Starting phenix.real_space_refine on Fri Feb 6 16:42:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9loy_63263/02_2026/9loy_63263_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9loy_63263/02_2026/9loy_63263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9loy_63263/02_2026/9loy_63263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9loy_63263/02_2026/9loy_63263.map" model { file = "/net/cci-nas-00/data/ceres_data/9loy_63263/02_2026/9loy_63263_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9loy_63263/02_2026/9loy_63263_neut.cif" } resolution = 2.66 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= -0.001 sd= 0.068 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 113 5.16 5 C 16607 2.51 5 N 4270 2.21 5 O 4981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25971 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7884 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 55, 'TRANS': 946} Chain breaks: 11 Chain: "B" Number of atoms: 6375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6375 Classifications: {'peptide': 818} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 41, 'TRANS': 776} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 8006 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 55, 'TRANS': 965} Chain breaks: 8 Chain: "E" 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: "F" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 764 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 91} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Restraints were copied for chains: H, I Time building chain proxies: 5.93, per 1000 atoms: 0.23 Number of scatterers: 25971 At special positions: 0 Unit cell: (143.56, 125.13, 222.13, 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 113 16.00 O 4981 8.00 N 4270 7.00 C 16607 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 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 E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 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 709 " " NAG A1303 " - " ASN A 717 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1098 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 354 " " NAG A1309 " - " ASN A 616 " " 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 343 " " NAG C1309 " - " ASN C 354 " Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 995.3 milliseconds 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6100 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 57 sheets defined 23.0% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 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 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.841A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.596A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.201A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.077A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.762A 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 919 removed outlier: 4.004A 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 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.723A 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: 4.130A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 624 removed outlier: 3.698A pdb=" N VAL B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.868A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.760A 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 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.976A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.583A 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: 4.682A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.842A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.596A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.201A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 638 through 640 No H-bonds generated for 'chain 'C' and resid 638 through 640' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.893A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.738A 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 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.664A 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: 4.178A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.740A pdb=" N LYS E 64 " --> pdb=" O ASP E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.741A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'I' and resid 28 through 31 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 3.561A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 6.836A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 172 removed outlier: 4.084A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.466A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.497A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.461A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N LYS A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.461A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N LYS A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.034A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 689 " --> pdb=" O GLN A 677 