Starting phenix.real_space_refine on Thu Mar 5 16:31:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lyp_23598/03_2026/7lyp_23598.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lyp_23598/03_2026/7lyp_23598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lyp_23598/03_2026/7lyp_23598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lyp_23598/03_2026/7lyp_23598.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lyp_23598/03_2026/7lyp_23598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lyp_23598/03_2026/7lyp_23598.map" } resolution = 4.05 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= 0.034 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 102 5.16 5 C 15020 2.51 5 N 3878 2.21 5 O 4504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23504 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7717 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 47, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7712 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 47, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 7683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7683 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 47, 'TRANS': 945} Chain breaks: 7 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.19, per 1000 atoms: 0.22 Number of scatterers: 23504 At special positions: 0 Unit cell: (129.349, 137.901, 192.42, 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 102 16.00 O 4504 8.00 N 3878 7.00 C 15020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 616 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 873.5 milliseconds 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 45 sheets defined 27.7% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.505A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.424A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.322A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.673A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.868A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.695A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.890A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.597A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.998A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.006A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.767A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.941A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.276A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.149A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.603A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.508A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.715A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.820A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) 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 966 removed outlier: 3.831A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.876A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.791A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 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 370 removed outlier: 3.749A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.349A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.723A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 757 removed outlier: 3.654A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 754 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.995A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.250A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.521A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.577A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.524A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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 Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.714A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N PHE A 220 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG A 34 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N LEU A 223 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.606A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.582A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.011A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.422A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.074A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (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: 6.713A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.097A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.553A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.795A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.902A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.339A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.343A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.620A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.509A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.155A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.852A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.852A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.995A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.855A 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: 