Starting phenix.real_space_refine on Tue Aug 26 02:24:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1v_35934/08_2025/8j1v_35934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1v_35934/08_2025/8j1v_35934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j1v_35934/08_2025/8j1v_35934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1v_35934/08_2025/8j1v_35934.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j1v_35934/08_2025/8j1v_35934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1v_35934/08_2025/8j1v_35934.map" } resolution = 3.01 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4143 atoms to isotropic. 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 138 5.16 5 C 18603 2.51 5 N 4833 2.21 5 O 5631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29205 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7910 Classifications: {'peptide': 1008} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 874 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Restraints were copied for chains: B, E, C, F, D, G Time building chain proxies: 7.85, per 1000 atoms: 0.27 Number of scatterers: 29205 At special positions: 0 Unit cell: (154.23, 146.47, 210.49, 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 138 16.00 O 5631 8.00 N 4833 7.00 C 18603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 63 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 122 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 331 " " NAG B1301 " - " ASN B 63 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 331 " " NAG E1301 " - " ASN E 63 " " NAG E1302 " - " ASN E 282 " " NAG E1303 " - " ASN E 603 " " NAG E1304 " - " ASN E 657 " " NAG E1305 " - " ASN E1074 " " NAG E1306 " - " ASN E 122 " " NAG E1307 " - " ASN E 165 " " NAG E1308 " - " ASN E 234 " " NAG E1309 " - " ASN E 331 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 918.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6870 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 54 sheets defined 21.5% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.850A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.093A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.573A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.632A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.646A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.027A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.731A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.260A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.781A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.860A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.815A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.518A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 33 removed outlier: 3.895A pdb=" N ASN H 33 " --> pdb=" O VAL H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.671A pdb=" N ARG H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.850A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.093A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.573A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.632A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.645A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.028A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 800 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.732A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.260A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.781A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (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 967 removed outlier: 3.860A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.815A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.518A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 removed outlier: 3.895A pdb=" N ASN C 33 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.671A pdb=" N ARG C 65 " --> pdb=" O ASP C 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 366 through 372 removed outlier: 3.851A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE E 371 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 388 removed outlier: 4.093A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.573A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.632A pdb=" N TYR E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 742 Processing helix chain 'E' and resid 746 through 755 removed outlier: 3.646A pdb=" N GLN E 755 " --> pdb=" O ASN E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 783 removed outlier: 4.027A pdb=" N GLN E 762 " --> pdb=" O SER E 758 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR E 778 " --> pdb=" O GLN E 774 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL E 781 " --> pdb=" O ASN E 777 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 783 " --> pdb=" O GLN E 779 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 800 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 886 through 891 removed outlier: 3.730A pdb=" N ALA E 890 " --> pdb=" O TRP E 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 910 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.260A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.781A pdb=" N SER E 939 " --> pdb=" O GLN E 935 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 967 removed outlier: 3.860A pdb=" N SER E 967 " --> pdb=" O VAL E 963 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.815A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.518A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 33 