) SS BOND : bond 0.00192 ( 8) SS BOND : angle 0.84819 ( 16) hydrogen bonds : bond 0.03445 ( 857) hydrogen bonds : angle 4.58546 ( 2499) link_ALPHA1-3 : bond 0.02091 ( 3) link_ALPHA1-3 : angle 3.13613 ( 9) link_ALPHA1-6 : bond 0.00919 ( 3) link_ALPHA1-6 : angle 1.61628 ( 9) link_BETA1-3 : bond 0.01716 ( 1) link_BETA1-3 : angle 5.95078 ( 3) link_BETA1-4 : bond 0.00686 ( 11) link_BETA1-4 : angle 3.03915 ( 33) link_NAG-ASN : bond 0.00678 ( 25) link_NAG-ASN : angle 3.83546 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 1.272 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: A 70 LEU cc_start: 0.7634 (mt) cc_final: 0.7364 (mt) REVERT: A 114 SER cc_start: 0.8621 (m) cc_final: 0.8341 (t) REVERT: A 223 GLU cc_start: 0.6324 (mt-10) cc_final: 0.6048 (mt-10) REVERT: A 340 MET cc_start: 0.5667 (mmm) cc_final: 0.4851 (mmm) REVERT: A 360 MET cc_start: 0.8359 (tpt) cc_final: 0.8151 (tpt) REVERT: A 620 MET cc_start: 0.9158 (mmt) cc_final: 0.8778 (mmt) REVERT: B 260 ASP cc_start: 0.7535 (m-30) cc_final: 0.7108 (m-30) REVERT: B 498 TRP cc_start: 0.5526 (m100) cc_final: 0.5204 (m100) REVERT: B 539 SER cc_start: 0.8612 (m) cc_final: 0.8323 (p) REVERT: B 620 MET cc_start: 0.8531 (tpp) cc_final: 0.8240 (mmt) REVERT: B 639 ILE cc_start: 0.8314 (tt) cc_final: 0.7750 (mm) REVERT: B 649 SER cc_start: 0.8183 (p) cc_final: 0.7641 (t) REVERT: B 709 MET cc_start: 0.4640 (tpt) cc_final: 0.4407 (tpt) REVERT: B 728 VAL cc_start: 0.8074 (m) cc_final: 0.7872 (m) REVERT: B 737 MET cc_start: 0.6557 (ttp) cc_final: 0.6112 (ttt) REVERT: B 834 SER cc_start: 0.7388 (m) cc_final: 0.6990 (t) REVERT: C 86 TYR cc_start: 0.6288 (m-80) cc_final: 0.5730 (m-80) REVERT: C 232 HIS cc_start: 0.7212 (p-80) cc_final: 0.6519 (p-80) REVERT: C 631 LEU cc_start: 0.8002 (tt) cc_final: 0.7763 (tt) REVERT: C 711 SER cc_start: 0.7991 (p) cc_final: 0.7603 (t) REVERT: C 764 TYR cc_start: 0.7033 (m-80) cc_final: 0.6802 (m-80) REVERT: D 90 GLU cc_start: 0.7756 (tt0) cc_final: 0.7462 (tt0) REVERT: D 140 ASP cc_start: 0.8346 (p0) cc_final: 0.7603 (p0) REVERT: D 323 MET cc_start: 0.8353 (tpp) cc_final: 0.8089 (tpp) REVERT: D 622 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8677 (mm110) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.1774 time to fit residues: 144.4444 Evaluate side-chains 387 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 162 optimal weight: 6.9990 chunk 277 optimal weight: 5.9990 chunk 317 optimal weight: 6.9990 chunk 269 optimal weight: 0.8980 chunk 321 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN A 677 GLN A 819 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 ASN D 98 GLN D 283 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.155628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.138877 restraints weight = 47349.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135149 restraints weight = 59762.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135068 restraints weight = 77373.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135257 restraints weight = 72908.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.135328 restraints weight = 58379.938| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27832 Z= 0.152 Angle : 0.767 12.970 37747 Z= 0.365 Chirality : 0.047 0.479 4311 Planarity : 0.005 0.061 4715 Dihedral : 12.749 111.652 4510 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.14 % Favored : 87.62 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.19 % 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: -2.79 (0.14), residues: 3344 helix: -0.07 (0.14), residues: 1425 sheet: -4.04 (0.24), residues: 374 loop : -3.06 (0.14), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 481 TYR 0.036 0.002 TYR B 86 PHE 0.022 0.002 PHE D 744 TRP 0.049 0.001 TRP B 613 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00354 (27781) covalent geometry : angle 0.73845 (37602) SS