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.769A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.769A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.462A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.708A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.560A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 30 Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.439A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.879A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 224 through 230 removed outlier: 5.534A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 171 through 172 removed outlier: 3.643A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.868A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC7, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.090A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.931A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.931A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.550A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.698A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 30 removed outlier: 7.883A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.936A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.843A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.021A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.858A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.461A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N LYS C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.461A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N LYS C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.102A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.796A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.796A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.459A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.618A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.563A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL E 5 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP E 72 " --> pdb=" O THR E 77 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.595A pdb=" N THR E 111 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR E 93 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.595A pdb=" N THR E 111 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR E 93 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS E 95 " --> pdb=" O TRP E 107 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TRP E 107 " --> pdb=" O CYS E 95 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG E 97 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR E 103 " --> pdb=" O TYR E 99 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 8 through 11 removed outlier: 6.391A pdb=" N TRP F 34 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 8 through 11 removed outlier: 3.548A pdb=" N HIS F 89 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 96 " --> pdb=" O HIS F 89 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 17 through 22 removed outlier: 3.608A pdb=" N ASP F 69 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.562A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL H 5 " --> pdb=" O GLU H 23 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.595A pdb=" N THR H 111 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR H 93 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.595A pdb=" N THR H 111 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR H 93 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS H 95 " --> pdb=" O TRP H 107 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP H 107 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG H 97 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR H 103 " --> pdb=" O TYR H 99 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 8 through 11 removed outlier: 6.391A pdb=" N TRP I 34 " --> pdb=" O LEU I 46 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 8 through 11 removed outlier: 3.548A pdb=" N HIS I 89 " --> pdb=" O THR I 96 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR I 96 " --> pdb=" O HIS I 89 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 17 through 22 removed outlier: 3.607A pdb=" N ASP I 69 " --> pdb=" O SER I 66 " (cutoff:3.500A) 1071 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.36 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 4193 1.27 - 1.41: 6963 1.41 - 1.56: 15274 1.56 - 1.70: 2 1.70 - 1.84: 145 Bond restraints: 26577 Sorted by residual: bond pdb=" C PRO B 899 " pdb=" O PRO B 899 " ideal model delta sigma weight residual 1.237 1.131 0.106 1.26e-02 6.30e+03 7.09e+01 bond pdb=" C PRO B 295 " pdb=" O PRO B 295 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.26e-02 6.30e+03 3.94e+01 bond pdb=" C TYR B 313 " pdb=" O TYR B 313 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.14e-02 7.69e+03 2.87e+01 bond pdb=" C PRO C 295 " pdb=" O PRO C 295 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.26e-02 6.30e+03 2.36e+01 bond pdb=" C TYR C 313 " pdb=" O TYR C 313 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.14e-02 7.69e+03 2.35e+01 ... (remaining 