removed outlier: 3.895A pdb=" N ASN F 33 " --> pdb=" O VAL F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 removed outlier: 3.671A pdb=" N ARG F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 5.947A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 38 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 57 removed outlier: 3.843A pdb=" N VAL A 49 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.656A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.460A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 355 removed outlier: 3.585A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.619A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.971A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.540A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.548A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.518A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.884A pdb=" N GLN H 4 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER H 22 " --> pdb=" O SER H 8 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.178A pdb=" N GLY H 11 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL H 114 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TYR H 34 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET H 35 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL H 51 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP H 37 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.931A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 45 through 48 removed outlier: 5.800A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 30 through 32 removed outlier: 5.947A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 38 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 49 through 57 removed outlier: 3.843A pdb=" N VAL B 49 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.656A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.460A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 355 removed outlier: 3.584A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.618A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.971A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.539A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.548A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 4 through 8 removed outlier: 3.884A pdb=" N GLN C 4 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 22 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.178A pdb=" N GLY C 11 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 114 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TYR C 34 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET C 35 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL C 51 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP C 37 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.931A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 45 through 48 removed outlier: 5.800A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 30 through 32 removed outlier: 5.947A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL E 38 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.842A pdb=" N VAL E 49 " --> pdb=" O TYR E 279 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.656A pdb=" N SER E 172 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.460A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 354 through 355 removed outlier: 3.584A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AE8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'E' and resid 538 through 543 removed outlier: 3.619A pdb=" N GLY E 550 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE E 543 " --> pdb=" O LEU E 546 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR E 553 " --> pdb=" O ASP E 586 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 654 through 660 removed outlier: 5.971A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N VAL E 656 " --> pdb=" O THR E 696 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER E 691 " --> pdb=" O GLN E 675 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE E 664 " --> pdb=" O ALA E 672 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 712 through 728 removed outlier: 6.540A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.548A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=AF6, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.884A pdb=" N GLN F 4 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER F 22 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.178A pdb=" N GLY F 11 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL F 114 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TYR F 34 " --> pdb=" O ASP F 99 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET F 35 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL F 51 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP F 37 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.932A pdb=" N VAL G 19 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 45 through 48 removed outlier: 5.800A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) 1052 hydrogen bonds defined for protein. 