BOND : bond 0.00167 ( 8) SS BOND : angle 0.73994 ( 16) hydrogen bonds : bond 0.03398 ( 857) hydrogen bonds : angle 4.56636 ( 2499) link_ALPHA1-3 : bond 0.02314 ( 3) link_ALPHA1-3 : angle 3.03302 ( 9) link_ALPHA1-6 : bond 0.00868 ( 3) link_ALPHA1-6 : angle 1.76755 ( 9) link_BETA1-3 : bond 0.01689 ( 1) link_BETA1-3 : angle 5.85848 ( 3) link_BETA1-4 : bond 0.00708 ( 11) link_BETA1-4 : angle 3.12525 ( 33) link_NAG-ASN : bond 0.00572 ( 25) link_NAG-ASN : angle 3.89175 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 493 time to evaluate : 0.947 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: A 114 SER cc_start: 0.8557 (m) cc_final: 0.8328 (t) REVERT: A 223 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6112 (mt-10) REVERT: A 620 MET cc_start: 0.9219 (mmt) cc_final: 0.8735 (mmt) REVERT: B 69 THR cc_start: 0.8106 (p) cc_final: 0.7883 (t) REVERT: B 87 ASP cc_start: 0.8422 (t70) cc_final: 0.8217 (t70) REVERT: B 539 SER cc_start: 0.8710 (m) cc_final: 0.8425 (p) REVERT: B 620 MET cc_start: 0.8573 (tpp) cc_final: 0.8084 (mmt) REVERT: B 639 ILE cc_start: 0.8611 (tt) cc_final: 0.8165 (mm) REVERT: B 649 SER cc_start: 0.8425 (p) cc_final: 0.7703 (t) REVERT: B 709 MET cc_start: 0.5238 (tpt) cc_final: 0.4890 (tpt) REVERT: B 737 MET cc_start: 0.6648 (ttp) cc_final: 0.6223 (ttt) REVERT: B 834 SER cc_start: 0.7490 (m) cc_final: 0.7093 (t) REVERT: B 861 MET cc_start: 0.7936 (pmm) cc_final: 0.7390 (pmm) REVERT: C 90 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7358 (mm-30) REVERT: C 620 MET cc_start: 0.8668 (mmm) cc_final: 0.8374 (mmt) REVERT: C 631 LEU cc_start: 0.8082 (tt) cc_final: 0.7869 (tt) REVERT: C 711 SER cc_start: 0.7877 (p) cc_final: 0.7549 (t) REVERT: C 823 ILE cc_start: 0.8073 (tp) cc_final: 0.7690 (tp) REVERT: D 622 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8714 (mm110) REVERT: D 626 LEU cc_start: 0.7277 (mt) cc_final: 0.6956 (mp) REVERT: D 704 LYS cc_start: 0.7448 (ptmt) cc_final: 0.7145 (pttt) outliers start: 0 outliers final: 0 residues processed: 493 average time/residue: 0.1673 time to fit residues: 135.1007 Evaluate side-chains 375 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 231 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 188 optimal weight: 0.0020 chunk 332 optimal weight: 20.0000 chunk 180 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN A 802 ASN A 819 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS C 622 GLN C 849 ASN ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.156291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.147414 restraints weight = 47712.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143171 restraints weight = 102265.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141703 restraints weight = 83544.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.140326 restraints weight = 94037.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.140734 restraints weight = 70343.353| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27832 Z= 0.145 Angle : 0.774 13.022 37747 Z= 0.369 Chirality : 0.047 0.429 4311 Planarity : 0.004 0.061 4715 Dihedral : 12.227 109.286 4510 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.14 % Favored : 87.62 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.19 % 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: -2.68 (0.14), residues: 3344 helix: 0.05 (0.14), residues: 1422 sheet: -3.95 (0.24), residues: 374 loop : -3.04 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 349 TYR 0.094 0.002 TYR B 86 PHE 0.039 0.002 PHE A 612 TRP 0.058 0.001 TRP B 613 HIS 0.024 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00334 (27781) covalent geometry : angle 0.74649 (37602) SS BOND : bond 0.01038 ( 8) SS BOND : angle 1.79995 ( 16) hydrogen bonds : bond 0.03304 ( 857) hydrogen bonds : angle 4.50608 ( 2499) link_ALPHA1-3 : bond 0.02496 ( 3) link_ALPHA1-3 : angle 3.15180 ( 9) link_ALPHA1-6 : bond 0.00992 ( 3) link_ALPHA1-6 : angle 1.88098 ( 9) link_BETA1-3 : bond 0.01756 ( 1) link_BETA1-3 : angle 5.73740 ( 3) link_BETA1-4 : bond 0.00726 ( 11) link_BETA1-4 : angle 3.10977 ( 33) link_NAG-ASN : bond 0.00586 ( 25) link_NAG-ASN : angle 3.80615 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 1.275 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: A 114 SER cc_start: 0.8603 (m) cc_final: 0.8376 (t) REVERT: A 223 GLU cc_start: 0.6349 (mt-10) cc_final: 0.6113 (mt-10) REVERT: A 620 MET cc_start: 0.9211 (mmt) cc_final: 0.8694 (mmt) REVERT: B 539 SER cc_start: 0.8645 (m) cc_final: 0.8359 (p) REVERT: B 620 MET cc_start: 0.8652 (mmt) cc_final: 0.8431 (mmt) REVERT: B 639 ILE cc_start: 0.8522 (tt) cc_final: 0.8057 (mm) REVERT: B 649 SER cc_start: 0.8425 (p) cc_final: 0.7699 (t) REVERT: B 709 MET cc_start: 0.4787 (tpt) cc_final: 0.4507 (tpt) REVERT: B 834 SER cc_start: 0.7316 (m) cc_final: 0.7022 (t) REVERT: B 861 MET cc_start: 0.7812 (pmm) cc_final: 0.7345 (pmm) REVERT: C 90 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7333 (mm-30) REVERT: C 397 GLU cc_start: 0.7166 (pm20) cc_final: 0.6830 (pm20) REVERT: C 631 LEU cc_start: 0.8057 (tt) cc_final: 0.7800 (tt) REVERT: C 711 SER cc_start: 0.7896 (p) cc_final: 0.7578 (t) REVERT: D 140 ASP cc_start: 0.8191 (p0) cc_final: 0.7832 (p0) REVERT: D 169 TRP cc_start: 0.8148 (m-10) cc_final: 0.7797 (m-10) REVERT: D 267 GLU cc_start: 0.8317 (tp30) cc_final: 0.8091 (mm-30) REVERT: D 622 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8727 (mm110) REVERT: D 626 LEU cc_start: 0.7229 (mt) cc_final: 0.6862 (mp) outliers start: 0 outliers final: 0 residues processed: 495 average time/residue: 0.1705 time to fit residues: 138.9767 Evaluate side-chains 378 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 70 optimal weight: 7.9990 chunk 127 optimal weight: 0.7980 chunk 331 optimal weight: 8.9990 chunk 279 optimal weight: 2.9990 chunk 300 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 199 optimal weight: 7.9990 chunk 312 optimal weight: 1.9990 chunk 253 optimal weight: 0.5980 chunk 68 optimal weight: 0.0010 chunk 1 optimal weight: 1.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 604 ASN A 754 GLN A 819 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 ASN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 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 = 0.3938 r_free = 0.3938 target = 0.156854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.149058 restraints weight = 47528.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.145028 restraints weight = 96653.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.143468 restraints weight = 106622.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142935 restraints weight = 102439.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142893 restraints weight = 74518.560| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27832 Z= 0.136 Angle : 0.767 12.918 37747 Z= 0.364 Chirality : 0.046 0.409 4311 Planarity : 0.004 0.062 4715 Dihedral : 11.837 108.123 4510 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.93 % Favored : 87.80 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.22 % 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: -2.58 (0.14), residues: 3344 helix: 0.12 (0.14), residues: 1417 sheet: -3.83 (0.25), residues: 362 loop : -3.00 (0.14), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 349 TYR 0.040 0.002 TYR B 86 PHE 0.030 0.001 PHE A 612 TRP 0.082 0.001 TRP B 613 HIS 0.019 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00311 (27781) covalent geometry : angle 0.73884 (37602) SS BOND : bond 0.00236 ( 8) SS BOND : angle 1.61201 ( 16) hydrogen bonds : bond 0.03314 ( 857) hydrogen bonds : angle 4.47352 ( 2499) link_ALPHA1-3 : bond 0.02239 ( 3) link_ALPHA1-3 : angle 3.27506 ( 9) link_ALPHA1-6 : bond 