Starting phenix.real_space_refine on Fri Feb 6 06:57:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lp0_63265/02_2026/9lp0_63265.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lp0_63265/02_2026/9lp0_63265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lp0_63265/02_2026/9lp0_63265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lp0_63265/02_2026/9lp0_63265.map" model { file = "/net/cci-nas-00/data/ceres_data/9lp0_63265/02_2026/9lp0_63265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lp0_63265/02_2026/9lp0_63265.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.075 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 97 5.16 5 C 14704 2.51 5 N 3783 2.21 5 O 4404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s 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: 22988 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7559 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 913} Chain breaks: 9 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 5893 Classifications: {'peptide': 756} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 719} Chain breaks: 10 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 7529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7529 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 911} Chain breaks: 11 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "E" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 771 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.53, per 1000 atoms: 0.20 Number of scatterers: 22988 At special positions: 0 Unit cell: (125.13, 118.34, 224.07, 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 97 16.00 O 4404 8.00 N 3783 7.00 C 14704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.06 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.06 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 87 " 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 NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1098 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 354 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C1098 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 354 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 694.9 milliseconds 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5410 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 48 sheets defined 27.4% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.221A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.803A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 372 " --> pdb=" O TYR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.504A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.962A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.635A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.020A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.621A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.726A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.551A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.086A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.628A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.152A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1144 removed outlier: 3.671A pdb=" N LEU B1143 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU B1144 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1144' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.605A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.979A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.563A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.611A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.274A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.733A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.076A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.632A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.994A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1145 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.509A pdb=" N ARG D 31 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.578A pdb=" N LYS D 64 " --> pdb=" O ASP D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.650A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 31 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 4.195A pdb=" N PHE A 32 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER A 60 " --> pdb=" O PHE A 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.200A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.200A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.528A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.596A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 103 through 107 removed outlier: 