3.696A 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 Processing sheet with id=AD8, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.462A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.025A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.025A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.821A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (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 656 removed outlier: 4.356A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.513A 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: 6.630A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.518A 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: 6.630A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.710A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 2814 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: 5.10 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6097 1.33 - 1.45: 4672 1.45 - 1.58: 13128 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 24023 Sorted by residual: bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 24018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 23917 1.87 - 3.74: 7709 3.74 - 5.61: 965 5.61 - 7.48: 100 7.48 - 9.35: 10 Bond angle restraints: 32701 Sorted by residual: angle pdb=" CA PHE C 456 " pdb=" CB PHE C 456 " pdb=" CG PHE C 456 " ideal model delta sigma weight residual 113.80 119.86 -6.06 1.00e+00 1.00e+00 3.67e+01 angle pdb=" CA PHE A 456 " pdb=" CB PHE A 456 " pdb=" CG PHE A 456 " ideal model delta sigma weight residual 113.80 119.73 -5.93 1.00e+00 1.00e+00 3.52e+01 angle pdb=" CA ASP A 571 " pdb=" CB ASP A 571 " pdb=" CG ASP A 571 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" CA ASP B 427 " pdb=" CB ASP B 427 " pdb=" CG ASP B 427 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.11e+01 angle pdb=" N ASN C 709 " pdb=" CA ASN C 709 " pdb=" C ASN C 709 " ideal model delta sigma weight residual 112.87 119.33 -6.46 1.20e+00 6.94e-01 2.90e+01 ... (remaining 32696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 13506 17.65 - 35.30: 915 35.30 - 52.94: 134 52.94 - 70.59: 47 70.59 - 88.24: 29 Dihedral angle restraints: 14631 sinusoidal: 5958 harmonic: 8673 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 164.50 -71.50 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 156.02 -63.02 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -143.28 57.28 1 1.00e+01 1.00e-02 4.41e+01 ... (remaining 14628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2357 0.083 - 0.166: 1253 0.166 - 0.249: 186 0.249 - 0.332: 35 0.332 - 0.416: 7 Chirality restraints: 3838 Sorted by residual: chirality pdb=" CB THR C 523 " pdb=" CA THR C 523 " pdb=" OG1 THR C 523 " pdb=" CG2 THR C 523 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CA ASN A 710 " pdb=" N ASN A 710 " pdb=" C ASN A 710 " pdb=" CB ASN A 710 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA SER C 112 " pdb=" N SER C 112 " pdb=" C SER C 112 " pdb=" CB SER C 112 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 3835 not shown) Planarity restraints: 4209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 707 " 0.240 2.00e-02 2.50e+03 1.33e-01 3.51e+02 pdb=" CG TYR C 707 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR C 707 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR C 707 " -0.118 2.00e-02 2.50e+03 pdb=" CE1 TYR C 707 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 TYR C 707 " -0.073 2.00e-02 2.50e+03 pdb=" CZ TYR C 707 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 707 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.138 2.00e-02 2.50e+03 1.49e-01 2.78e+02 pdb=" CG ASN B 331 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.233 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " 0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " 0.143 2.00e-02 2.50e+03 1.47e-01 2.68e+02 pdb=" CG ASN C 709 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " -0.217 2.00e-02 2.50e+03 pdb=" C1 NAG C1306 " 0.178 2.00e-02 2.50e+03 ... (remaining 4206 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 12029 2.99 - 3.47: 24261 3.47 - 3.94: 39025 3.94 - 4.42: 43397 4.42 - 4.90: 71642 Nonbonded interactions: 190354 Sorted by model distance: nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.509 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.513 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.522 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.548 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.553 3.040 ... (remaining 190349 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 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 through 166 and (name N or name CA or name C or name \ O or name CB )) or resid 167 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 171 or (resid 172 and (nam \ e N or name CA or name C or name O or name CB )) or resid 186 through 190 or (re \ sid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 th \ rough 196 or (resid 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 213 or (resid 214 and (name N or name CA or name C or name \ O or name CB )) or resid 215 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (nam \ e N or name CA or