26572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 35577 3.61 - 7.22: 526 7.22 - 10.84: 38 10.84 - 14.45: 7 14.45 - 18.06: 1 Bond angle restraints: 36149 Sorted by residual: angle pdb=" N PRO A 631 " pdb=" CA PRO A 631 " pdb=" C PRO A 631 " ideal model delta sigma weight residual 113.47 131.53 -18.06 1.43e+00 4.89e-01 1.59e+02 angle pdb=" N PRO C 631 " pdb=" CA PRO C 631 " pdb=" C PRO C 631 " ideal model delta sigma weight residual 113.53 101.56 11.97 1.39e+00 5.18e-01 7.41e+01 angle pdb=" C VAL C 83 " pdb=" N LEU C 84 " pdb=" CA LEU C 84 " ideal model delta sigma weight residual 120.68 133.06 -12.38 1.52e+00 4.33e-01 6.63e+01 angle pdb=" C ASN A 641 " pdb=" CA ASN A 641 " pdb=" CB ASN A 641 " ideal model delta sigma weight residual 110.85 123.46 -12.61 1.70e+00 3.46e-01 5.50e+01 angle pdb=" C VAL A 635 " pdb=" N TYR A 636 " pdb=" CA TYR A 636 " ideal model delta sigma weight residual 123.05 112.76 10.29 1.40e+00 5.10e-01 5.40e+01 ... (remaining 36144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14872 17.97 - 35.93: 976 35.93 - 53.90: 190 53.90 - 71.87: 46 71.87 - 89.83: 23 Dihedral angle restraints: 16107 sinusoidal: 6612 harmonic: 9495 Sorted by residual: dihedral pdb=" C ASN A 641 " pdb=" N ASN A 641 " pdb=" CA ASN A 641 " pdb=" CB ASN A 641 " ideal model delta harmonic sigma weight residual -122.60 -147.52 24.92 0 2.50e+00 1.60e-01 9.94e+01 dihedral pdb=" N ASN A 641 " pdb=" C ASN A 641 " pdb=" CA ASN A 641 " pdb=" CB ASN A 641 " ideal model delta harmonic sigma weight residual 122.80 143.13 -20.33 0 2.50e+00 1.60e-01 6.61e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -17.22 -68.78 1 1.00e+01 1.00e-02 6.12e+01 ... (remaining 16104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 4108 0.248 - 0.496: 38 0.496 - 0.743: 6 0.743 - 0.991: 1 0.991 - 1.239: 2 Chirality restraints: 4155 Sorted by residual: chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.16 -1.24 2.00e-01 2.50e+01 3.84e+01 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.16 -1.24 2.00e-01 2.50e+01 3.82e+01 chirality pdb=" CA ASN A 641 " pdb=" N ASN A 641 " pdb=" C ASN A 641 " pdb=" CB ASN A 641 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.24e+01 ... (remaining 4152 not shown) Planarity restraints: 4649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1302 " -0.335 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG C1302 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG C1302 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG C1302 " 0.506 2.00e-02 2.50e+03 pdb=" O7 NAG C1302 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1308 " 0.313 2.00e-02 2.50e+03 2.74e-01 9.39e+02 pdb=" C7 NAG C1308 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C1308 " 0.098 2.00e-02 2.50e+03 pdb=" N2 NAG C1308 " -0.491 2.00e-02 2.50e+03 pdb=" O7 NAG C1308 " 0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " -0.313 2.00e-02 2.50e+03 2.74e-01 9.39e+02 pdb=" C7 NAG A1307 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " -0.098 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " 0.491 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " -0.149 2.00e-02 2.50e+03 ... (remaining 4646 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 283 2.63 - 3.20: 22359 3.20 - 3.77: 37317 3.77 - 4.33: 55547 4.33 - 4.90: 91999 Nonbonded interactions: 207505 Sorted by model distance: nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.063 3.040 nonbonded pdb=" O THR A 108 " pdb=" OG1 THR A 236 " model vdw 2.170 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE2 GLU C 191 " model vdw 2.179 3.040 nonbonded pdb=" OG SER H 17 " pdb=" O MET H 82 " model vdw 2.183 3.040 nonbonded pdb=" OG SER E 17 " pdb=" O MET E 82 " model vdw 2.183 3.040 ... (remaining 207500 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 143 or resid 163 through 177 or resid 187 throu \ gh 1309)) selection = (chain 'C' and (resid 28 through 65 or resid 84 through 95 or resid 100 through \ 108 or resid 117 through 177 or resid 187 through 210 or resid 216 through 242 o \ r resid 264 through 1309)) } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'I' } 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: 5.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 25.210 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 : 0.012 0.106 26641 Z= 0.570 Angle : 1.135 18.059 36302 Z= 0.698 Chirality : 0.082 1.239 4155 Planarity : 0.014 0.287 4624 Dihedral : 13.051 89.834 9890 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.73 % Rotamer: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 0.00 % 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: -1.10 (0.14), residues: 3207 helix: 0.88 (0.20), residues: 657 sheet: -0.45 (0.18), residues: 764 loop : -1.52 (0.13), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 273 TYR 0.035 0.003 TYR C 37 PHE 0.040 0.003 PHE A 855 TRP 0.103 0.004 TRP B 886 HIS 0.013 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01163 (26577) covalent geometry : angle 1.11534 (36149) SS BOND : bond 0.00678 ( 39) SS BOND : angle 1.61451 ( 78) hydrogen bonds : bond 0.20395 ( 1033) hydrogen bonds : angle 8.81844 ( 2910) link_NAG-ASN : bond 0.01067 ( 