3.797A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.894A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.469A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.762A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.464A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.769A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.038A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.645A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.895A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.337A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.756A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 63 through 64 removed outlier: 3.581A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 104 through 106 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.889A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.110A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.602A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.003A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.419A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 787 through 790 removed outlier: 5.896A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.440A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 63 through 64 removed outlier: 7.169A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.864A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 357 through 358 removed outlier: 4.105A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD9, first strand: chain 'C' and resid 538 through 543 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.117A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.646A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.917A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.313A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.986A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D 18 " --> pdb=" O MET D 82 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.986A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 70 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.539A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N MET D 34 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 96 through 98 Processing sheet with id=AF1, first strand: chain 'E' and resid 8 through 11 removed outlier: 5.757A pdb=" N LEU E 9 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN E 88 " --> pdb=" O ALA E 33 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP E 34 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 8 through 11 removed outlier: 5.757A pdb=" N LEU E 9 " --> pdb=" O ASP E 104 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 17 through 22 removed outlier: 3.971A pdb=" N ASP E 69 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER E 66 " --> pdb=" O ASP E 69 " (cutoff:3.500A) 970 hydrogen bonds defined for protein. 2652 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: 4.92 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3707 1.28 - 1.42: 6222 1.42 - 1.56: 13455 1.56 - 1.69: 1 1.69 - 1.83: 124 Bond restraints: 23509 Sorted by residual: bond pdb=" C ILE C 712 " pdb=" O ILE C 712 " ideal model delta sigma weight residual 1.235 1.149 0.086 9.90e-03 1.02e+04 7.49e+01 bond pdb=" C ILE B 712 " pdb=" O ILE B 712 " ideal model delta sigma weight residual 1.235 1.179 0.056 9.90e-03 1.02e+04 3.21e+01 bond pdb=" N ASN A 334 " pdb=" CA ASN A 334 " ideal model delta sigma weight residual 1.457 1.490 -0.034 6.40e-03 2.44e+04 2.76e+01 bond pdb=" CA SER A 711 " pdb=" CB SER A 711 " ideal model delta sigma weight residual 1.531 1.454 0.077 1.52e-02 4.33e+03 2.53e+01 bond pdb=" CA SER A 530 " pdb=" CB SER A 530 " ideal model delta sigma weight residual 1.529 1.452 0.077 1.69e-02 3.50e+03 2.08e+01 ... (remaining 23504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 31235 3.03 - 6.06: 650 6.06 - 9.08: 78 9.08 - 12.11: 8 12.11 - 15.14: 4 Bond angle restraints: 31975 Sorted by residual: angle pdb=" N PRO B 631 " pdb=" CA PRO B 631 " pdb=" C PRO B 631 " ideal model delta sigma weight residual 113.84 98.82 15.02 1.30e+00 5.92e-01 1.34e+02 angle pdb=" N LYS C 481 " pdb=" CA LYS C 481 " pdb=" C LYS C 481 " ideal model delta sigma weight residual 114.56 101.03 13.53 1.27e+00 6.20e-01 1.13e+02 angle pdb=" C PRO B 631 " pdb=" CA PRO B 631 " pdb=" CB PRO B 631 " ideal model delta sigma weight residual 111.85 123.49 -11.64 1.42e+00 4.96e-01 6.72e+01 angle pdb=" N ASN B 125 " pdb=" CA ASN B 125 " pdb=" C ASN B 125 " ideal model delta sigma weight residual 110.36 120.17 -9.81 1.55e+00 4.16e-01 4.00e+01 angle pdb=" N ASP B 88 " pdb=" CA ASP B 88 " pdb=" C ASP B 88 " ideal model delta sigma weight residual 114.31 106.16 8.15 1.29e+00 6.01e-01 3.99e+01 ... (remaining 31970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 13110 17.84 - 35.68: 945 35.68 - 53.52: 136 53.52 - 71.36: 50 71.36 - 89.19: 19 Dihedral angle restraints: 14260 sinusoidal: 5850 harmonic: 8410 Sorted by residual: dihedral pdb=" C THR B 167 " pdb=" N THR B 167 " pdb=" CA THR B 167 " pdb=" CB THR B 167 " ideal model delta harmonic sigma weight residual -122.00 -141.44 19.44 0 2.50e+00 1.60e-01 6.05e+01 dihedral pdb=" N THR B 167 " pdb=" C THR B 167 " pdb=" CA THR B 167 " pdb=" CB THR B 167 " ideal model delta harmonic sigma weight residual 