name C or name O or name CB )) or resid 240 through 308 or (re \ sid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 th \ rough 479 or (resid 480 and (name N or name CA or name C or name O or name CB )) \ or resid 481 through 527 or (resid 528 and (name N or name CA or name C or name \ O or name CB )) or resid 529 through 810 or (resid 811 and (name N or name CA o \ r name C or name O or name CB )) or resid 812 through 827 or resid 855 through 8 \ 66 or (resid 867 through 868 and (name N or name CA or name C or name O or name \ CB )) or resid 869 through 1141 or (resid 1142 and (name N or name CA or name C \ or name O or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1147 through 13 \ 08)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or (resid 1 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 167 through \ 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or r \ esid 170 through 190 or (resid 191 and (name N or name CA or name C or name O or \ name CB )) or resid 192 through 195 or (resid 196 through 197 and (name N or na \ me CA or name C or name O or name CB )) or resid 198 through 241 or (resid 242 t \ hrough 264 and (name N or name CA or name C or name O or name CB )) or resid 265 \ through 280 or (resid 281 and (name N or name CA or name C or name O or name CB \ )) or resid 282 through 479 or (resid 480 and (name N or name CA or name C or n \ ame O or name CB )) or resid 481 through 567 or (resid 568 and (name N or name C \ A or name C or name O or name CB )) or resid 569 through 582 or (resid 583 and ( \ name N or name CA or name C or name O or name CB )) or resid 584 through 585 or \ (resid 586 and (name N or name CA or name C or name O or name CB )) or resid 587 \ through 618 or (resid 619 and (name N or name CA or name C or name O or name CB \ )) or resid 620 through 676 or resid 690 through 744 or (resid 745 and (name N \ or name CA or name C or name O or name CB )) or resid 746 through 747 or (resid \ 748 and (name N or name CA or name C or name O or name CB )) or resid 749 throug \ h 810 or (resid 811 and (name N or name CA or name C or name O or name CB )) or \ resid 812 through 827 or resid 855 through 866 or (resid 867 through 868 and (na \ me N or name CA or name C or name O or name CB )) or resid 869 through 1091 or ( \ resid 1092 and (name N or name CA or name C or name O or name CB )) or resid 109 \ 3 through 1143 or (resid 1144 through 1146 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1147 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 through 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 195 or ( \ resid 196 through 197 and (name N or name CA or name C or name O or name CB )) o \ r resid 198 through 213 or (resid 214 and (name N or name CA or name C or name O \ or name CB )) or resid 215 through 217 or (resid 218 and (name N or name CA or \ name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (name \ N or name CA or name C or name O or name CB )) or resid 240 through 308 or (resi \ d 309 and (name N or name CA or name C or name O or name CB )) or resid 310 thro \ ugh 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) o \ r resid 529 through 567 or (resid 568 and (name N or name CA or name C or name O \ or name CB )) or resid 569 through 582 or (resid 583 and (name N or name CA or \ name C or name O or name CB )) or resid 584 through 585 or (resid 586 and (name \ N or name CA or name C or name O or name CB )) or resid 587 through 618 or (resi \ d 619 and (name N or name CA or name C or name O or name CB )) or resid 620 thro \ ugh 1091 or (resid 1092 and (name N or name CA or name C or name O or name CB )) \ or resid 1093 through 1141 or (resid 1142 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1147 through 1308)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.860 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.013 0.075 24088 Z= 0.732 Angle : 1.743 9.347 32859 Z= 1.150 Chirality : 0.093 0.416 3838 Planarity : 0.015 0.150 4181 Dihedral : 12.971 88.242 8940 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.67 % Favored : 92.71 % Rotamer: Outliers : 0.71 % Allowed : 2.04 % Favored : 97.26 % 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: -1.22 (0.14), residues: 2937 helix: -0.65 (0.17), residues: 686 sheet: 0.47 (0.24), residues: 417 loop : -1.21 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B 102 TYR 0.240 0.023 TYR C 707 PHE 0.088 0.013 PHE A1095 TRP 0.082 0.021 TRP A 436 HIS 0.023 0.004 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01293 (24023) covalent geometry : angle 1.73157 (32701) SS BOND : bond 0.00950 ( 37) SS BOND : angle 1.77135 ( 74) hydrogen bonds : bond 0.14194 ( 1022) hydrogen bonds : angle 8.62606 ( 2814) link_NAG-ASN : bond 0.01119 ( 28) link_NAG-ASN : angle 4.35506 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 SER cc_start: 0.8929 (m) cc_final: 0.8709 (p) REVERT: A 417 ASN cc_start: 0.9355 (m-40) cc_final: 0.9093 (p0) REVERT: A 557 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7289 (mmtm) REVERT: B 63 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.7949 (p) REVERT: B 198 ASP cc_start: 0.9051 (m-30) cc_final: 0.8627 (p0) REVERT: B 238 PHE cc_start: 0.8800 (p90) cc_final: 