2859 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.01 Time building geometry restraints manager: 2.60 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: 7795 1.33 - 1.45: 6388 1.45 - 1.58: 15514 1.58 - 1.70: 0 1.70 - 1.82: 183 Bond restraints: 29880 Sorted by residual: bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.35e-02 5.49e+03 9.83e+00 bond pdb=" N ILE E 233 " pdb=" CA ILE E 233 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.35e-02 5.49e+03 9.79e+00 bond pdb=" N ILE B 233 " pdb=" CA ILE B 233 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.35e-02 5.49e+03 9.76e+00 bond pdb=" N THR E 912 " pdb=" CA THR E 912 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.31e-02 5.83e+03 8.26e+00 bond pdb=" N THR A 912 " pdb=" CA THR A 912 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 8.09e+00 ... (remaining 29875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 39554 1.82 - 3.65: 969 3.65 - 5.47: 94 5.47 - 7.30: 9 7.30 - 9.12: 3 Bond angle restraints: 40629 Sorted by residual: angle pdb=" C PRO E 230 " pdb=" CA PRO E 230 " pdb=" CB PRO E 230 " ideal model delta sigma weight residual 112.97 103.85 9.12 1.43e+00 4.89e-01 4.07e+01 angle pdb=" C PRO A 230 " pdb=" CA PRO A 230 " pdb=" CB PRO A 230 " ideal model delta sigma weight residual 112.97 103.87 9.10 1.43e+00 4.89e-01 4.05e+01 angle pdb=" C PRO B 230 " pdb=" CA PRO B 230 " pdb=" CB PRO B 230 " ideal model delta sigma weight residual 112.97 103.88 9.09 1.43e+00 4.89e-01 4.04e+01 angle pdb=" N VAL E 159 " pdb=" CA VAL E 159 " pdb=" C VAL E 159 " ideal model delta sigma weight residual 113.53 109.45 4.08 9.80e-01 1.04e+00 1.73e+01 angle pdb=" N VAL A 159 " pdb=" CA VAL A 159 " pdb=" C VAL A 159 " ideal model delta sigma weight residual 113.53 109.47 4.06 9.80e-01 1.04e+00 1.72e+01 ... (remaining 40624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 16686 17.20 - 34.39: 1124 34.39 - 51.59: 239 51.59 - 68.78: 50 68.78 - 85.98: 15 Dihedral angle restraints: 18114 sinusoidal: 7401 harmonic: 10713 Sorted by residual: dihedral pdb=" CB CYS E 662 " pdb=" SG CYS E 662 " pdb=" SG CYS E 671 " pdb=" CB CYS E 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.02 -85.98 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.06 -85.94 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.08 -85.92 1 1.00e+01 1.00e-02 8.92e+01 ... (remaining 18111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3960 0.066 - 0.133: 620 0.133 - 0.199: 49 0.199 - 0.265: 3 0.265 - 0.331: 6 Chirality restraints: 4638 Sorted by residual: chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C1 NAG E1308 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E1308 " pdb=" O5 NAG E1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 4635 not shown) Planarity restraints: 5241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E1309 " 0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG E1309 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG E1309 " 0.116 2.00e-02 2.50e+03 pdb=" N2 NAG E1309 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG E1309 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.349 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG B1309 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.115 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " -0.349 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG A1309 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " -0.105 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " -0.166 2.00e-02 2.50e+03 ... (remaining 5238 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3882 2.76 - 3.29: 27463 3.29 - 3.83: 44813 3.83 - 4.36: 52667 4.36 - 4.90: 94036 Nonbonded interactions: 222861 Sorted by model distance: nonbonded pdb=" OH TYR D 36 " pdb=" OE1 GLN D 89 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR K 36 " pdb=" OE1 GLN K 89 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR G 36 " pdb=" OE1 GLN G 89 " model vdw 2.220 3.040 nonbonded pdb=" O ILE B 742 " pdb=" NH1 ARG B1000 " model vdw 2.230 3.120 nonbonded pdb=" O ILE A 742 " pdb=" NH1 ARG A1000 " model vdw 2.230 3.120 ... (remaining 222856 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'H' selection = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'K' selection = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.900 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 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 : 0.004 0.042 29952 Z= 0.230 Angle : 0.650 12.781 40800 Z= 0.382 Chirality : 0.047 0.331 4638 Planarity : 0.009 0.302 5214 Dihedral : 12.040 75.257 11109 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.63 % 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 aren not related in a simple way. whole: -0.38 (0.14), residues: 3627 helix: 2.17 (0.21), residues: 648 sheet: -0.01 (0.17), residues: 996 loop : -1.25 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 355 TYR 0.019 0.001 TYR E 396 PHE 0.017 0.001 PHE A 45 TRP 0.012 0.001 TRP E 353 HIS 0.005 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00402 (29880) covalent geometry : angle 0.63026 (40629) SS BOND : bond 0.00414 ( 45) SS BOND : angle 1.07325 ( 90) hydrogen bonds : bond 0.22274 ( 1052) hydrogen bonds : angle 7.60740 ( 2859) link_NAG-ASN : bond 0.01034 ( 27) link_NAG-ASN : angle 3.46504 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 705 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 THR cc_start: 0.7048 (p) cc_final: 0.6844 (p) REVERT: A 121 ASN cc_start: 0.7684 (m-40) cc_final: 0.7378 (t0) REVERT: A 191 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6909 (mt-10) REVERT: A 200 TYR cc_start: 0.6778 (m-80) cc_final: 0.6499 (m-80) REVERT: A 542 ASN cc_start: 0.7073 (t0) cc_final: 0.6834 (t0) REVERT: A 646 ARG cc_start: 0.6866 (ttt90) cc_final: 0.6621 (ttt90) REVERT: A 945 LEU cc_start: 0.7859 (mm) cc_final: 0.7515 (mp) REVERT: A 1084 ASP cc_start: 0.6998 (t0) cc_final: 0.6549 (t0) REVERT: B 190 ARG cc_start: 0.6965 (mpt180) cc_final: 