0.00860 ( 3) link_ALPHA1-6 : angle 1.85710 ( 9) link_BETA1-3 : bond 0.01645 ( 1) link_BETA1-3 : angle 5.66282 ( 3) link_BETA1-4 : bond 0.00680 ( 11) link_BETA1-4 : angle 3.09175 ( 33) link_NAG-ASN : bond 0.00581 ( 25) link_NAG-ASN : angle 3.78734 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 0.999 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: A 114 SER cc_start: 0.8610 (m) cc_final: 0.8358 (t) REVERT: A 223 GLU cc_start: 0.6355 (mt-10) cc_final: 0.6069 (mt-10) REVERT: A 340 MET cc_start: 0.5573 (mmm) cc_final: 0.5309 (mmm) REVERT: A 620 MET cc_start: 0.9234 (mmt) cc_final: 0.8676 (mmt) REVERT: B 69 THR cc_start: 0.8138 (p) cc_final: 0.7894 (t) REVERT: B 539 SER cc_start: 0.8600 (m) cc_final: 0.8379 (p) REVERT: B 620 MET cc_start: 0.8702 (mmt) cc_final: 0.8501 (mmt) REVERT: B 639 ILE cc_start: 0.8464 (tt) cc_final: 0.8034 (mm) REVERT: B 649 SER cc_start: 0.8415 (p) cc_final: 0.7652 (t) REVERT: B 709 MET cc_start: 0.4805 (tpt) cc_final: 0.4493 (tpt) REVERT: B 737 MET cc_start: 0.6337 (ttp) cc_final: 0.5946 (ttt) REVERT: B 834 SER cc_start: 0.7250 (m) cc_final: 0.6909 (t) REVERT: B 861 MET cc_start: 0.7758 (pmm) cc_final: 0.7369 (pmm) REVERT: C 90 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7285 (mm-30) REVERT: C 711 SER cc_start: 0.7907 (p) cc_final: 0.7534 (t) REVERT: D 169 TRP cc_start: 0.8178 (m-10) cc_final: 0.7910 (m-10) REVERT: D 234 MET cc_start: 0.7839 (ttm) cc_final: 0.7598 (ttm) REVERT: D 267 GLU cc_start: 0.8359 (tp30) cc_final: 0.8119 (mm-30) REVERT: D 337 PHE cc_start: 0.7444 (t80) cc_final: 0.7152 (t80) REVERT: D 622 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8657 (mm110) REVERT: D 626 LEU cc_start: 0.7216 (mt) cc_final: 0.6918 (mp) outliers start: 0 outliers final: 0 residues processed: 473 average time/residue: 0.1673 time to fit residues: 130.4445 Evaluate side-chains 379 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 297 optimal weight: 6.9990 chunk 289 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 185 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 295 optimal weight: 8.9990 chunk 216 optimal weight: 0.0270 chunk 55 optimal weight: 20.0000 chunk 135 optimal weight: 0.4980 chunk 132 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 819 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.159259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.152547 restraints weight = 47720.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142868 restraints weight = 93010.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143322 restraints weight = 87935.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.141786 restraints weight = 78437.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142102 restraints weight = 61783.865| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27832 Z= 0.125 Angle : 0.760 12.707 37747 Z= 0.361 Chirality : 0.045 0.404 4311 Planarity : 0.005 0.077 4715 Dihedral : 11.397 105.518 4510 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.15 % Favored : 88.64 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.22 % 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: -2.49 (0.14), residues: 3344 helix: 0.17 (0.14), residues: 1417 sheet: -3.76 (0.25), residues: 356 loop : -2.94 (0.14), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 634 TYR 0.051 0.002 TYR C 733 PHE 0.029 0.002 PHE D 579 TRP 0.077 0.001 TRP B 613 HIS 0.014 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00277 (27781) covalent geometry : angle 0.73390 (37602) SS BOND : bond 0.00204 ( 8) SS BOND : angle 1.27027 ( 16) hydrogen bonds : bond 0.03163 ( 857) hydrogen bonds : angle 4.39794 ( 2499) link_ALPHA1-3 : bond 0.02048 ( 3) link_ALPHA1-3 : angle 3.41546 ( 9) link_ALPHA1-6 : bond 0.00946 ( 3) link_ALPHA1-6 : angle 1.95723 ( 9) link_BETA1-3 : bond 0.01647 ( 1) link_BETA1-3 : angle 5.50835 ( 3) link_BETA1-4 : bond 0.00711 ( 11) link_BETA1-4 : angle 3.09094 ( 33) link_NAG-ASN : bond 0.00600 ( 25) link_NAG-ASN : angle 3.65401 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.6284 (mt-10) cc_final: 0.6043 (mt-10) REVERT: A 620 MET cc_start: 0.9240 (mmt) cc_final: 0.8710 (mmt) REVERT: B 69 THR cc_start: 0.8190 (p) cc_final: 0.7951 (t) REVERT: B 260 ASP cc_start: 0.7832 (m-30) cc_final: 0.7048 (m-30) REVERT: B 539 SER cc_start: 0.8685 (m) cc_final: 0.8424 (p) REVERT: B 620 MET cc_start: 0.8668 (mmt) cc_final: 0.8360 (mmt) REVERT: B 639 ILE cc_start: 0.8596 (tt) cc_final: 0.8168 (mm) REVERT: B 647 ILE cc_start: 0.9044 (mm) cc_final: 0.8459 (mm) REVERT: B 649 SER cc_start: 0.8368 (p) cc_final: 0.7602 (t) REVERT: B 728 VAL cc_start: 0.8321 (m) cc_final: 0.8113 (m) REVERT: B 737 MET cc_start: 0.6487 (ttp) cc_final: 0.6009 (ttt) REVERT: B 834 SER cc_start: 0.7388 (m) cc_final: 0.7067 (t) REVERT: B 861 MET cc_start: 0.8124 (pmm) cc_final: 0.7486 (pmm) REVERT: C 248 MET cc_start: 0.8588 (tpp) cc_final: 0.8307 (mmm) REVERT: C 340 MET cc_start: 0.6330 (mmm) cc_final: 0.6064 (tpp) REVERT: C 631 LEU cc_start: 0.8226 (tt) cc_final: 0.7982 (tt) REVERT: C 711 SER cc_start: 0.7874 (p) cc_final: 0.7525 (t) REVERT: D 169 TRP cc_start: 0.8115 (m-10) cc_final: 0.7877 (m-10) REVERT: D 194 ARG cc_start: 0.7165 (ptt180) cc_final: 0.6691 (mtm180) REVERT: D 337 PHE cc_start: 0.7421 (t80) cc_final: 0.7079 (t80) REVERT: D 622 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8536 (mm-40) REVERT: D 626 LEU cc_start: 0.7434 (mt) cc_final: 0.7072 (mp) outliers start: 0 outliers final: 0 residues processed: 487 average time/residue: 0.1689 time to fit residues: 136.0280 Evaluate side-chains 373 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 115 optimal weight: 7.9990 chunk 286 optimal weight: 0.7980 chunk 259 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 325 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 819 ASN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 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 = 0.3954 r_free = 0.3954 target = 0.158479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.151878 restraints weight = 47437.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141663 restraints weight = 93960.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.142222 restraints weight = 92322.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140786 restraints weight = 84639.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.141092 restraints weight = 62362.232| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27832 Z= 0.133 Angle : 0.752 12.582 37747 Z= 0.357 Chirality : 0.045 0.406 4311 Planarity : 0.005 0.077 4715 Dihedral : 11.118 105.190 4510 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.72 % Favored : 88.04 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.22 % 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: -2.37 (0.15), residues: 3344 helix: 0.26 (0.14), residues: 1418 sheet: -3.69 (0.27), residues: 336 loop : -2.89 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 133 TYR 0.042 0.002 TYR C 733 PHE 0.028 0.001 PHE A 612 TRP 0.083 0.002 TRP B 613 HIS 0.015 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00303 (27781) covalent geometry : angle 0.72581 (37602) SS BOND : bond 0.00143 ( 8) SS BOND : angle 1.21834 ( 16) hydrogen bonds : bond 0.03160 ( 857) hydrogen bonds : angle 4.38185 ( 2499) link_ALPHA1-3 : bond 0.02349 ( 3) link_ALPHA1-3 : angle 3.51003 ( 9) link_ALPHA1-6 : bond 0.00922 ( 3) link_ALPHA1-6 : angle 2.02694 ( 9) link_BETA1-3 : bond 0.01549 ( 1) link_BETA1-3 : angle 5.47072 ( 3) link_BETA1-4 : bond 0.00649 ( 11) link_BETA1-4 : angle 3.08605 ( 33) link_NAG-ASN : bond 0.00554 ( 25) link_NAG-ASN : angle 3.55602 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4419.90 seconds wall clock time: 77 minutes 45.34 seconds (4665.34 seconds total)