0.8535 (p90) REVERT: B 365 TYR cc_start: 0.9333 (m-80) cc_final: 0.9101 (m-80) REVERT: B 427 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: B 650 LEU cc_start: 0.9340 (tp) cc_final: 0.9028 (tt) REVERT: B 752 LEU cc_start: 0.9404 (mt) cc_final: 0.9064 (mp) REVERT: B 864 LEU cc_start: 0.8853 (tp) cc_final: 0.8440 (tp) REVERT: C 509 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7418 (mtp85) REVERT: C 611 LEU cc_start: 0.9211 (tp) cc_final: 0.9006 (tt) REVERT: C 613 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8446 (mp10) REVERT: C 902 MET cc_start: 0.9568 (mmm) cc_final: 0.9365 (tpp) outliers start: 18 outliers final: 4 residues processed: 252 average time/residue: 0.1575 time to fit residues: 62.6240 Evaluate side-chains 116 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 354 ASN A 710 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 498 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 965 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.072148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.052643 restraints weight = 123031.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053838 restraints weight = 74837.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.054809 restraints weight = 46806.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.055125 restraints weight = 33481.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.055235 restraints weight = 31158.740| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24088 Z= 0.160 Angle : 0.682 9.911 32859 Z= 0.358 Chirality : 0.047 0.291 3838 Planarity : 0.004 0.079 4181 Dihedral : 6.981 57.269 3776 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.81 % Favored : 96.02 % Rotamer: Outliers : 0.12 % Allowed : 1.76 % Favored : 98.12 % 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: -0.22 (0.15), residues: 2937 helix: 1.30 (0.20), residues: 664 sheet: 0.19 (0.21), residues: 542 loop : -0.85 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 355 TYR 0.023 0.002 TYR B 200 PHE 0.026 0.002 PHE C 906 TRP 0.013 0.002 TRP B 64 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00355 (24023) covalent geometry : angle 0.66311 (32701) SS BOND : bond 0.00329 ( 37) SS BOND : angle 1.14028 ( 74) hydrogen bonds : bond 0.04781 ( 1022) hydrogen bonds : angle 6.31781 ( 2814) link_NAG-ASN : bond 0.00349 ( 28) link_NAG-ASN : angle 3.11450 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9187 (mm) cc_final: 0.8517 (tp) REVERT: A 168 PHE cc_start: 0.8302 (t80) cc_final: 0.7995 (t80) REVERT: A 297 SER cc_start: 0.8997 (m) cc_final: 0.8670 (p) REVERT: A 417 ASN cc_start: 0.9540 (m-40) cc_final: 0.9034 (p0) REVERT: A 456 PHE cc_start: 0.8683 (p90) cc_final: 0.8429 (p90) REVERT: A 557 LYS cc_start: 0.7737 (mmtt) cc_final: 0.7236 (mmtm) REVERT: B 90 VAL cc_start: 0.9454 (t) cc_final: 0.8945 (m) REVERT: B 223 LEU cc_start: 0.8822 (mp) cc_final: 0.8459 (mp) REVERT: B 360 ASN cc_start: 0.8552 (p0) cc_final: 0.8245 (p0) REVERT: B 650 LEU cc_start: 0.9392 (tp) cc_final: 0.9104 (tt) REVERT: B 864 LEU cc_start: 0.8887 (tp) cc_final: 0.8587 (tp) REVERT: B 1002 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8151 (tm-30) REVERT: C 395 VAL cc_start: 0.8197 (m) cc_final: 0.7848 (p) REVERT: C 417 ASN cc_start: 0.9473 (m110) cc_final: 0.9062 (p0) REVERT: C 509 ARG cc_start: 0.8010 (mtt180) cc_final: 0.7505 (mtp85) outliers start: 3 outliers final: 0 residues processed: 166 average time/residue: 0.1533 time to fit residues: 40.8624 Evaluate side-chains 92 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 147 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 236 optimal weight: 30.0000 chunk 259 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 675 GLN A1048 HIS B1119 ASN B1135 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 965 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.070113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.050569 restraints weight = 124982.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.051813 restraints weight = 71321.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.052368 restraints weight = 44094.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.052651 restraints weight = 36296.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.052725 restraints weight = 32132.159| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 24088 Z= 0.234 Angle : 0.693 9.971 32859 Z= 0.359 Chirality : 0.046 0.257 3838 Planarity : 0.005 0.062 4181 Dihedral : 6.601 56.689 3776 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.14 % Favored : 94.72 % Rotamer: Outliers : 0.12 % Allowed : 2.27 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.27 (0.15), residues: 2937 helix: 1.28 (0.20), residues: 671 sheet: -0.07 (0.20), residues: 596 loop : -0.83 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 408 TYR 0.039 0.002 TYR B 505 PHE 0.029 0.002 PHE C 559 TRP 0.020 0.002 TRP A 64 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00515 (24023) covalent geometry : angle 0.67568 (32701) SS BOND : bond 0.00404 ( 37) SS BOND : angle 1.18364 ( 74) hydrogen bonds : bond 0.04629 ( 1022) hydrogen bonds : angle 6.19526 ( 2814) link_NAG-ASN : bond 0.00454 ( 28) link_NAG-ASN : angle 2.94461 