0.6661 (mtt90) REVERT: B 227 VAL cc_start: 0.8139 (t) cc_final: 0.7930 (m) REVERT: B 239 GLN cc_start: 0.7101 (tt0) cc_final: 0.6669 (tt0) REVERT: B 531 THR cc_start: 0.8128 (m) cc_final: 0.7731 (p) REVERT: B 555 SER cc_start: 0.8174 (t) cc_final: 0.7764 (t) REVERT: B 583 GLU cc_start: 0.6402 (tp30) cc_final: 0.6104 (tp30) REVERT: B 584 ILE cc_start: 0.7992 (pt) cc_final: 0.7791 (pt) REVERT: B 586 ASP cc_start: 0.7205 (m-30) cc_final: 0.7004 (m-30) REVERT: B 587 ILE cc_start: 0.8064 (mm) cc_final: 0.7785 (mt) REVERT: B 646 ARG cc_start: 0.6730 (ttt90) cc_final: 0.6508 (ttt90) REVERT: B 674 TYR cc_start: 0.8312 (t80) cc_final: 0.7998 (t80) REVERT: B 704 SER cc_start: 0.8286 (t) cc_final: 0.8042 (m) REVERT: B 735 SER cc_start: 0.8249 (t) cc_final: 0.7826 (p) REVERT: B 1084 ASP cc_start: 0.6794 (t0) cc_final: 0.6439 (t0) REVERT: B 1139 ASP cc_start: 0.7286 (t0) cc_final: 0.6971 (t0) REVERT: D 92 ASN cc_start: 0.6331 (m-40) cc_final: 0.6091 (m-40) REVERT: E 121 ASN cc_start: 0.7676 (m-40) cc_final: 0.7363 (t0) REVERT: E 239 GLN cc_start: 0.6917 (tt0) cc_final: 0.6491 (tt0) REVERT: E 541 PHE cc_start: 0.7485 (p90) cc_final: 0.7245 (p90) REVERT: E 567 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7550 (mtt180) REVERT: E 578 ASP cc_start: 0.6500 (p0) cc_final: 0.6297 (p0) REVERT: E 735 SER cc_start: 0.8335 (t) cc_final: 0.7880 (p) REVERT: E 784 GLN cc_start: 0.8503 (mt0) cc_final: 0.8284 (mt0) REVERT: E 883 THR cc_start: 0.8510 (m) cc_final: 0.7831 (p) REVERT: E 904 TYR cc_start: 0.7371 (m-10) cc_final: 0.6632 (m-10) REVERT: E 1084 ASP cc_start: 0.6841 (t0) cc_final: 0.6487 (t0) REVERT: E 1102 TRP cc_start: 0.8350 (m100) cc_final: 0.7958 (m100) REVERT: E 1136 THR cc_start: 0.8509 (p) cc_final: 0.8216 (p) REVERT: E 1139 ASP cc_start: 0.7538 (t0) cc_final: 0.7306 (t0) outliers start: 3 outliers final: 1 residues processed: 708 average time/residue: 0.1825 time to fit residues: 202.0085 Evaluate side-chains 590 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 589 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.0270 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 207 HIS A 239 GLN A 417 ASN A 544 ASN A 762 GLN A 774 GLN A 784 GLN A 853 GLN H 100 HIS K 38 GLN K 55 GLN ** K 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 207 HIS B 564 GLN B 762 GLN B 774 GLN B 784 GLN B 853 GLN B 913 GLN C 100 HIS D 55 GLN E 196 ASN E 207 HIS E 417 ASN E 450 ASN E 762 GLN E 774 GLN E 853 GLN F 100 HIS G 38 GLN G 55 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.170000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.135284 restraints weight = 47018.715| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.74 r_work: 0.3662 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 29952 Z= 0.174 Angle : 0.625 13.103 40800 Z= 0.318 Chirality : 0.047 0.417 4638 Planarity : 0.005 0.061 5214 Dihedral : 6.586 54.493 4550 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.96 % Allowed : 8.22 % Favored : 90.82 % 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 aren not related in a simple way. whole: -0.30 (0.14), residues: 3627 helix: 2.11 (0.21), residues: 651 sheet: 0.40 (0.18), residues: 885 loop : -1.30 (0.12), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E1000 TYR 0.021 0.002 TYR E 170 PHE 0.030 0.002 PHE E 497 TRP 0.021 0.002 TRP H 48 HIS 0.014 0.002 HIS H 100 Details of bonding type rmsd covalent geometry : bond 0.00396 (29880) covalent geometry : angle 0.60104 (40629) SS BOND : bond 0.00685 ( 45) SS BOND : angle 1.97891 ( 90) hydrogen bonds : bond 0.05098 ( 1052) hydrogen bonds : angle 5.51836 ( 2859) link_NAG-ASN : bond 0.00797 ( 27) link_NAG-ASN : angle 3.34832 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 604 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7940 (m-40) cc_final: 0.7507 (t0) REVERT: A 168 PHE cc_start: 0.7667 (t80) cc_final: 0.7328 (t80) REVERT: A 190 ARG cc_start: 0.7758 (mpt180) cc_final: 0.7399 (mtt90) REVERT: A 200 TYR cc_start: 0.7201 (m-80) cc_final: 0.6913 (m-80) REVERT: A 229 LEU cc_start: 0.8170 (mt) cc_final: 0.7890 (mp) REVERT: A 424 LYS cc_start: 0.8530 (tptm) cc_final: 0.8199 (tptm) REVERT: A 465 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6869 (mt-10) REVERT: A 498 ARG cc_start: 0.7452 (mpt180) cc_final: 0.7188 (mpt180) REVERT: A 537 LYS cc_start: 0.8103 (mtmm) cc_final: 0.7903 (mtpt) REVERT: A 542 ASN cc_start: 0.7356 (t0) cc_final: 0.7139 (t0) REVERT: A 558 LYS cc_start: 0.8054 (mmtm) cc_final: 0.7809 (mmmm) REVERT: A 574 ASP cc_start: 0.7477 (t0) cc_final: 0.7190 (t0) REVERT: A 646 ARG cc_start: 0.8113 (ttt90) cc_final: 0.7802 (ttt90) REVERT: A 779 GLN cc_start: 0.8231 (tp40) cc_final: 0.7962 (tm-30) REVERT: A 1084 ASP cc_start: 0.7614 (t0) cc_final: 0.7066 (t0) REVERT: A 1139 ASP cc_start: 0.7850 (t0) cc_final: 0.7639 (t0) REVERT: K 90 HIS cc_start: 0.8391 (t70) cc_final: 0.8126 (t-90) REVERT: K 97 MET cc_start: 0.7362 (mmm) cc_final: 0.6827 (mmm) REVERT: B 158 ARG cc_start: 0.6500 (tpt90) cc_final: 0.6261 (tpt170) REVERT: B 190 ARG cc_start: 0.7858 (mpt180) cc_final: 0.7561 (mtt90) REVERT: B 239 GLN cc_start: 0.7685 (tt0) cc_final: 0.7201 (tt0) REVERT: B 305 SER cc_start: 0.8364 (t) cc_final: 0.8153 (p) REVERT: B 356 LYS cc_start: 0.7686 (tppt) cc_final: 0.7478 (tptp) REVERT: B 403 ARG cc_start: 0.7135 (mtt180) cc_final: 0.6670 (mtt180) REVERT: B 465 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6920 (mt-10) REVERT: B 467 ASP cc_start: 0.7735 (t0) cc_final: 0.7265 (t0) REVERT: B 531 THR cc_start: 0.8215 (m) cc_final: 0.7876 (p) REVERT: B 583 GLU cc_start: 