123.40 138.07 -14.67 0 2.50e+00 1.60e-01 3.44e+01 dihedral pdb=" CA VAL C 635 " pdb=" C VAL C 635 " pdb=" N TYR C 636 " pdb=" CA TYR C 636 " ideal model delta harmonic sigma weight residual -180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 14257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 3638 0.194 - 0.388: 62 0.388 - 0.583: 8 0.583 - 0.777: 1 0.777 - 0.971: 1 Chirality restraints: 3710 Sorted by residual: chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -3.37 0.97 2.00e-01 2.50e+01 2.36e+01 chirality pdb=" CA THR B 167 " pdb=" N THR B 167 " pdb=" C THR B 167 " pdb=" CB THR B 167 " both_signs ideal model delta sigma weight residual False 2.53 1.85 0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 354 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.83e+00 ... (remaining 3707 not shown) Planarity restraints: 4097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.337 2.00e-02 2.50e+03 2.93e-01 1.07e+03 pdb=" C7 NAG B1302 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.111 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " -0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1308 " 0.272 2.00e-02 2.50e+03 2.35e-01 6.88e+02 pdb=" C7 NAG C1308 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG C1308 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG C1308 " -0.412 2.00e-02 2.50e+03 pdb=" O7 NAG C1308 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1302 " 0.263 2.00e-02 2.50e+03 2.23e-01 6.21e+02 pdb=" C7 NAG A1302 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG A1302 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG A1302 " -0.380 2.00e-02 2.50e+03 pdb=" O7 NAG A1302 " 0.015 2.00e-02 2.50e+03 ... (remaining 4094 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.23: 12 2.23 - 2.90: 9103 2.90 - 3.57: 30289 3.57 - 4.23: 53337 4.23 - 4.90: 91234 Nonbonded interactions: 183975 Sorted by model distance: nonbonded pdb=" OG SER B 803 " pdb=" C1 NAG B1305 " model vdw 1.568 3.470 nonbonded pdb=" O ASN A 125 " pdb=" OD1 ASN A 125 " model vdw 2.002 3.040 nonbonded pdb=" O ILE A 119 " pdb=" OD1 ASN A 121 " model vdw 2.012 3.040 nonbonded pdb=" O ALA A 292 " pdb=" OG1 THR A 632 " model vdw 2.079 3.040 nonbonded pdb=" OG SER A 383 " pdb=" OD2 ASP C 985 " model vdw 2.091 3.040 ... (remaining 183970 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 28 through 171 or resid 189 through 199 or (resid 200 and \ (name N or name CA or name C or name O or name CB )) or resid 201 through 240 or \ resid 265 through 328 or resid 334 through 368 or (resid 369 and (name N or nam \ e CA or name C or name O or name CB )) or resid 370 through 528 or resid 530 thr \ ough 828 or resid 855 through 1308)) selection = (chain 'C' and (resid 28 through 95 or resid 102 through 130 or resid 166 throug \ h 240 or resid 265 through 457 or (resid 458 and (name N or name CA or name C or \ name O or name CB )) or resid 459 through 576 or (resid 577 and (name N or name \ CA or name C or name O or name CB )) or resid 578 through 676 or resid 689 thro \ ugh 1308)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.590 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:5.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 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 : 0.008 0.086 23566 Z= 0.421 Angle : 1.036 18.108 32112 Z= 0.626 Chirality : 0.071 0.971 3710 Planarity : 0.011 0.293 4074 Dihedral : 13.225 89.194 8748 Min Nonbonded Distance : 1.568 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.13 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.15), residues: 2831 helix: 1.38 (0.20), residues: 686 sheet: -0.35 (0.20), residues: 596 loop : -1.19 (0.14), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 634 TYR 0.029 0.002 TYR C 873 PHE 0.054 0.003 PHE C 823 TRP 0.059 0.004 TRP A 886 HIS 0.010 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00774 (23509) covalent geometry : angle 1.00435 (31975) SS BOND : bond 0.00869 ( 34) SS BOND : angle 2.09375 ( 68) hydrogen bonds : bond 0.17841 ( 951) hydrogen bonds : angle 7.81428 ( 2652) link_NAG-ASN : bond 0.01500 ( 23) link_NAG-ASN : angle 5.25270 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.8004 (p) cc_final: 0.7742 (m) REVERT: A 271 GLN cc_start: 0.7638 (mt0) cc_final: 0.7330 (tt0) REVERT: A 432 CYS cc_start: 0.5997 (m) cc_final: 0.5517 (m) REVERT: A 571 ASP cc_start: 0.7425 (t70) cc_final: 0.7209 (t0) REVERT: B 239 GLN cc_start: 0.6427 (tt0) cc_final: 0.5719 (pt0) REVERT: B 628 GLN cc_start: 0.7272 (mt0) cc_final: 0.7048 (mt0) REVERT: C 190 ARG cc_start: 0.6451 (mpt180) cc_final: 0.6241 (mmp80) REVERT: C 869 MET cc_start: 0.9084 (mtt) cc_final: 0.8728 (mtt) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.5995 time to fit residues: 161.6013 Evaluate side-chains 182 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 394 ASN A 613 GLN A 955 ASN A1002 GLN A1005 GLN A1106 GLN B 314 GLN B 613 GLN B 628 GLN B1101 HIS C 122 ASN C 196 ASN C 321 GLN C 755 GLN C 955 ASN C 957 