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9093 (mm) cc_final: 0.8401 (tp) REVERT: A 168 PHE cc_start: 0.8348 (t80) cc_final: 0.7951 (t80) REVERT: A 297 SER cc_start: 0.9043 (m) cc_final: 0.8687 (p) REVERT: A 417 ASN cc_start: 0.9595 (m-40) cc_final: 0.9183 (p0) REVERT: A 557 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7278 (mmtm) REVERT: B 223 LEU cc_start: 0.8836 (mp) cc_final: 0.8599 (mp) REVERT: B 360 ASN cc_start: 0.8452 (p0) cc_final: 0.8246 (p0) REVERT: B 864 LEU cc_start: 0.9042 (tp) cc_final: 0.8746 (tp) REVERT: C 55 PHE cc_start: 0.8648 (m-80) cc_final: 0.8267 (m-80) REVERT: C 395 VAL cc_start: 0.7959 (m) cc_final: 0.7667 (p) REVERT: C 417 ASN cc_start: 0.9492 (m110) cc_final: 0.9067 (p0) REVERT: C 611 LEU cc_start: 0.9153 (tp) cc_final: 0.8882 (tt) REVERT: C 613 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8287 (mp10) REVERT: C 699 LEU cc_start: 0.9001 (mt) cc_final: 0.8729 (mp) REVERT: C 878 LEU cc_start: 0.9365 (tp) cc_final: 0.9156 (tt) outliers start: 3 outliers final: 0 residues processed: 129 average time/residue: 0.1503 time to fit residues: 32.0955 Evaluate side-chains 85 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 249 optimal weight: 5.9990 chunk 277 optimal weight: 0.2980 chunk 221 optimal weight: 10.0000 chunk 234 optimal weight: 30.0000 chunk 42 optimal weight: 0.0170 chunk 88 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 269 optimal weight: 3.9990 chunk 225 optimal weight: 0.1980 chunk 49 optimal weight: 20.0000 overall best weight: 1.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN C 762 GLN C 901 GLN C 926 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.071919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.052571 restraints weight = 123578.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.053893 restraints weight = 75144.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.054485 restraints weight = 44921.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.054818 restraints weight = 37352.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.054883 restraints weight = 32795.175| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24088 Z= 0.114 Angle : 0.567 7.947 32859 Z= 0.296 Chirality : 0.044 0.234 3838 Planarity : 0.004 0.065 4181 Dihedral : 5.985 54.592 3776 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 0.04 % Allowed : 1.41 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.05 (0.15), residues: 2937 helix: 1.87 (0.21), residues: 661 sheet: -0.02 (0.19), residues: 623 loop : -0.71 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.025 0.001 TYR A 369 PHE 0.022 0.001 PHE C 906 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00244 (24023) covalent geometry : angle 0.55265 (32701) SS BOND : bond 0.00263 ( 37) SS BOND : angle 1.16978 ( 74) hydrogen bonds : bond 0.03943 ( 1022) hydrogen bonds : angle 5.67070 ( 2814) link_NAG-ASN : bond 0.00333 ( 28) link_NAG-ASN : angle 2.41731 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8218 (t80) cc_final: 0.7977 (t80) REVERT: A 297 SER cc_start: 0.8976 (m) cc_final: 0.8601 (p) REVERT: A 354 ASN cc_start: 0.8483 (m110) cc_final: 0.8201 (m-40) REVERT: A 417 ASN cc_start: 0.9559 (m-40) cc_final: 0.9134 (p0) REVERT: A 557 LYS cc_start: 0.7735 (mmtt) cc_final: 0.7255 (mmtm) REVERT: B 52 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8432 (tm-30) REVERT: B 90 VAL cc_start: 0.9465 (t) cc_final: 0.9107 (t) REVERT: B 238 PHE cc_start: 0.8706 (p90) cc_final: 0.8193 (p90) REVERT: B 864 LEU cc_start: 0.8977 (tp) cc_final: 0.8688 (tp) REVERT: B 979 ASP cc_start: 0.9322 (m-30) cc_final: 0.9115 (m-30) REVERT: C 297 SER cc_start: 0.9483 (m) cc_final: 0.9212 (p) REVERT: C 395 VAL cc_start: 0.8155 (m) cc_final: 0.7760 (p) REVERT: C 417 ASN cc_start: 0.9457 (m110) cc_final: 0.9068 (p0) REVERT: C 509 ARG cc_start: 0.7942 (mtt180) cc_final: 0.7238 (mtp85) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1430 time to fit residues: 32.6435 Evaluate side-chains 86 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 218 optimal weight: 0.9980 chunk 281 optimal weight: 0.9990 chunk 129 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1048 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.070984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.051539 restraints weight = 123944.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.052435 restraints weight = 79617.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.053279 restraints weight = 48168.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.053839 restraints weight = 36934.