0.6859 (tp30) cc_final: 0.6540 (tp30) REVERT: B 585 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7333 (pp) REVERT: B 587 ILE cc_start: 0.8401 (mm) cc_final: 0.8199 (mt) REVERT: B 646 ARG cc_start: 0.7915 (ttt90) cc_final: 0.7693 (ttt90) REVERT: B 702 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7144 (mt-10) REVERT: B 779 GLN cc_start: 0.8345 (tp40) cc_final: 0.8055 (tm-30) REVERT: B 804 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7950 (mm-40) REVERT: B 1084 ASP cc_start: 0.7540 (t0) cc_final: 0.7068 (t0) REVERT: B 1139 ASP cc_start: 0.7761 (t0) cc_final: 0.7420 (t0) REVERT: C 39 ARG cc_start: 0.7170 (ttm-80) cc_final: 0.6834 (ttt180) REVERT: C 48 TRP cc_start: 0.8212 (t60) cc_final: 0.7574 (t60) REVERT: D 4 MET cc_start: 0.7065 (mmm) cc_final: 0.6791 (mmm) REVERT: D 55 GLN cc_start: 0.7004 (tm130) cc_final: 0.6378 (mp10) REVERT: E 47 SER cc_start: 0.8284 (t) cc_final: 0.8009 (t) REVERT: E 121 ASN cc_start: 0.7881 (m-40) cc_final: 0.7470 (t0) REVERT: E 239 GLN cc_start: 0.7559 (tt0) cc_final: 0.7078 (tt0) REVERT: E 355 ARG cc_start: 0.8057 (tpp80) cc_final: 0.7637 (tpp80) REVERT: E 424 LYS cc_start: 0.8442 (tptm) cc_final: 0.8207 (tptm) REVERT: E 425 LEU cc_start: 0.7990 (mt) cc_final: 0.7670 (mt) REVERT: E 465 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7005 (mt-10) REVERT: E 513 LEU cc_start: 0.7799 (mt) cc_final: 0.7492 (mt) REVERT: E 559 PHE cc_start: 0.8019 (m-10) cc_final: 0.7439 (m-10) REVERT: E 784 GLN cc_start: 0.8543 (mt0) cc_final: 0.8270 (mt0) REVERT: E 790 LYS cc_start: 0.8668 (mttm) cc_final: 0.8220 (mttm) REVERT: E 859 THR cc_start: 0.8288 (p) cc_final: 0.8061 (t) REVERT: E 904 TYR cc_start: 0.8156 (m-10) cc_final: 0.7519 (m-10) REVERT: E 1084 ASP cc_start: 0.7551 (t0) cc_final: 0.7084 (t0) REVERT: E 1114 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7968 (mt) REVERT: E 1139 ASP cc_start: 0.7907 (t0) cc_final: 0.7543 (t0) REVERT: F 35 MET cc_start: 0.7777 (mmm) cc_final: 0.7555 (mmm) REVERT: F 59 PHE cc_start: 0.8102 (m-80) cc_final: 0.7880 (m-80) REVERT: F 83 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6745 (mtp) REVERT: G 97 MET cc_start: 0.7517 (mmm) cc_final: 0.7199 (mmm) outliers start: 31 outliers final: 10 residues processed: 616 average time/residue: 0.1769 time to fit residues: 171.3336 Evaluate side-chains 579 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 566 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 304 LYS Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain F residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 290 optimal weight: 0.0570 chunk 107 optimal weight: 0.6980 chunk 128 optimal weight: 0.0000 chunk 255 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 258 optimal weight: 0.7980 chunk 250 optimal weight: 0.6980 chunk 322 optimal weight: 2.9990 overall best weight: 0.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 544 ASN A 774 GLN K 55 GLN B 115 GLN B 207 HIS B 417 ASN B 542 ASN B 774 GLN D 38 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 207 HIS E 460 ASN E 564 GLN E 774 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.170050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.135261 restraints weight = 46752.132| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.74 r_work: 0.3669 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 29952 Z= 0.127 Angle : 0.592 16.130 40800 Z= 0.296 Chirality : 0.045 0.370 4638 Planarity : 0.004 0.052 5214 Dihedral : 6.100 54.180 4548 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.37 % Allowed : 11.05 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.14), residues: 3627 helix: 2.39 (0.21), residues: 627 sheet: 0.25 (0.17), residues: 963 loop : -1.28 (0.12), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 357 TYR 0.021 0.001 TYR B 266 PHE 0.017 0.001 PHE A 592 TRP 0.027 0.001 TRP D 35 HIS 0.007 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00293 (29880) covalent geometry : angle 0.56340 (40629) SS BOND : bond 0.00747 ( 45) SS BOND : angle 2.26910 ( 90) hydrogen bonds : bond 0.04421 ( 1052) hydrogen bonds : angle 5.19638 ( 2859) link_NAG-ASN : bond 0.00811 ( 27) link_NAG-ASN : angle 3.42222 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 573 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.7184 (mm) cc_final: 0.6942 (mm) REVERT: A 121 ASN cc_start: 0.7885 (m-40) cc_final: 0.7425 (t0) REVERT: A 168 PHE cc_start: 0.7514 (t80) cc_final: 0.7189 (t80) REVERT: A 190 ARG cc_start: 0.7751 (mpt180) cc_final: 0.7396 (mtt90) REVERT: A 200 TYR cc_start: 0.7189 (m-80) cc_final: 0.6914 (m-80) REVERT: A 229 LEU cc_start: 0.8114 (mt) cc_final: 0.7847 (mp) REVERT: A 266 TYR cc_start: 0.7515 (m-10) cc_final: 0.7291 (m-80) REVERT: A 424 LYS cc_start: 0.8487 (tptm) cc_final: 0.8252 (tptm) REVERT: A 465 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6945 (mt-10) REVERT: A 537 LYS cc_start: 0.8096 (mtmm) cc_final: 0.7871 (mtpt) REVERT: A 542 ASN cc_start: 0.7386 (t0) cc_final: 0.7184 (t0) REVERT: A 567 ARG cc_start: 0.7945 (ttm170) cc_final: 0.7591 (mtt90) REVERT: A 574 ASP cc_start: 0.7406 (t0) cc_final: 0.7158 (t0) REVERT: A 646 ARG cc_start: 0.8027 (ttt90) cc_final: 0.7729 (ttt90) REVERT: A 749 CYS cc_start: 0.6108 (OUTLIER) cc_final: 0.5799 (t) REVERT: A 776 LYS cc_start: 0.8411 (ttpt) cc_final: 0.8096 (tttp) REVERT: A 779 GLN cc_start: 0.8175 (tp40) cc_final: 0.7929 (tm-30) REVERT: A 945 LEU cc_start: 0.8121 (mt) cc_final: 0.7866 (mp) REVERT: A 1084 ASP cc_start: 0.7589 (t0) cc_final: 0.7030 (t0) REVERT: A 1139 ASP cc_start: 0.7901 (t0) cc_final: 