25) link_NAG-ASN : angle 4.63749 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1588 (mmt) cc_final: 0.0479 (mpt) REVERT: A 633 TRP cc_start: 0.6913 (m-10) cc_final: 0.6076 (m-10) REVERT: A 995 ARG cc_start: 0.7802 (mtp85) cc_final: 0.7373 (mtp-110) REVERT: B 629 LEU cc_start: 0.7867 (tp) cc_final: 0.7574 (tp) REVERT: B 751 ASN cc_start: 0.8482 (m110) cc_final: 0.8276 (m-40) REVERT: B 950 ASP cc_start: 0.7180 (m-30) cc_final: 0.6963 (m-30) REVERT: C 294 ASP cc_start: 0.8597 (p0) cc_final: 0.8379 (p0) REVERT: C 780 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7354 (pt0) REVERT: C 936 ASP cc_start: 0.6718 (m-30) cc_final: 0.6367 (m-30) outliers start: 1 outliers final: 1 residues processed: 229 average time/residue: 0.6274 time to fit residues: 167.1069 Evaluate side-chains 182 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 556 ASN A 580 GLN A 628 GLN A 751 ASN A 804 GLN B 165 ASN B 239 GLN B 321 GLN B 606 ASN B 751 ASN B 755 GLN B 901 GLN B 935 GLN B1101 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 564 GLN C 613 GLN C1101 HIS E 3 GLN H 3 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.213301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130278 restraints weight = 30925.789| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.46 r_work: 0.3123 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 26641 Z= 0.132 Angle : 0.586 10.061 36302 Z= 0.301 Chirality : 0.047 0.335 4155 Planarity : 0.004 0.059 4624 Dihedral : 6.653 58.962 4038 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.12 % Allowed : 5.78 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.14), residues: 3207 helix: 2.21 (0.20), residues: 653 sheet: 0.01 (0.17), residues: 788 loop : -1.08 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 31 TYR 0.019 0.001 TYR C 170 PHE 0.020 0.001 PHE C 855 TRP 0.022 0.001 TRP B 886 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00304 (26577) covalent geometry : angle 0.57301 (36149) SS BOND : bond 0.00225 ( 39) SS BOND : angle 0.96380 ( 78) hydrogen bonds : bond 0.05164 ( 1033) hydrogen bonds : angle 6.00277 ( 2910) link_NAG-ASN : bond 0.00701 ( 25) link_NAG-ASN : angle 2.67643 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 634 ARG cc_start: 0.5837 (OUTLIER) cc_final: 0.5620 (tmt170) REVERT: B 755 GLN cc_start: 0.7764 (mt0) cc_final: 0.7176 (mp-120) REVERT: B 765 ARG cc_start: 0.8398 (ptm-80) cc_final: 0.8036 (ptp90) REVERT: B 821 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8259 (tp) REVERT: B 935 GLN cc_start: 0.7866 (tt0) cc_final: 0.7535 (tt0) REVERT: B 950 ASP cc_start: 0.7633 (m-30) cc_final: 0.7378 (m-30) REVERT: B 984 LEU cc_start: 0.6397 (tt) cc_final: 0.6092 (tt) REVERT: C 52 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7797 (tm130) REVERT: C 65 PHE cc_start: 0.8106 (m-80) cc_final: 0.7849 (m-80) REVERT: C 319 ARG cc_start: 0.8148 (mmm160) cc_final: 0.7687 (mmm-85) REVERT: C 675 GLN cc_start: 0.7329 (mt0) cc_final: 0.6945 (pt0) REVERT: C 751 ASN cc_start: 0.8306 (m110) cc_final: 0.8006 (m-40) REVERT: C 776 LYS cc_start: 0.9155 (tttp) cc_final: 0.8829 (ttmp) REVERT: C 780 GLU cc_start: 0.8585 (mt-10) cc_final: 0.7924 (pt0) REVERT: C 787 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8154 (mt0) REVERT: E 82 MET cc_start: -0.2445 (mtm) cc_final: -0.2683 (tpt) outliers start: 32 outliers final: 11 residues processed: 213 average time/residue: 0.5983 time to fit residues: 148.6071 Evaluate side-chains 180 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 84 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 142 optimal weight: 0.9980 chunk 294 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 213 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 195 optimal weight: 0.3980 chunk 310 optimal weight: 20.0000 chunk 131 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A 804 GLN A 955 ASN B 239 GLN B 628 GLN B 751 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.213024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131564 restraints weight = 31062.384| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.39 r_work: 0.3154 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26641 Z= 0.129 Angle : 0.533 7.408 36302 Z= 0.276 Chirality : 0.045 0.262 4155 Planarity : 0.004 0.051 4624 Dihedral : 5.990 59.546 4038 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.37 % Allowed : 8.38 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.14), residues: 3207 helix: 2.54 (0.20), residues: 654 sheet: 0.15 (0.17), residues: 801 loop : -0.96 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 31 TYR 0.019 0.001 TYR A1067 PHE 0.017 0.001 PHE C 855 TRP 0.015 0.001 TRP C 633 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00303 (26577) covalent geometry : angle 0.52340 (36149) SS BOND : bond 0.00264 ( 39) SS BOND : angle 0.86799 ( 78) hydrogen bonds : bond 0.04900 ( 1033) hydrogen bonds : angle 5.52517 ( 2910) link_NAG-ASN : bond 0.00283 ( 25) link_NAG-ASN : angle 2.12939 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8012 (mtp180) REVERT: B 619 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7237 (tp30) REVERT: B 634 ARG cc_start: 0.5738 (OUTLIER) cc_final: 0.5528 (tmt170) REVERT: B 765 ARG cc_start: 0.8333 (ptm-80) cc_final: 0.8020 (ptp90) REVERT: B 821 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8237 (tp) REVERT: B 935 GLN cc_start: 0.7703 (tt0) cc_final: 0.7269 (tp-100) REVERT: B 950 ASP cc_start: 0.7557 (m-30) cc_final: 0.7298 (m-30) REVERT: C 52 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7646 (tm130) REVERT: C 65 PHE cc_start: 0.8146 (m-80) cc_final: 0.7784 (m-80) REVERT: C 319 ARG cc_start: 0.8214 (mmm160) cc_final: 0.7751 (mmm-85) REVERT: C 751 ASN cc_start: 0.8246 (m110) cc_final: 0.7990 (m110) REVERT: C 780 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7976 (pt0) REVERT: C 983 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7439 (ptp90) outliers start: 39 outliers final: 18 residues processed: 206 average time/residue: 0.6453 time to fit residues: 155.7019 Evaluate side-chains 191 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain H residue 78 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 28 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 275 optimal weight: 2.9990 chunk 315 optimal weight: 3.9990 chunk 294 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 556 ASN B 317 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 239 GLN C 580 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.212981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129676 restraints weight = 31044.518| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.94 r_work: 0.3124 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26641 Z= 0.129 Angle : 0.521 9.532 36302 Z= 0.269 Chirality : 0.045 0.319 4155 Planarity : 0.004 0.046 4624 Dihedral : 5.858 59.172 4038 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.47 % Allowed : 9.57 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.14), residues: 3207 helix: 2.70 (0.20), residues: 647 sheet: 0.25 (0.17), residues: 821 loop : -0.87 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 273 TYR 0.018 0.001 TYR A1067 PHE 0.016 0.001 PHE C 855 TRP 0.014 0.001 TRP C 633 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00306 (26577) covalent geometry : angle 0.51343 (36149) SS BOND : bond 0.00243 ( 39) SS BOND : angle 0.83163 ( 78) hydrogen bonds : bond 0.04709 ( 1033) hydrogen bonds : angle 5.35303 ( 2910) link_NAG-ASN : bond 0.00222 ( 25) link_NAG-ASN : angle 1.94060 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.8483 (m-30) cc_final: 0.8221 (m-30) REVERT: A 646 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8072 (mtp180) REVERT: A 1038 LYS cc_start: 0.9212 (mmmt) cc_final: 0.8611 (mmtm) REVERT: B 619 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7154 (tp30) REVERT: B 765 ARG cc_start: 0.8339 (ptm-80) cc_final: 0.7978 (ptp90) REVERT: B 821 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8192 (tp) REVERT: B 935 GLN cc_start: 0.7625 (tt0) cc_final: 0.7169 (tp-100) REVERT: B 950 ASP cc_start: 0.7578 (m-30) cc_final: 0.7356 (m-30) REVERT: C 52 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7811 (tm130) REVERT: C 65 PHE cc_start: 0.8038 (m-80) cc_final: 0.7607 (m-80) REVERT: C 776 LYS cc_start: 0.9116 (tttt) cc_final: 0.8610 (ttmm) REVERT: C 780 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7823 (pt0) REVERT: C 787 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8137 (mt0) REVERT: C 791 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8502 (p) outliers start: 42 outliers final: 18 residues processed: 206 average time/residue: 0.6299 time to fit residues: 152.5994 Evaluate side-chains 192 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 131 optimal weight: 0.7980 chunk 300 optimal weight: 4.9990 chunk 262 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 287 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 235 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN B 762 GLN C 196 ASN C 207 HIS C 751 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.213220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.130225 restraints weight = 30800.431| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.20 r_work: 0.3132 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26641 Z= 0.116 Angle : 0.510 10.677 36302 Z= 0.262 Chirality : 0.044 0.346 4155 Planarity : 0.004 0.044 4624 Dihedral : 5.747 58.740 4038 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.47 % Allowed : 10.09 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.15), residues: 3207 helix: 2.78 (0.20), residues: 647 sheet: 0.26 (0.17), residues: 831 loop : -0.81 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.017 0.001 TYR A1067 PHE 0.015 0.001 PHE C 855 TRP 0.014 0.001 TRP C 633 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00273 (26577) covalent geometry : angle 0.50307 (36149) SS BOND : bond 0.00226 ( 39) SS BOND : angle 0.78753 ( 78) hydrogen bonds : bond 0.04509 ( 1033) hydrogen bonds : angle 5.24440 ( 2910) link_NAG-ASN : bond 0.00218 ( 25) link_NAG-ASN : angle 1.87279 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.8516 (m-30) cc_final: 0.8263 (m-30) REVERT: A 646 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8126 (mtp180) REVERT: A 1038 LYS