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.053812 restraints weight = 33889.614| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24088 Z= 0.156 Angle : 0.575 8.039 32859 Z= 0.298 Chirality : 0.044 0.246 3838 Planarity : 0.004 0.060 4181 Dihedral : 5.863 54.766 3776 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.66 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.05 (0.15), residues: 2937 helix: 1.82 (0.21), residues: 663 sheet: 0.03 (0.20), residues: 592 loop : -0.70 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 408 TYR 0.021 0.001 TYR B 505 PHE 0.026 0.001 PHE C 392 TRP 0.010 0.001 TRP A 64 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00344 (24023) covalent geometry : angle 0.56223 (32701) SS BOND : bond 0.00732 ( 37) SS BOND : angle 1.06782 ( 74) hydrogen bonds : bond 0.03965 ( 1022) hydrogen bonds : angle 5.61496 ( 2814) link_NAG-ASN : bond 0.00318 ( 28) link_NAG-ASN : angle 2.27761 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.936 Fit side-chains REVERT: A 168 PHE cc_start: 0.8148 (t80) cc_final: 0.7904 (t80) REVERT: A 297 SER cc_start: 0.8950 (m) cc_final: 0.8632 (p) REVERT: A 417 ASN cc_start: 0.9619 (m-40) cc_final: 0.9196 (p0) REVERT: A 557 LYS cc_start: 0.7819 (mmtt) cc_final: 0.7283 (mmtm) REVERT: A 979 ASP cc_start: 0.8946 (m-30) cc_final: 0.8526 (t0) REVERT: B 52 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8508 (tm-30) REVERT: B 56 LEU cc_start: 0.8862 (tp) cc_final: 0.8651 (tp) REVERT: B 864 LEU cc_start: 0.9019 (tp) cc_final: 0.8694 (tp) REVERT: B 1002 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8006 (tm-30) REVERT: C 297 SER cc_start: 0.9472 (m) cc_final: 0.9184 (p) REVERT: C 395 VAL cc_start: 0.8101 (m) cc_final: 0.7775 (p) REVERT: C 417 ASN cc_start: 0.9464 (m110) cc_final: 0.9061 (p0) REVERT: C 509 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7257 (mtp85) REVERT: C 528 LYS cc_start: 0.9058 (tptp) cc_final: 0.8811 (tppt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1496 time to fit residues: 27.3447 Evaluate side-chains 81 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 138 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 39 optimal weight: 30.0000 chunk 150 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 191 optimal weight: 0.0770 chunk 149 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 229 optimal weight: 0.0870 overall best weight: 2.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.071058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.051385 restraints weight = 123897.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.052832 restraints weight = 72433.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.053529 restraints weight = 47311.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.054004 restraints weight = 33709.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054106 restraints weight = 29899.001| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24088 Z= 0.144 Angle : 0.562 11.749 32859 Z= 0.290 Chirality : 0.044 0.279 3838 Planarity : 0.004 0.058 4181 Dihedral : 5.763 54.446 3776 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.32 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.08 (0.15), residues: 2937 helix: 1.88 (0.21), residues: 663 sheet: 0.03 (0.20), residues: 620 loop : -0.69 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.023 0.001 TYR B 200 PHE 0.022 0.001 PHE C 342 TRP 0.010 0.001 TRP C 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00317 (24023) covalent geometry : angle 0.54942 (32701) SS BOND : bond 0.00280 ( 37) SS BOND : angle 0.93080 ( 74) hydrogen bonds : bond 0.03829 ( 1022) hydrogen bonds : angle 5.52496 ( 2814) link_NAG-ASN : bond 0.00310 ( 28) link_NAG-ASN : angle 2.31810 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.919 Fit side-chains REVERT: A 168 PHE cc_start: 0.8140 (t80) cc_final: 0.7885 (t80) REVERT: A 297 SER cc_start: 0.8934 (m) cc_final: 0.8607 (p) REVERT: A 417 ASN cc_start: 0.9641 (m-40) cc_final: 0.9247 (p0) REVERT: A 456 PHE cc_start: 0.8733 (p90) cc_final: 0.8450 (p90) REVERT: A 473 TYR cc_start: 0.6832 (t80) cc_final: 0.6085 (t80) REVERT: A 979 ASP cc_start: 0.8905 (m-30) cc_final: 0.8519 (t0) REVERT: B 52 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8482 (tm-30) REVERT: B 56 LEU cc_start: 0.8781 (tp) cc_final: 0.8572 (tp) REVERT: B 864 LEU cc_start: 0.8991 (tp) cc_final: 0.8637 (tp) REVERT: B 1002 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8261 (tm-30) REVERT: C 297 SER cc_start: 0.9470 (m) cc_final: 0.9207 (p) REVERT: C 395 VAL cc_start: 0.8073 (m) cc_final: 0.7832 (p) REVERT: C 417 ASN cc_start: 0.9469 (m110) cc_final: 0.9064 (p0) REVERT: C 509 ARG cc_start: 0.7916 (mtt180) cc_final: 0.7176 (mtp85) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1504 time to fit residues: 28.9025 Evaluate side-chains 85 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.2980 chunk 9 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 247 optimal weight: 6.9990 chunk 268 optimal weight: 3.9990 chunk 279 optimal weight: 0.0970 chunk 48 optimal weight: 20.0000 chunk 202 optimal weight: 0.0070 chunk 122 optimal weight: 6.9990 chunk 293 optimal weight: 2.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C1108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.072100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.052499 restraints weight = 122866.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.054352 restraints weight = 68837.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.054818 restraints weight = 40618.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.055221 restraints weight = 32428.