0.7660 (t0) REVERT: K 97 MET cc_start: 0.7131 (mmm) cc_final: 0.6814 (mmm) REVERT: B 188 ASN cc_start: 0.7205 (p0) cc_final: 0.6957 (p0) REVERT: B 239 GLN cc_start: 0.7710 (tt0) cc_final: 0.7226 (tt0) REVERT: B 305 SER cc_start: 0.8373 (t) cc_final: 0.8151 (p) REVERT: B 403 ARG cc_start: 0.7154 (mtt180) cc_final: 0.6626 (mtt180) REVERT: B 425 LEU cc_start: 0.8200 (mt) cc_final: 0.7986 (mt) REVERT: B 453 TYR cc_start: 0.7817 (p90) cc_final: 0.7564 (p90) REVERT: B 467 ASP cc_start: 0.7689 (t0) cc_final: 0.7402 (t0) REVERT: B 498 ARG cc_start: 0.7368 (mmt180) cc_final: 0.7009 (mmp-170) REVERT: B 567 ARG cc_start: 0.8081 (ttm170) cc_final: 0.7814 (mtt90) REVERT: B 583 GLU cc_start: 0.6892 (tp30) cc_final: 0.6476 (tp30) REVERT: B 585 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7277 (pp) REVERT: B 587 ILE cc_start: 0.8292 (mm) cc_final: 0.8080 (mt) REVERT: B 646 ARG cc_start: 0.7838 (ttt90) cc_final: 0.7610 (ttt90) REVERT: B 749 CYS cc_start: 0.6143 (OUTLIER) cc_final: 0.5673 (t) REVERT: B 779 GLN cc_start: 0.8305 (tp40) cc_final: 0.8021 (tm-30) REVERT: B 804 GLN cc_start: 0.8428 (mm-40) cc_final: 0.7996 (mm-40) REVERT: B 1084 ASP cc_start: 0.7569 (t0) cc_final: 0.7037 (t0) REVERT: B 1139 ASP cc_start: 0.7757 (t0) cc_final: 0.7411 (t0) REVERT: C 39 ARG cc_start: 0.7266 (ttm-80) cc_final: 0.6787 (ttt180) REVERT: C 48 TRP cc_start: 0.8326 (t60) cc_final: 0.7699 (t60) REVERT: D 4 MET cc_start: 0.7091 (mmm) cc_final: 0.6814 (mmm) REVERT: E 121 ASN cc_start: 0.7845 (m-40) cc_final: 0.7456 (t0) REVERT: E 129 LYS cc_start: 0.8010 (ptmt) cc_final: 0.7572 (ptmm) REVERT: E 239 GLN cc_start: 0.7601 (tt0) cc_final: 0.7120 (tt0) REVERT: E 355 ARG cc_start: 0.7958 (tpp80) cc_final: 0.7674 (tpp80) REVERT: E 424 LYS cc_start: 0.8471 (tptm) cc_final: 0.8175 (tptm) REVERT: E 425 LEU cc_start: 0.7986 (mt) cc_final: 0.7642 (mt) REVERT: E 434 ILE cc_start: 0.7978 (mt) cc_final: 0.7753 (mt) REVERT: E 465 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6991 (mt-10) REVERT: E 513 LEU cc_start: 0.7772 (mt) cc_final: 0.7443 (mt) REVERT: E 559 PHE cc_start: 0.8069 (m-10) cc_final: 0.7831 (m-10) REVERT: E 690 GLN cc_start: 0.7719 (mm110) cc_final: 0.7317 (mm-40) REVERT: E 784 GLN cc_start: 0.8516 (mt0) cc_final: 0.8281 (mt0) REVERT: E 859 THR cc_start: 0.8292 (p) cc_final: 0.8090 (t) REVERT: E 869 MET cc_start: 0.8360 (mtt) cc_final: 0.8080 (mtt) REVERT: E 894 LEU cc_start: 0.8770 (mt) cc_final: 0.8523 (mt) REVERT: E 904 TYR cc_start: 0.8176 (m-10) cc_final: 0.7572 (m-10) REVERT: E 1084 ASP cc_start: 0.7569 (t0) cc_final: 0.7107 (t0) REVERT: E 1102 TRP cc_start: 0.8483 (m100) cc_final: 0.8146 (m100) REVERT: E 1139 ASP cc_start: 0.7878 (t0) cc_final: 0.7535 (t0) REVERT: F 59 PHE cc_start: 0.8076 (m-80) cc_final: 0.7850 (m-80) REVERT: F 83 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6810 (mtp) REVERT: G 97 MET cc_start: 0.7549 (mmm) cc_final: 0.7185 (mmm) outliers start: 44 outliers final: 22 residues processed: 599 average time/residue: 0.1906 time to fit residues: 178.2429 Evaluate side-chains 585 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 559 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 369 TYR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 5 optimal weight: 0.2980 chunk 122 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 302 optimal weight: 0.0980 chunk 220 optimal weight: 0.8980 chunk 257 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 207 HIS A 774 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN B 115 GLN B 125 ASN B 207 HIS B 544 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 207 HIS E 460 ASN E 564 GLN E 856 ASN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.170061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.135389 restraints weight = 46771.871| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.74 r_work: 0.3663 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 29952 Z= 0.119 Angle : 0.581 15.851 40800 Z= 0.287 Chirality : 0.044 0.310 4638 Planarity : 0.004 0.050 5214 Dihedral : 5.845 59.680 4548 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.46 % Allowed : 12.95 % Favored : 85.59 % 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 aren not related in a simple way. whole: -0.18 (0.14), residues: 3627 helix: 2.44 (0.21), residues: 627 sheet: 0.38 (0.17), residues: 921 loop : -1.23 (0.12), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.018 0.001 TYR B1067 PHE 0.016 0.001 PHE A 592 TRP 0.025 0.001 TRP D 35 HIS 0.013 0.001 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00272 (29880) covalent geometry : angle 0.54810 (40629) SS BOND : bond 0.00562 ( 45) SS BOND : angle 1.80051 ( 90) hydrogen bonds : bond 0.04159 ( 1052) hydrogen bonds : angle 4.97800 ( 2859) link_NAG-ASN : bond 0.00904 ( 27) link_NAG-ASN : angle 3.95144 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 577 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.7165 (mm) cc_final: 0.6910 (mm) REVERT: A 121 ASN cc_start: 0.7907 (m-40) cc_final: 0.7383 (t0) REVERT: A 190 ARG cc_start: 0.7770 (mpt180) cc_final: 0.7401 (mtt90) REVERT: A 200 TYR cc_start: 0.7158 (m-80) cc_final: 0.6875 (m-80) REVERT: A 266 TYR cc_start: 0.7479 (m-10) cc_final: 0.7173 (m-80) REVERT: A 356 LYS cc_start: 0.7680 (tptp) cc_final: 0.7474 (tptp) REVERT: A 465 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6955 (mt-10) REVERT: A 492 LEU cc_start: 0.9067 (pp) cc_final: 0.8620 (pp) REVERT: A 537 LYS cc_start: 0.8054 (mtmm) cc_final: 0.7841 (mtpt) REVERT: A 542 ASN cc_start: 0.7412 (t0) cc_final: 0.7163 (t0) REVERT: A 567 ARG cc_start: 0.7908 (ttm170) cc_final: 0.7699 (mtt90) REVERT: A 574 ASP cc_start: 0.7457 (t0) cc_final: 0.7255 (t0) REVERT: A 646 ARG cc_start: 0.8020 (ttt90) cc_final: 0.7713 (ttt90) REVERT: A 776 LYS cc_start: 0.8376 (ttpt) cc_final: 0.8075 (tttp) REVERT: A 779 GLN cc_start: 0.8189 (tp40) cc_final: 0.7928 (tm-30) REVERT: A 790 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8177 (mttt) REVERT: A 945 LEU cc_start: 0.8074 (mt) cc_final: 0.7855 (mp) REVERT: A 1084 ASP cc_start: 0.7613 (t0) cc_final: 0.7054 (t0) REVERT: A 1139 ASP cc_start: 0.7919 (t0) cc_final: 0.7691 (t0) REVERT: H 93 VAL cc_start: 0.7372 (OUTLIER) cc_final: 0.7155 (p) REVERT: K 97 MET cc_start: 0.7284 (mmm) cc_final: 0.6868 (mmm) REVERT: B 188 ASN cc_start: 0.7198 (p0) cc_final: 0.6905 (p0) REVERT: B 239 GLN cc_start: 0.7679 (tt0) cc_final: 0.7187 (tt0) REVERT: B 298 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7750 (tt0) REVERT: B 305 SER cc_start: 0.8366 (t) cc_final: 0.8145 (p) REVERT: B 356 LYS cc_start: 0.7494 (tptp) cc_final: 0.7202 (tptp) REVERT: B 403 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6664 (mtt180) REVERT: B 424 LYS cc_start: 0.8610 (tptp) cc_final: 0.8388 (tptp) REVERT: B 425 LEU cc_start: 0.8314 (mt) cc_final: 0.7931 (mt) REVERT: B 453 TYR cc_start: 0.7768 (p90) cc_final: 0.7528 (p90) REVERT: B 467 ASP cc_start: 0.7650 (t0) cc_final: 0.7292 (t0) REVERT: B 498 ARG cc_start: 0.7665 (mmt180) cc_final: 0.7103 (mmp-170) REVERT: B 567 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7855 (mtt90) REVERT: B 583 GLU cc_start: 0.6903 (tp30) cc_final: 0.6465 (tp30) REVERT: B 585 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7237 (pp) REVERT: B 646 ARG cc_start: 0.7872 (ttt90) cc_final: 0.7649 (ttt90) REVERT: B 749 CYS cc_start: 0.6058 (OUTLIER) cc_final: 0.5723 (t) REVERT: B 779 GLN cc_start: 0.8285 (tp40) cc_final: 0.8015 (tm-30) REVERT: B 804 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8010 (mm-40) REVERT: B 1031 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7753 (mt-10) REVERT: B 1084 ASP cc_start: 0.7571 (t0) cc_final: 0.6988 (t0) REVERT: B 1139 ASP cc_start: 0.7770 (t0) cc_final: 0.7432 (t0) REVERT: C 39 ARG cc_start: 0.7284 (ttm-80) cc_final: 0.6740 (ttt180) REVERT: C 48 TRP cc_start: 0.8467 (t60) cc_final: 0.7724 (t60) REVERT: D 4 MET cc_start: 0.7145 (mmm) cc_final: 0.6913 (mmm) REVERT: D 97 MET cc_start: 0.7795 (mmm) cc_final: 0.7430 (mmm) REVERT: E 129 LYS cc_start: 0.7960 (ptmt) cc_final: 0.7587 (ptmm) REVERT: E 239 GLN cc_start: 0.7603 (tt0) cc_final: 0.7109 (tt0) REVERT: E 355 ARG cc_start: 0.7940 (tpp80) cc_final: 0.7714 (tpp80) REVERT: E 465 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6948 (mt-10) REVERT: E 513 LEU cc_start: 0.7828 (mt) cc_final: 0.7510 (mt) REVERT: E 559 PHE cc_start: 0.8075 (m-10) cc_final: 0.7837 (m-10) REVERT: E 675 GLN cc_start: 0.7245 (tt0) cc_final: 0.7006 (mt0) REVERT: E 690 GLN cc_start: 0.7723 (mm110) cc_final: 0.7307 (mm110) REVERT: E 784 GLN cc_start: 0.8525 (mt0) cc_final: 0.8267 (mt0) REVERT: E 790 LYS cc_start: 0.8633 (mttm) cc_final: 0.8410 (mttm) REVERT: E 804 GLN cc_start: 0.8395 (mm-40) cc_final: 0.7756 (mm-40) REVERT: E 869 MET cc_start: 0.8342 (mtt) cc_final: 0.8071 (mtt) REVERT: E 904 TYR cc_start: 0.8197 (m-10) cc_final: 0.7562 (m-10) REVERT: E 1084 ASP cc_start: 0.7633 (t0) cc_final: 0.7146 (t0) REVERT: E 1102 TRP cc_start: 0.8488 (m100) cc_final: 0.8154 (m100) REVERT: E 1139 ASP cc_start: 0.7864 (t0) cc_final: 0.7505 (t0) REVERT: F 39 ARG cc_start: 0.6875 (ttm-80) cc_final: 0.6406 (ttt180) REVERT: F 59 PHE cc_start: 0.8257 (m-80) cc_final: 0.8012 (m-80) REVERT: F 83 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6575 (mtp) REVERT: G 55 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6683 (tm130) REVERT: G 97 MET cc_start: 0.7677 (mmm) cc_final: 0.7217 (mmm) outliers start: 47 outliers final: 24 residues processed: 605 average time/residue: 0.2020 time to fit residues: 191.4785 Evaluate side-chains 588 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 558 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain G residue 55 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 221 optimal weight: 0.0970 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 243 optimal weight: 0.0040 chunk 58 optimal weight: 2.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 544 ASN A 774 GLN A 853 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN B 115 GLN B 207 HIS B 542 ASN B 544 ASN B 774 GLN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 207 HIS E 460 ASN E 564 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.167533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.132850 restraints weight = 46421.537| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.73 r_work: 0.3624 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 29952 Z= 0.188 Angle : 0.611 13.744 40800 Z= 0.307 Chirality : 0.046 0.308 4638 Planarity : 0.004 0.051 5214 Dihedral : 5.720 54.670 4548 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.84 % Allowed : 13.41 % Favored : 84.75 % 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 aren not related in a simple way. whole: -0.27 (0.13), residues: 3627 helix: 2.29 (0.21), residues: 627 sheet: 0.29 (0.17), residues: 936 loop : -1.25 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 357 TYR 0.023 0.002 TYR B 266 PHE 0.020 0.002 PHE A 45 TRP 0.029 0.002 TRP K 35 HIS 0.006 0.001 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00443 (29880) covalent geometry : angle 0.58085 (40629) SS