GLN C1101 HIS D 32 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.190146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122497 restraints weight = 27841.743| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.22 r_work: 0.3154 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23566 Z= 0.165 Angle : 0.626 11.824 32112 Z= 0.328 Chirality : 0.047 0.261 3710 Planarity : 0.005 0.053 4074 Dihedral : 5.629 57.239 3582 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.35 % Allowed : 6.61 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 2831 helix: 1.79 (0.20), residues: 684 sheet: 0.18 (0.20), residues: 568 loop : -1.10 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 995 TYR 0.022 0.002 TYR A1067 PHE 0.017 0.002 PHE B 802 TRP 0.026 0.002 TRP B 633 HIS 0.004 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00379 (23509) covalent geometry : angle 0.61481 (31975) SS BOND : bond 0.00385 ( 34) SS BOND : angle 1.27271 ( 68) hydrogen bonds : bond 0.05990 ( 951) hydrogen bonds : angle 5.89453 ( 2652) link_NAG-ASN : bond 0.00494 ( 23) link_NAG-ASN : angle 2.36756 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7042 (ptt90) cc_final: 0.6520 (ptp90) REVERT: A 271 GLN cc_start: 0.7961 (mt0) cc_final: 0.7480 (tt0) REVERT: A 357 ARG cc_start: 0.6931 (ttm-80) cc_final: 0.6119 (mtt180) REVERT: A 515 PHE cc_start: 0.8317 (m-80) cc_final: 0.8026 (m-80) REVERT: A 571 ASP cc_start: 0.7541 (t70) cc_final: 0.7286 (t70) REVERT: A 697 MET cc_start: 0.8945 (ptm) cc_final: 0.8528 (ptp) REVERT: A 738 CYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7658 (t) REVERT: B 619 GLU cc_start: 0.7678 (mp0) cc_final: 0.7067 (mp0) REVERT: B 902 MET cc_start: 0.9294 (mmt) cc_final: 0.9068 (tpt) REVERT: C 88 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6742 (t0) REVERT: C 190 ARG cc_start: 0.6512 (mpt180) cc_final: 0.6019 (mpp80) REVERT: C 237 ARG cc_start: 0.6812 (ptm160) cc_final: 0.6330 (ttm-80) REVERT: C 271 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7804 (mp10) outliers start: 34 outliers final: 9 residues processed: 227 average time/residue: 0.5371 time to fit residues: 142.1956 Evaluate side-chains 200 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 50 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 613 GLN A 779 GLN B 49 HIS B 540 ASN B 628 GLN B 751 ASN B 957 GLN C 314 GLN C 321 GLN C 532 ASN C 957 GLN C1101 HIS D 13 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.187508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121228 restraints weight = 27799.257| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.47 r_work: 0.3123 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 23566 Z= 0.274 Angle : 0.680 10.452 32112 Z= 0.356 Chirality : 0.051 0.296 3710 Planarity : 0.005 0.046 4074 Dihedral : 5.837 59.518 3582 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.22 % Allowed : 9.07 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.15), residues: 2831 helix: 1.66 (0.20), residues: 686 sheet: 0.19 (0.20), residues: 577 loop : -1.15 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.028 0.002 TYR A1067 PHE 0.024 0.002 PHE B 898 TRP 0.022 0.002 TRP A 633 HIS 0.006 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00671 (23509) covalent geometry : angle 0.66956 (31975) SS BOND : bond 0.00357 ( 34) SS BOND : angle 1.34825 ( 68) hydrogen bonds : bond 0.07162 ( 951) hydrogen bonds : angle 5.83236 ( 2652) link_NAG-ASN : bond 0.00364 ( 23) link_NAG-ASN : angle 2.42566 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 189 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8122 (tp40) REVERT: A 237 ARG cc_start: 0.6954 (ptt90) cc_final: 0.6464 (ptp90) REVERT: A 271 GLN cc_start: 0.7980 (mt0) cc_final: 0.7506 (tt0) REVERT: A 357 ARG cc_start: 0.6996 (ttm-80) cc_final: 0.6131 (mtt180) REVERT: A 515 PHE cc_start: 0.8484 (m-80) cc_final: 0.8248 (m-80) REVERT: A 571 ASP cc_start: 0.7724 (t70) cc_final: 0.7358 (t70) REVERT: A 697 MET cc_start: 0.9045 (ptm) cc_final: 0.8756 (ptp) REVERT: A 738 CYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7721 (t) REVERT: B 314 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7943 (tm130) REVERT: B 902 MET cc_start: 0.9310 (mmt) cc_final: 0.9109 (tpt) REVERT: C 32 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.6065 (m-80) REVERT: C 88 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6881 (t0) REVERT: C 190 ARG cc_start: 0.6578 (mpt180) cc_final: 0.6302 (mmt90) REVERT: C 237 ARG cc_start: 0.6837 (ptm160) cc_final: 0.6463 (ttt90) REVERT: C 271 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: C 745 ASP cc_start: 0.8156 (m-30) cc_final: 0.7949 (OUTLIER) outliers start: 56 outliers final: 26 residues processed: 221 average time/residue: 0.5589 time to fit residues: 142.8662 Evaluate side-chains 213 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 10 optimal weight: 7.9990 chunk 259 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 181 optimal weight: 30.0000 chunk 71 