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.055279 restraints weight = 29367.067| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24088 Z= 0.099 Angle : 0.522 7.836 32859 Z= 0.269 Chirality : 0.043 0.237 3838 Planarity : 0.004 0.059 4181 Dihedral : 5.436 53.475 3776 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.88 % Favored : 96.08 % Rotamer: Outliers : 0.04 % Allowed : 0.74 % Favored : 99.22 % 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: 0.30 (0.16), residues: 2937 helix: 2.09 (0.21), residues: 657 sheet: 0.20 (0.20), residues: 603 loop : -0.56 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.019 0.001 TYR B 200 PHE 0.022 0.001 PHE A 275 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00211 (24023) covalent geometry : angle 0.51012 (32701) SS BOND : bond 0.00332 ( 37) SS BOND : angle 0.99540 ( 74) hydrogen bonds : bond 0.03502 ( 1022) hydrogen bonds : angle 5.27478 ( 2814) link_NAG-ASN : bond 0.00300 ( 28) link_NAG-ASN : angle 2.06111 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.722 Fit side-chains REVERT: A 168 PHE cc_start: 0.7989 (t80) cc_final: 0.7741 (t80) REVERT: A 297 SER cc_start: 0.8917 (m) cc_final: 0.8587 (p) REVERT: A 400 PHE cc_start: 0.9383 (p90) cc_final: 0.8498 (p90) REVERT: A 456 PHE cc_start: 0.8584 (p90) cc_final: 0.8358 (p90) REVERT: A 473 TYR cc_start: 0.6879 (t80) cc_final: 0.6112 (t80) REVERT: A 979 ASP cc_start: 0.8941 (m-30) cc_final: 0.8683 (t0) REVERT: B 52 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8517 (tm-30) REVERT: B 238 PHE cc_start: 0.8745 (p90) cc_final: 0.8314 (p90) REVERT: B 1002 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8066 (tm-30) REVERT: C 55 PHE cc_start: 0.8660 (m-80) cc_final: 0.8256 (m-80) REVERT: C 238 PHE cc_start: 0.8313 (p90) cc_final: 0.8096 (p90) REVERT: C 297 SER cc_start: 0.9459 (m) cc_final: 0.9167 (p) REVERT: C 395 VAL cc_start: 0.8184 (m) cc_final: 0.7901 (p) REVERT: C 417 ASN cc_start: 0.9472 (m110) cc_final: 0.9109 (p0) REVERT: C 509 ARG cc_start: 0.7862 (mtt180) cc_final: 0.7109 (mtp85) outliers start: 1 outliers final: 1 residues processed: 126 average time/residue: 0.1401 time to fit residues: 30.0213 Evaluate side-chains 86 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 130 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 76 optimal weight: 0.0370 chunk 204 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 overall best weight: 2.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.071167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.051567 restraints weight = 123744.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.053237 restraints weight = 71957.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053675 restraints weight = 44075.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.054069 restraints weight = 35159.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.054143 restraints weight = 31614.261| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24088 Z= 0.141 Angle : 0.542 7.274 32859 Z= 0.281 Chirality : 0.043 0.238 3838 Planarity : 0.004 0.058 4181 Dihedral : 5.483 54.150 3776 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 0.27 (0.16), residues: 2937 helix: 1.95 (0.21), residues: 663 sheet: 0.20 (0.20), residues: 626 loop : -0.55 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 408 TYR 0.033 0.001 TYR A 266 PHE 0.026 0.001 PHE C 329 TRP 0.027 0.001 TRP A 64 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00313 (24023) covalent geometry : angle 0.53086 (32701) SS BOND : bond 0.00330 ( 37) SS BOND : angle 1.17215 ( 74) hydrogen bonds : bond 0.03632 ( 1022) hydrogen bonds : angle 5.32908 ( 2814) link_NAG-ASN : bond 0.00289 ( 28) link_NAG-ASN : angle 2.01604 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8062 (t80) cc_final: 0.7798 (t80) REVERT: A 297 SER cc_start: 0.9012 (m) cc_final: 0.8670 (p) REVERT: A 473 TYR cc_start: 0.7235 (t80) cc_final: 0.6556 (t80) REVERT: A 979 ASP cc_start: 0.8958 (m-30) cc_final: 0.8678 (t0) REVERT: B 52 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8546 (tm-30) REVERT: B 1002 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8207 (tm-30) REVERT: C 238 PHE cc_start: 0.8452 (p90) cc_final: 0.8200 (p90) REVERT: C 297 SER cc_start: 0.9507 (m) cc_final: 0.9248 (p) REVERT: C 395 VAL cc_start: 0.8179 (m) cc_final: 0.7868 (p) REVERT: C 417 ASN cc_start: 0.9494 (m110) cc_final: 0.9094 (p0) REVERT: C 509 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7122 (mtp85) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1404 time to fit residues: 26.7960 Evaluate side-chains 81 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 63 optimal weight: 7.9990 chunk 258 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 126 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 241 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.070391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.051189 restraints weight = 124573.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.052239 restraints weight = 71473.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.052816 restraints weight = 46165.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.053168 restraints weight = 37566.