cc_start: 0.9245 (mmmt) cc_final: 0.8654 (mmtm) REVERT: B 619 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7168 (tp30) REVERT: B 752 LEU cc_start: 0.8354 (mt) cc_final: 0.7764 (tp) REVERT: B 765 ARG cc_start: 0.8412 (ptm-80) cc_final: 0.8067 (ptp90) REVERT: B 821 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8256 (tp) REVERT: B 935 GLN cc_start: 0.7648 (tt0) cc_final: 0.7215 (tp-100) REVERT: B 950 ASP cc_start: 0.7661 (m-30) cc_final: 0.7450 (m-30) REVERT: C 52 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7798 (tm130) REVERT: C 65 PHE cc_start: 0.8066 (m-80) cc_final: 0.7587 (m-80) REVERT: C 239 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8056 (pt0) REVERT: C 567 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7781 (mtm180) REVERT: C 675 GLN cc_start: 0.7420 (mt0) cc_final: 0.6972 (pt0) REVERT: C 776 LYS cc_start: 0.9161 (tttt) cc_final: 0.8678 (ttmm) REVERT: C 780 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7867 (pt0) REVERT: C 787 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8145 (mt0) outliers start: 42 outliers final: 25 residues processed: 205 average time/residue: 0.6169 time to fit residues: 148.9867 Evaluate side-chains 206 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 787 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 247 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 271 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 313 optimal weight: 30.0000 overall best weight: 1.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A 710 ASN C 207 HIS C 239 GLN C 751 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.211597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128752 restraints weight = 30820.765| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.90 r_work: 0.3114 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26641 Z= 0.179 Angle : 0.560 11.183 36302 Z= 0.289 Chirality : 0.046 0.385 4155 Planarity : 0.004 0.042 4624 Dihedral : 5.971 59.940 4038 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.47 % Allowed : 10.69 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.14), residues: 3207 helix: 2.69 (0.20), residues: 638 sheet: 0.21 (0.17), residues: 842 loop : -0.83 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.019 0.001 TYR C1067 PHE 0.020 0.002 PHE A 855 TRP 0.014 0.001 TRP C 633 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00436 (26577) covalent geometry : angle 0.55202 (36149) SS BOND : bond 0.00323 ( 39) SS BOND : angle 0.92861 ( 78) hydrogen bonds : bond 0.05339 ( 1033) hydrogen bonds : angle 5.39902 ( 2910) link_NAG-ASN : bond 0.00242 ( 25) link_NAG-ASN : angle 2.01574 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.8422 (m-30) cc_final: 0.8162 (m-30) REVERT: A 646 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8076 (mtp180) REVERT: B 765 ARG cc_start: 0.8387 (ptm-80) cc_final: 0.8033 (ptp90) REVERT: B 821 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8202 (tp) REVERT: B 935 GLN cc_start: 0.7703 (tt0) cc_final: 0.7236 (tp-100) REVERT: B 950 ASP cc_start: 0.7588 (m-30) cc_final: 0.7322 (m-30) REVERT: B 976 VAL cc_start: 0.7576 (OUTLIER) cc_final: 0.7371 (m) REVERT: C 52 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7850 (tm130) REVERT: C 65 PHE cc_start: 0.8035 (m-80) cc_final: 0.7576 (m-80) REVERT: C 329 PHE cc_start: 0.7406 (m-80) cc_final: 0.7159 (m-80) REVERT: C 567 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7909 (mtt180) REVERT: C 780 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7890 (pt0) REVERT: C 787 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8144 (mt0) outliers start: 42 outliers final: 30 residues processed: 202 average time/residue: 0.6237 time to fit residues: 147.9576 Evaluate side-chains 200 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain E residue 82 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 202 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 291 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 30.0000 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 285 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 288 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A 628 GLN B 165 ASN C 207 HIS C 321 GLN C 580 GLN C 603 ASN C 613 GLN C1106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.210803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126704 restraints weight = 31223.452| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.15 r_work: 0.3136 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 26641 Z= 0.258 Angle : 0.626 9.187 36302 Z= 0.324 Chirality : 0.049 0.355 4155 Planarity : 0.005 0.044 4624 Dihedral : 6.225 59.825 4038 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.89 % Allowed : 10.83 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3207 helix: 2.42 (0.21), residues: 636 sheet: 0.16 (0.17), residues: 801 loop : -0.96 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 319 TYR 0.021 0.002 TYR B1067 PHE 0.024 0.002 PHE A 855 TRP 0.013 0.002 TRP C 633 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00636 (26577) covalent geometry : angle 0.61654 (36149) SS BOND : bond 0.00444 ( 