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 275 optimal weight: 0.4980 chunk 221 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 439 ASN A 613 GLN B 314 GLN B 628 GLN B 957 GLN C 314 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.190647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125154 restraints weight = 27684.245| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.37 r_work: 0.3174 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23566 Z= 0.114 Angle : 0.535 8.458 32112 Z= 0.281 Chirality : 0.044 0.172 3710 Planarity : 0.004 0.044 4074 Dihedral : 5.212 56.444 3582 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.76 % Favored : 97.21 % Rotamer: Outliers : 2.02 % Allowed : 10.21 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 2831 helix: 2.19 (0.20), residues: 677 sheet: 0.45 (0.20), residues: 584 loop : -1.02 (0.14), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.017 0.001 TYR A1067 PHE 0.022 0.001 PHE A 92 TRP 0.019 0.001 TRP B 633 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00250 (23509) covalent geometry : angle 0.52591 (31975) SS BOND : bond 0.00195 ( 34) SS BOND : angle 1.00790 ( 68) hydrogen bonds : bond 0.05172 ( 951) hydrogen bonds : angle 5.38941 ( 2652) link_NAG-ASN : bond 0.00226 ( 23) link_NAG-ASN : angle 2.00559 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 198 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6841 (ptt90) cc_final: 0.6459 (ptp90) REVERT: A 271 GLN cc_start: 0.7979 (mt0) cc_final: 0.7511 (tt0) REVERT: A 357 ARG cc_start: 0.6983 (ttm-80) cc_final: 0.6269 (mtt180) REVERT: A 571 ASP cc_start: 0.7598 (t70) cc_final: 0.7248 (t70) REVERT: A 772 VAL cc_start: 0.9048 (m) cc_final: 0.8843 (t) REVERT: A 1038 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8417 (mppt) REVERT: B 619 GLU cc_start: 0.7652 (mp0) cc_final: 0.6966 (mp0) REVERT: C 88 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6775 (t0) REVERT: C 190 ARG cc_start: 0.6496 (mpt180) cc_final: 0.6209 (mmt90) REVERT: C 237 ARG cc_start: 0.6811 (ptm160) cc_final: 0.6306 (ttm-80) REVERT: C 745 ASP cc_start: 0.7998 (m-30) cc_final: 0.7752 (OUTLIER) outliers start: 51 outliers final: 12 residues processed: 228 average time/residue: 0.5642 time to fit residues: 149.7750 Evaluate side-chains 197 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 902 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 275 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 chunk 282 optimal weight: 20.0000 chunk 245 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 chunk 194 optimal weight: 0.2980 chunk 148 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 779 GLN A1002 GLN A1010 GLN B 314 GLN B 957 GLN C 314 GLN C 321 GLN C 613 GLN C 955 ASN C 957 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.191850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126717 restraints weight = 27682.945| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.23 r_work: 0.3212 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 23566 Z= 0.103 Angle : 0.508 7.823 32112 Z= 0.265 Chirality : 0.043 0.164 3710 Planarity : 0.004 0.044 4074 Dihedral : 4.908 56.980 3582 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 1.66 % Allowed : 11.48 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 2831 helix: 2.45 (0.20), residues: 673 sheet: 0.59 (0.20), residues: 594 loop : -0.86 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.018 0.001 TYR A1067 PHE 0.017 0.001 PHE C 759 TRP 0.018 0.001 TRP B 633 HIS 0.002 0.000 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00221 (23509) covalent geometry : angle 0.49900 (31975) SS BOND : bond 0.00387 ( 34) SS BOND : angle 1.35112 ( 68) hydrogen bonds : bond 0.04615 ( 951) hydrogen bonds : angle 5.16412 ( 2652) link_NAG-ASN : bond 0.00179 ( 23) link_NAG-ASN : angle 1.76595 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6824 (ptt90) cc_final: 0.6553 (ptp90) REVERT: A 271 GLN cc_start: 0.7945 (mt0) cc_final: 0.7458 (tt0) REVERT: A 357 ARG cc_start: 0.6969 (ttm-80) cc_final: 0.6234 (mtt180) REVERT: A 571 ASP cc_start: 0.7483 (t70) cc_final: 0.7150 (t70) REVERT: A 697 MET cc_start: 0.8962 (ptm) cc_final: 0.8674 (ptp) REVERT: A 1038 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8402 (mppt) REVERT: B 269 TYR cc_start: 0.7627 (m-10) cc_final: 0.7380 (m-80) REVERT: B 1142 GLN cc_start: 0.8265 (mt0) cc_final: 0.8051 (mm110) REVERT: C 33 THR cc_start: 0.7554 (p) cc_final: 0.7076 (m) REVERT: C 190 ARG cc_start: 0.6583 (mpt180) cc_final: 0.6267 (mmt90) REVERT: C 237 ARG cc_start: 0.6818 (ptm160) cc_final: 0.6280 (ttm-80) REVERT: C 271 GLN cc_start: 0.7825 (mp10) cc_final: 0.7594 (pt0) REVERT: C 745 ASP cc_start: 0.7952 (m-30) cc_final: 0.7630 (t0) REVERT: C 900 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.9045 (mtm) outliers start: 42 outliers final: 13 residues processed: 222 average time/residue: 0.5688 time to fit residues: 146.1567 Evaluate side-chains 195 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 107 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 187 optimal weight: 0.8980 chunk 205 optimal weight: 10.0000 chunk 249 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 138 optimal weight: 0.0980 chunk 183 optimal weight: 9.9990 chunk 284 optimal weight: 30.