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.053228 restraints weight = 32451.140| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24088 Z= 0.186 Angle : 0.582 6.927 32859 Z= 0.302 Chirality : 0.044 0.242 3838 Planarity : 0.004 0.061 4181 Dihedral : 5.696 54.464 3776 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 0.15 (0.16), residues: 2937 helix: 1.74 (0.21), residues: 670 sheet: 0.21 (0.20), residues: 625 loop : -0.63 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 408 TYR 0.021 0.002 TYR A 266 PHE 0.034 0.002 PHE A 559 TRP 0.024 0.002 TRP A 64 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00413 (24023) covalent geometry : angle 0.57181 (32701) SS BOND : bond 0.00309 ( 37) SS BOND : angle 1.16194 ( 74) hydrogen bonds : bond 0.03876 ( 1022) hydrogen bonds : angle 5.47438 ( 2814) link_NAG-ASN : bond 0.00317 ( 28) link_NAG-ASN : angle 2.04818 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8057 (t80) cc_final: 0.7827 (t80) REVERT: A 297 SER cc_start: 0.8970 (m) cc_final: 0.8619 (p) REVERT: A 473 TYR cc_start: 0.6766 (t80) cc_final: 0.6490 (t80) REVERT: A 557 LYS cc_start: 0.7640 (mmtp) cc_final: 0.7199 (mmtm) REVERT: B 52 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8521 (tm-30) REVERT: B 1002 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8205 (tm-30) REVERT: C 297 SER cc_start: 0.9477 (m) cc_final: 0.9272 (p) REVERT: C 395 VAL cc_start: 0.8218 (m) cc_final: 0.7898 (p) REVERT: C 417 ASN cc_start: 0.9483 (m110) cc_final: 0.9080 (p0) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1415 time to fit residues: 23.7319 Evaluate side-chains 69 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 69 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 36 optimal weight: 0.1980 chunk 122 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.069837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.050511 restraints weight = 125000.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.051489 restraints weight = 72406.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.052270 restraints weight = 45792.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.052476 restraints weight = 36988.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052487 restraints weight = 33530.773| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24088 Z= 0.217 Angle : 0.612 8.029 32859 Z= 0.315 Chirality : 0.045 0.248 3838 Planarity : 0.004 0.061 4181 Dihedral : 5.861 54.363 3776 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -0.07 (0.15), residues: 2937 helix: 1.49 (0.20), residues: 676 sheet: 0.12 (0.20), residues: 637 loop : -0.77 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 408 TYR 0.021 0.002 TYR A 873 PHE 0.037 0.002 PHE A 559 TRP 0.028 0.002 TRP A 64 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00479 (24023) covalent geometry : angle 0.60119 (32701) SS BOND : bond 0.00322 ( 37) SS BOND : angle 1.14558 ( 74) hydrogen bonds : bond 0.03975 ( 1022) hydrogen bonds : angle 5.62873 ( 2814) link_NAG-ASN : bond 0.00345 ( 28) link_NAG-ASN : angle 2.10212 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8095 (t80) cc_final: 0.7829 (t80) REVERT: A 297 SER cc_start: 0.8960 (m) cc_final: 0.8589 (p) REVERT: A 557 LYS cc_start: 0.7676 (mmtp) cc_final: 0.7236 (mmtm) REVERT: B 52 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8505 (tm-30) REVERT: B 864 LEU cc_start: 0.9109 (tp) cc_final: 0.8668 (tp) REVERT: C 297 SER cc_start: 0.9485 (m) cc_final: 0.9267 (p) REVERT: C 395 VAL cc_start: 0.8169 (m) cc_final: 0.7820 (p) REVERT: C 417 ASN cc_start: 0.9520 (m110) cc_final: 0.9091 (p0) REVERT: C 509 ARG cc_start: 0.7929 (mtt180) cc_final: 0.6759 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1377 time to fit residues: 22.0156 Evaluate side-chains 68 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 172 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 256 optimal weight: 0.8980 chunk 273 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 540 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.071373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.051910 restraints weight = 121866.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.053847 restraints weight = 68540.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.054314 restraints weight = 38129.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.054655 restraints weight = 30249.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.054748 restraints weight = 28055.005| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24088 Z= 0.104 Angle : 0.525 6.881 32859 Z= 0.272 Chirality : 0.043 0.245 3838 Planarity : 0.004 0.059 4181 Dihedral : 5.480 52.950 3776 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.15 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 0.20 (0.16), residues: 2937 helix: 1.87 (0.21), residues: 669 sheet: 0.27 (0.20), residues: 610 loop : -0.64 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 408 TYR 0.018 0.001 TYR A 873 PHE 0.029 0.001 PHE A 559 TRP 0.019 0.001 TRP A 64 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00224 (24023) covalent geometry : angle 0.51604 (32701) SS BOND : bond 0.00252 ( 37) SS BOND : angle 0.92377 ( 74) hydrogen bonds : bond 0.03541 ( 1022) hydrogen bonds : angle 5.30042 ( 2814) link_NAG-ASN : bond 0.00287 ( 28) link_NAG-ASN : angle 1.89395 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3079.81 seconds wall clock time: 54 minutes 26.29 seconds (3266.29 seconds total)