39) SS BOND : angle 1.10792 ( 78) hydrogen bonds : bond 0.06157 ( 1033) hydrogen bonds : angle 5.61321 ( 2910) link_NAG-ASN : bond 0.00316 ( 25) link_NAG-ASN : angle 2.23768 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8146 (mtp180) REVERT: B 539 VAL cc_start: 0.8099 (p) cc_final: 0.7813 (m) REVERT: B 675 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7000 (mp10) REVERT: B 765 ARG cc_start: 0.8503 (ptm-80) cc_final: 0.8172 (ptp90) REVERT: B 821 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8366 (tp) REVERT: B 950 ASP cc_start: 0.7714 (m-30) cc_final: 0.7437 (m-30) REVERT: B 976 VAL cc_start: 0.7811 (OUTLIER) cc_final: 0.7606 (m) REVERT: C 52 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7844 (tm130) REVERT: C 65 PHE cc_start: 0.8129 (m-80) cc_final: 0.7690 (m-80) REVERT: C 196 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.8025 (m110) REVERT: C 567 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7975 (mtt180) REVERT: C 780 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8038 (pt0) REVERT: C 787 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8310 (mt0) REVERT: C 936 ASP cc_start: 0.6558 (m-30) cc_final: 0.6139 (m-30) outliers start: 54 outliers final: 30 residues processed: 216 average time/residue: 0.5695 time to fit residues: 145.4417 Evaluate side-chains 205 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain E residue 82 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 93 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 216 optimal weight: 0.0570 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 196 optimal weight: 0.0980 chunk 41 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 233 optimal weight: 0.4980 chunk 188 optimal weight: 7.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A 751 ASN A 955 ASN B 165 ASN B 544 ASN B 613 GLN C 207 HIS C 613 GLN C 751 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.214885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130768 restraints weight = 31589.102| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.57 r_work: 0.3215 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 26641 Z= 0.095 Angle : 0.500 12.594 36302 Z= 0.257 Chirality : 0.044 0.381 4155 Planarity : 0.004 0.041 4624 Dihedral : 5.614 56.917 4038 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.16 % Allowed : 11.88 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3207 helix: 2.86 (0.20), residues: 640 sheet: 0.37 (0.18), residues: 797 loop : -0.77 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 97 TYR 0.016 0.001 TYR A1067 PHE 0.021 0.001 PHE C 855 TRP 0.019 0.001 TRP C 633 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00210 (26577) covalent geometry : angle 0.49336 (36149) SS BOND : bond 0.00267 ( 39) SS BOND : angle 0.83359 ( 78) hydrogen bonds : bond 0.03926 ( 1033) hydrogen bonds : angle 5.04823 ( 2910) link_NAG-ASN : bond 0.00209 ( 25) link_NAG-ASN : angle 1.68280 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7939 (tm-30) REVERT: A 586 ASP cc_start: 0.8544 (m-30) cc_final: 0.8290 (m-30) REVERT: B 675 GLN cc_start: 0.8140 (tp40) cc_final: 0.7561 (mp10) REVERT: B 752 LEU cc_start: 0.8266 (mt) cc_final: 0.7772 (tp) REVERT: B 765 ARG cc_start: 0.8280 (ptm-80) cc_final: 0.7959 (ptp90) REVERT: B 821 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8161 (tp) REVERT: B 935 GLN cc_start: 0.7703 (tt0) cc_final: 0.7165 (tp-100) REVERT: C 52 GLN cc_start: 0.8774 (tm130) cc_final: 0.8259 (tm-30) REVERT: C 65 PHE cc_start: 0.8098 (m-80) cc_final: 0.7655 (m-80) REVERT: C 309 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8082 (mm-30) REVERT: C 534 VAL cc_start: 0.8573 (t) cc_final: 0.8342 (t) REVERT: C 630 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.7253 (t) REVERT: C 675 GLN cc_start: 0.7274 (mt0) cc_final: 0.7015 (pt0) REVERT: C 776 LYS cc_start: 0.9088 (tttt) cc_final: 0.8591 (ttmm) REVERT: C 780 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7842 (pt0) outliers start: 33 outliers final: 19 residues processed: 211 average time/residue: 0.5697 time to fit residues: 142.3607 Evaluate side-chains 192 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain E residue 82 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 129 optimal weight: 1.9990 chunk 315 optimal weight: 6.9990 chunk 221 optimal weight: 30.0000 chunk 27 optimal weight: 20.0000 chunk 153 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 20.0000 chunk 223 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN B 165 ASN B 613 GLN B 628 GLN B 762 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.212176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132402 restraints weight = 31307.936| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.76 r_work: 0.3157 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26641 Z= 0.176 Angle : 0.557 12.517 36302 Z= 0.286 Chirality : 0.046 0.393 4155 Planarity : 0.004 0.041 4624 Dihedral : 5.802 58.754 4038 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.23 % Allowed : 12.09 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.15), residues: 3207 helix: 2.73 (0.20), residues: 641 sheet: 0.32 (0.17), residues: 826 loop : -0.83 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.018 0.001 TYR B1067 PHE 0.018 0.002 PHE A 855 TRP 0.014 0.001 TRP C 633 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00432 (26577) covalent geometry : angle 0.54935 (36149) SS BOND : bond 0.00316 ( 39) SS BOND : angle 1.00638 ( 78) hydrogen bonds : bond 0.05201 ( 1033) hydrogen bonds : angle 5.30779 ( 2910) link_NAG-ASN : bond 0.00234 ( 25) link_NAG-ASN : angle 1.90841 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.8481 (m-30) cc_final: 0.8238 (m-30) REVERT: B 765 ARG cc_start: 0.8444 (ptm-80) cc_final: 0.8081 (ptp90) REVERT: B 976 VAL cc_start: 0.7534 (t) cc_final: 0.7316 (m) REVERT: C 52 GLN cc_start: 0.8754 (tm130) cc_final: 0.8235 (tm-30) REVERT: C 65 PHE cc_start: 0.8086 (m-80) cc_final: 0.7519 (m-80) REVERT: C 196 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7996 (m110) REVERT: C 534 VAL cc_start: 0.8572 (t) cc_final: 0.8323 (t) REVERT: C 675 GLN cc_start: 0.7565 (mt0) cc_final: 0.7071 (pt0) REVERT: C 780 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7948 (pt0) outliers start: 35 outliers final: 24 residues processed: 192 average time/residue: 0.5699 time to fit residues: 128.4843 Evaluate side-chains 192 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain E residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 111 optimal weight: 10.0000 chunk 312 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 288 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 313 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN B 628 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.212939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.131904 restraints weight = 31184.383| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.33 r_work: 0.3191 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26641 Z= 0.131 Angle : 0.524 11.901 36302 Z= 0.269 Chirality : 0.045 0.369 4155 Planarity : 0.004 0.041 4624 Dihedral : 5.693 57.465 4038 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.09 % Allowed : 12.37 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.15), residues: 3207 helix: 2.80 (0.20), residues: 641 sheet: 0.36 (0.17), residues: 821 loop : -0.78 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.017 0.001 TYR A1067 PHE 0.019 0.001 PHE C 855 TRP 0.015 0.001 TRP C 633 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00314 (26577) covalent geometry : angle 0.51690 (36149) SS BOND : bond 0.00250 ( 39) SS BOND : angle 0.93790 ( 78) hydrogen bonds : bond 0.04680 ( 1033) hydrogen bonds : angle 5.17390 ( 2910) link_NAG-ASN : bond 0.00202 ( 25) link_NAG-ASN : angle 1.81104 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.8468 (m-30) cc_final: 0.8234 (m-30) REVERT: B 752 LEU cc_start: 0.8327 (mt) cc_final: 0.7751 (tp) REVERT: B 765 ARG cc_start: 0.8415 (ptm-80) cc_final: 0.8068 (ptp90) REVERT: C 52 GLN cc_start: 0.8754 (tm130) cc_final: 0.8250 (tm-30) REVERT: C 65 PHE cc_start: 0.8108 (m-80) cc_final: 0.7668 (m-80) REVERT: C 196 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7958 (m110) REVERT: C 234 ASN cc_start: 0.7143 (t0) cc_final: 0.6724 (m110) REVERT: C 534 VAL cc_start: 0.8564 (t) cc_final: 0.8329 (t) REVERT: C 675 GLN cc_start: 0.7545 (mt0) cc_final: 0.7055 (pt0) REVERT: C 780 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7907 (pt0) outliers start: 31 outliers final: 23 residues processed: 188 average time/residue: 0.5785 time to fit residues: 128.0045 Evaluate side-chains 190 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain H residue 84 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 288 optimal weight: 5.9990 chunk 279 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 229 optimal weight: 0.0010 chunk 182 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 40.0000 chunk 18 optimal weight: 0.1980 chunk 149 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN B 165 ASN B 628 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.214614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.131875 restraints weight = 31355.727| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.65 r_work: 0.3185 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26641 Z= 0.095 Angle : 0.488 11.254 36302 Z= 0.251 Chirality : 0.043 0.343 4155 Planarity : 0.004 0.041 4624 Dihedral : 5.434 54.999 4038 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.91 % Allowed : 12.51 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.15), residues: 3207 helix: 3.03 (0.20), residues: 640 sheet: 0.45 (0.17), residues: 833 loop : -0.68 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.017 0.001 TYR A1067 PHE 0.019 0.001 PHE C 855 TRP 0.018 0.001 TRP C 633 HIS 0.003 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00218 (26577) covalent geometry : angle 0.48201 (36149) SS BOND : bond 0.00201 ( 39) SS BOND : angle 0.83772 ( 78) hydrogen bonds : bond 0.03913 ( 1033) hydrogen bonds : angle 4.92176 ( 2910) link_NAG-ASN : bond 0.00200 ( 25) link_NAG-ASN : angle 1.60308 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13152.91 seconds wall clock time: 223 minutes 40.17 seconds (13420.17 seconds total)