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 613 GLN A 779 GLN A1010 GLN B 314 GLN B 957 GLN C 314 GLN C 321 GLN C 613 GLN C 957 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.188073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122370 restraints weight = 27703.174| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.46 r_work: 0.3105 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 23566 Z= 0.241 Angle : 0.628 10.092 32112 Z= 0.328 Chirality : 0.048 0.209 3710 Planarity : 0.005 0.042 4074 Dihedral : 5.409 59.795 3582 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 2.30 % Allowed : 11.72 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.15), residues: 2831 helix: 2.02 (0.20), residues: 681 sheet: 0.50 (0.19), residues: 614 loop : -1.06 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1039 TYR 0.026 0.002 TYR A1067 PHE 0.022 0.002 PHE B 898 TRP 0.019 0.002 TRP A 633 HIS 0.006 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00595 (23509) covalent geometry : angle 0.61527 (31975) SS BOND : bond 0.00349 ( 34) SS BOND : angle 1.90210 ( 68) hydrogen bonds : bond 0.06488 ( 951) hydrogen bonds : angle 5.50374 ( 2652) link_NAG-ASN : bond 0.00317 ( 23) link_NAG-ASN : angle 2.12655 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 186 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6772 (ptt90) cc_final: 0.6448 (ptp90) REVERT: A 271 GLN cc_start: 0.8045 (mt0) cc_final: 0.7529 (tt0) REVERT: A 357 ARG cc_start: 0.7050 (ttm-80) cc_final: 0.6224 (mtt180) REVERT: A 571 ASP cc_start: 0.7683 (t70) cc_final: 0.7373 (t70) REVERT: A 697 MET cc_start: 0.9055 (ptm) cc_final: 0.8760 (ptp) REVERT: A 702 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8324 (mp0) REVERT: A 738 CYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7645 (t) REVERT: A 1038 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8582 (mppt) REVERT: B 619 GLU cc_start: 0.7719 (mp0) cc_final: 0.7070 (mp0) REVERT: B 702 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7750 (tp30) REVERT: B 1142 GLN cc_start: 0.8315 (mt0) cc_final: 0.8089 (mm110) REVERT: C 32 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.6076 (m-80) REVERT: C 88 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.6854 (t0) REVERT: C 190 ARG cc_start: 0.6430 (mpt180) cc_final: 0.6122 (mmt90) REVERT: C 237 ARG cc_start: 0.6856 (ptm160) cc_final: 0.6347 (ttm-80) REVERT: C 271 GLN cc_start: 0.8134 (mp10) cc_final: 0.7901 (pt0) REVERT: C 814 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7751 (mptt) outliers start: 58 outliers final: 24 residues processed: 220 average time/residue: 0.5971 time to fit residues: 152.4081 Evaluate side-chains 211 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 82 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 1 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 160 optimal weight: 0.3980 chunk 256 optimal weight: 0.9980 chunk 211 optimal weight: 0.8980 chunk 286 optimal weight: 0.6980 chunk 280 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 208 optimal weight: 7.9990 chunk 193 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 613 GLN B 87 ASN B 957 GLN C 239 GLN C 314 GLN C 321 GLN C 957 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.191183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125692 restraints weight = 27769.887| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.51 r_work: 0.3169 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23566 Z= 0.108 Angle : 0.516 7.757 32112 Z= 0.271 Chirality : 0.043 0.166 3710 Planarity : 0.004 0.042 4074 Dihedral : 4.974 56.169 3582 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.37 % Favored : 97.56 % Rotamer: Outliers : 1.70 % Allowed : 12.63 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 2831 helix: 2.43 (0.20), residues: 672 sheet: 0.63 (0.20), residues: 603 loop : -0.92 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.016 0.001 TYR A1067 PHE 0.016 0.001 PHE C 759 TRP 0.018 0.001 TRP B 633 HIS 0.002 0.000 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00236 (23509) covalent geometry : angle 0.50626 (31975) SS BOND : bond 0.00201 ( 34) SS BOND : angle 1.44881 ( 68) hydrogen bonds : bond 0.04748 ( 951) hydrogen bonds : angle 5.19105 ( 2652) link_NAG-ASN : bond 0.00202 ( 23) link_NAG-ASN : angle 1.81854 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6787 (ptt90) cc_final: 0.6513 (ptp90) REVERT: A 271 GLN cc_start: 0.8050 (mt0) cc_final: 0.7541 (tt0) REVERT: A 281 GLU cc_start: 0.7802 (pm20) cc_final: 0.7583 (mp0) REVERT: A 357 ARG cc_start: 0.6976 (ttm-80) cc_final: 0.6224 (mtt180) REVERT: A 571 ASP cc_start: 0.7605 (t70) cc_final: 0.7270 (t70) REVERT: A 697 MET cc_start: 0.9005 (ptm) cc_final: 0.8713 (ptp) REVERT: A 1038 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8500 (mppt) REVERT: B 619 GLU cc_start: 0.7706 (mp0) cc_final: 0.7080 (mp0) REVERT: B 979 ASP cc_start: 0.7647 (m-30) cc_final: 0.7413 (m-30) REVERT: C 190 ARG cc_start: 0.6497 (mpt180) cc_final: 0.6156 (mmt90) REVERT: C 237 ARG cc_start: 0.6819 (ptm160) cc_final: 0.6334 (ttm-80) REVERT: C 814 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7760 (mptt) REVERT: C 900 MET cc_start: 0.9223 (mtm) cc_final: 0.8970 (ttm) outliers start: 43 outliers final: 21 residues processed: 216 average time/residue: 0.5551 time to fit residues: 139.2975 Evaluate side-chains 206 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 82 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 182 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 191 optimal weight: 20.0000 chunk 248 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 239 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A1002 GLN B 87 ASN B 314 GLN B 957 GLN C 314 GLN C 321 GLN C 957 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.190058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124387 restraints weight = 27432.407| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.31 r_work: 0.3157 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23566 Z= 0.139 Angle : 0.534 8.213 32112 Z= 0.279 Chirality : 0.044 0.171 3710 Planarity : 0.004 0.042 4074 Dihedral : 5.035 58.299 3582 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 1.82 % Allowed : 12.55 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 2831 helix: 2.42 (0.20), residues: 673 sheet: 0.62 (0.20), residues: 609 loop : -0.94 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 319 TYR 0.023 0.001 TYR A1067 PHE 0.022 0.001 PHE A 92 TRP 0.015 0.001 TRP B 633 HIS 0.003 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00330 (23509) covalent geometry : angle 0.52306 (31975) SS BOND : bond 0.00245 ( 34) SS BOND : angle 1.54041 ( 68) hydrogen bonds : bond 0.05193 ( 951) hydrogen bonds : angle 5.19939 ( 2652) link_NAG-ASN : bond 0.00195 ( 23) link_NAG-ASN : angle 1.83283 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6758 (ptt90) cc_final: 0.6499 (ptp90) REVERT: A 271 GLN cc_start: 0.8031 (mt0) cc_final: 0.7515 (tt0) REVERT: A 357 ARG cc_start: 0.6998 (ttm-80) cc_final: 0.6302 (mtt180) REVERT: A 571 ASP cc_start: 0.7561 (t70) cc_final: 0.7235 (t70) REVERT: A 697 MET cc_start: 0.8992 (ptm) cc_final: 0.8703 (ptp) REVERT: A 1038 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8427 (mppt) REVERT: B 979 ASP cc_start: 0.7639 (m-30) cc_final: 0.7406 (m-30) REVERT: B 1142 GLN cc_start: 0.8055 (mm110) cc_final: 0.7840 (mm110) REVERT: C 190 ARG cc_start: 0.6468 (mpt180) cc_final: 0.5974 (mmp80) REVERT: C 237 ARG cc_start: 0.6830 (ptm160) cc_final: 0.6344 (ttm-80) REVERT: C 745 ASP cc_start: 0.8131 (m-30) cc_final: 0.7803 (t0) REVERT: C 814 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7749 (mptt) REVERT: C 900 MET cc_start: 0.9223 (mtm) cc_final: 0.8975 (ttm) outliers start: 46 outliers final: 29 residues processed: 215 average time/residue: 0.5321 time to fit residues: 132.7344 Evaluate side-chains 214 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 82 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 117 optimal weight: 7.9990 chunk 247 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 257 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 279 optimal weight: 0.0470 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 439 ASN A1002 GLN B 87 ASN B 314 GLN B 957 GLN C 314 GLN C 321 GLN C 957 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.191205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125589 restraints weight = 27783.294| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.32 r_work: 0.3175 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23566 Z= 0.114 Angle : 0.512 8.100 32112 Z= 0.268 Chirality : 0.043 0.167 3710 Planarity : 0.004 0.042 4074 Dihedral : 4.939 57.110 3582 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.58 % Favored : 97.35 % Rotamer: Outliers : 1.66 % Allowed : 12.83 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.15), residues: 2831 helix: 2.49 (0.20), residues: 673 sheet: 0.65 (0.20), residues: 611 loop : -0.86 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 319 TYR 0.019 0.001 TYR A1067 PHE 0.020 0.001 PHE A 192 TRP 0.016 0.001 TRP B 633 HIS 0.002 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00258 (23509) covalent geometry : angle 0.50220 (31975) SS BOND : bond 0.00185 ( 34) SS BOND : angle 1.46843 ( 68) hydrogen bonds : bond 0.04771 ( 951) hydrogen bonds : angle 5.10665 ( 2652) link_NAG-ASN : bond 0.00182 ( 23) link_NAG-ASN : angle 1.75760 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6630 (ptt90) cc_final: 0.6272 (ptp90) REVERT: A 271 GLN cc_start: 0.8024 (mt0) cc_final: 0.7541 (tt0) REVERT: A 357 ARG cc_start: 0.6989 (ttm-80) cc_final: 0.6347 (mtt180) REVERT: A 571 ASP cc_start: 0.7521 (t70) cc_final: 0.7219 (t70) REVERT: A 697 MET cc_start: 0.8982 (ptm) cc_final: 0.8687 (ptp) REVERT: A 1038 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8423 (mppt) REVERT: B 619 GLU cc_start: 0.7657 (mp0) cc_final: 0.7101 (mp0) REVERT: B 979 ASP cc_start: 0.7614 (m-30) cc_final: 0.7378 (m-30) REVERT: C 190 ARG cc_start: 0.6520 (mpt180) cc_final: 0.6056 (mmp80) REVERT: C 237 ARG cc_start: 0.6885 (ptm160) cc_final: 0.6370 (ttm-80) REVERT: C 745 ASP cc_start: 0.8003 (m-30) cc_final: 0.7677 (t0) REVERT: C 814 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7753 (mptt) REVERT: C 900 MET cc_start: 0.9227 (mtm) cc_final: 0.8964 (ttm) outliers start: 42 outliers final: 27 residues processed: 213 average time/residue: 0.5486 time to fit residues: 135.8580 Evaluate side-chains 210 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 203 optimal weight: 9.9990 chunk 162 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 53 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN A1002 GLN B 87 ASN B 314 GLN B 957 GLN C 239 GLN C 314 GLN C 321 GLN C 957 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.191678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126585 restraints weight = 27755.121| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.34 r_work: 0.3189 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23566 Z= 0.109 Angle : 0.502 7.892 32112 Z= 0.263 Chirality : 0.043 0.164 3710 Planarity : 0.004 0.042 4074 Dihedral : 4.873 59.801 3582 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.72 % Favored : 97.21 % Rotamer: Outliers : 1.54 % Allowed : 12.95 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 2831 helix: 2.68 (0.20), residues: 664 sheet: 0.64 (0.20), residues: 623 loop : -0.77 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 319 TYR 0.019 0.001 TYR A1067 PHE 0.025 0.001 PHE A 92 TRP 0.018 0.001 TRP B 633 HIS 0.002 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00246 (23509) covalent geometry : angle 0.49357 (31975) SS BOND : bond 0.00170 ( 34) SS BOND : angle 1.30353 ( 68) hydrogen bonds : bond 0.04560 ( 951) hydrogen bonds : angle 5.00635 ( 2652) link_NAG-ASN : bond 0.00172 ( 23) link_NAG-ASN : angle 1.66188 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.6722 (mttp) cc_final: 0.6336 (mmtp) REVERT: A 237 ARG cc_start: 0.6616 (ptt90) cc_final: 0.5688 (ttt90) REVERT: A 271 GLN cc_start: 0.8043 (mt0) cc_final: 0.7529 (tt0) REVERT: A 357 ARG cc_start: 0.7028 (ttm-80) cc_final: 0.6376 (mtt180) REVERT: A 571 ASP cc_start: 0.7631 (t70) cc_final: 0.7281 (t70) REVERT: A 697 MET cc_start: 0.8986 (ptm) cc_final: 0.8687 (ptp) REVERT: A 1038 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8465 (mppt) REVERT: B 619 GLU cc_start: 0.7670 (mp0) cc_final: 0.7167 (mp0) REVERT: B 979 ASP cc_start: 0.7580 (m-30) cc_final: 0.7363 (m-30) REVERT: C 190 ARG cc_start: 0.6409 (mpt180) cc_final: 0.5949 (mmp80) REVERT: C 237 ARG cc_start: 0.6897 (ptm160) cc_final: 0.6363 (ttm-80) REVERT: C 745 ASP cc_start: 0.7984 (m-30) cc_final: 0.7663 (OUTLIER) REVERT: C 814 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7904 (mptt) REVERT: C 900 MET cc_start: 0.9234 (mtm) cc_final: 0.8968 (ttm) outliers start: 39 outliers final: 28 residues processed: 215 average time/residue: 0.5613 time to fit residues: 139.8050 Evaluate side-chains 219 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 210 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 233 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 153 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 186 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A1002 GLN B 87 ASN B 314 GLN B 957 GLN C 314 GLN C 321 GLN C 613 GLN C 957 GLN C1142 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.192134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126036 restraints weight = 27749.760| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.36 r_work: 0.3202 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23566 Z= 0.103 Angle : 0.496 8.113 32112 Z= 0.259 Chirality : 0.043 0.164 3710 Planarity : 0.004 0.042 4074 Dihedral : 4.796 57.221 3582 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.24 % Rotamer: Outliers : 1.23 % Allowed : 13.46 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2831 helix: 2.75 (0.20), residues: 664 sheet: 0.62 (0.20), residues: 627 loop : -0.69 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 319 TYR 0.019 0.001 TYR A1067 PHE 0.019 0.001 PHE A 192 TRP 0.018 0.001 TRP B 633 HIS 0.002 0.000 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00230 (23509) covalent geometry : angle 0.48833 (31975) SS BOND : bond 0.00178 ( 34) SS BOND : angle 1.24324 ( 68) hydrogen bonds : bond 0.04425 ( 951) hydrogen bonds : angle 4.94822 ( 2652) link_NAG-ASN : bond 0.00176 ( 23) link_NAG-ASN : angle 1.61614 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9616.39 seconds wall clock time: 163 minutes 52.54 seconds (9832.54 seconds total)