BOND : bond 0.00622 ( 45) SS BOND : angle 2.14580 ( 90) hydrogen bonds : bond 0.04785 ( 1052) hydrogen bonds : angle 5.00383 ( 2859) link_NAG-ASN : bond 0.00870 ( 27) link_NAG-ASN : angle 3.73210 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 584 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7776 (mpt180) cc_final: 0.7400 (mtt90) REVERT: A 266 TYR cc_start: 0.7543 (m-10) cc_final: 0.7091 (m-80) REVERT: A 357 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.8066 (ttm-80) REVERT: A 542 ASN cc_start: 0.7437 (t0) cc_final: 0.7173 (t0) REVERT: A 567 ARG cc_start: 0.7964 (ttm170) cc_final: 0.7733 (mtt90) REVERT: A 646 ARG cc_start: 0.8063 (ttt90) cc_final: 0.7748 (ttt90) REVERT: A 779 GLN cc_start: 0.8267 (tp40) cc_final: 0.8004 (tm-30) REVERT: A 790 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7905 (mttp) REVERT: A 945 LEU cc_start: 0.8189 (mt) cc_final: 0.7980 (mp) REVERT: A 1084 ASP cc_start: 0.7680 (t0) cc_final: 0.7132 (t0) REVERT: A 1139 ASP cc_start: 0.7919 (t0) cc_final: 0.7501 (t0) REVERT: H 95 TYR cc_start: 0.8376 (m-80) cc_final: 0.8100 (m-80) REVERT: K 97 MET cc_start: 0.7401 (mmm) cc_final: 0.7012 (mmm) REVERT: B 110 LEU cc_start: 0.7416 (mm) cc_final: 0.7165 (mm) REVERT: B 188 ASN cc_start: 0.7271 (p0) cc_final: 0.6997 (p0) REVERT: B 239 GLN cc_start: 0.7627 (tt0) cc_final: 0.7192 (tt0) REVERT: B 298 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7577 (mt-10) REVERT: B 305 SER cc_start: 0.8413 (t) cc_final: 0.8178 (p) REVERT: B 467 ASP cc_start: 0.7675 (t0) cc_final: 0.7336 (t0) REVERT: B 534 VAL cc_start: 0.8356 (p) cc_final: 0.8152 (p) REVERT: B 537 LYS cc_start: 0.8580 (mtmt) cc_final: 0.8312 (mttp) REVERT: B 583 GLU cc_start: 0.6959 (tp30) cc_final: 0.6593 (tp30) REVERT: B 585 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7345 (pp) REVERT: B 646 ARG cc_start: 0.7930 (ttt90) cc_final: 0.7708 (ttt90) REVERT: B 749 CYS cc_start: 0.5888 (OUTLIER) cc_final: 0.5605 (t) REVERT: B 779 GLN cc_start: 0.8369 (tp40) cc_final: 0.8123 (tm-30) REVERT: B 804 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8118 (mm-40) REVERT: B 1002 GLN cc_start: 0.7633 (mm110) cc_final: 0.7332 (mm-40) REVERT: B 1031 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7700 (mt-10) REVERT: B 1084 ASP cc_start: 0.7663 (t0) cc_final: 0.7110 (t0) REVERT: B 1139 ASP cc_start: 0.7767 (t0) cc_final: 0.7423 (t0) REVERT: C 39 ARG cc_start: 0.7313 (ttm-80) cc_final: 0.6760 (ttt180) REVERT: D 4 MET cc_start: 0.7240 (mmm) cc_final: 0.6960 (mmm) REVERT: D 55 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6348 (tm130) REVERT: D 97 MET cc_start: 0.7819 (mmm) cc_final: 0.7445 (mmm) REVERT: E 110 LEU cc_start: 0.7236 (mm) cc_final: 0.7011 (mm) REVERT: E 129 LYS cc_start: 0.8073 (ptmt) cc_final: 0.7685 (ptmm) REVERT: E 239 GLN cc_start: 0.7644 (tt0) cc_final: 0.7149 (tt0) REVERT: E 355 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7529 (ttt180) REVERT: E 356 LYS cc_start: 0.8094 (tptp) cc_final: 0.7841 (tptp) REVERT: E 434 ILE cc_start: 0.8001 (mt) cc_final: 0.7786 (mt) REVERT: E 465 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6958 (mt-10) REVERT: E 513 LEU cc_start: 0.7834 (mt) cc_final: 0.7464 (mt) REVERT: E 586 ASP cc_start: 0.7851 (m-30) cc_final: 0.7645 (m-30) REVERT: E 675 GLN cc_start: 0.7403 (tt0) cc_final: 0.7150 (mt0) REVERT: E 690 GLN cc_start: 0.7729 (mm110) cc_final: 0.7242 (mm-40) REVERT: E 735 SER cc_start: 0.8560 (t) cc_final: 0.8058 (p) REVERT: E 784 GLN cc_start: 0.8570 (mt0) cc_final: 0.8275 (mt0) REVERT: E 804 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7793 (mm-40) REVERT: E 869 MET cc_start: 0.8311 (mtt) cc_final: 0.8028 (mtt) REVERT: E 894 LEU cc_start: 0.8723 (mt) cc_final: 0.8475 (mt) REVERT: E 904 TYR cc_start: 0.8253 (m-10) cc_final: 0.7567 (m-10) REVERT: E 1084 ASP cc_start: 0.7755 (t0) cc_final: 0.7267 (t0) REVERT: E 1139 ASP cc_start: 0.7884 (t0) cc_final: 0.7544 (t0) REVERT: F 39 ARG cc_start: 0.7030 (ttm-80) cc_final: 0.6492 (ttt180) REVERT: F 59 PHE cc_start: 0.8309 (m-80) cc_final: 0.8067 (m-80) REVERT: F 83 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6386 (mtp) REVERT: G 55 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6904 (tm130) REVERT: G 97 MET cc_start: 0.7666 (mmm) cc_final: 0.7226 (mmm) outliers start: 59 outliers final: 34 residues processed: 614 average time/residue: 0.1715 time to fit residues: 166.6799 Evaluate side-chains 598 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 558 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 464 PHE Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 961 THR Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain G residue 55 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 0.9990 chunk 243 optimal weight: 0.1980 chunk 167 optimal weight: 0.6980 chunk 151 optimal weight: 20.0000 chunk 122 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 176 optimal weight: 0.4980 chunk 139 optimal weight: 0.0270 chunk 265 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 544 ASN A1010 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN B 207 HIS B 317 ASN B 542 ASN B 853 GLN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 115 GLN E 207 HIS E 564 GLN E 774 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.168571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.133877 restraints weight = 46392.935| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.73 r_work: 0.3646 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 29952 Z= 0.119 Angle : 0.607 16.561 40800 Z= 0.295 Chirality : 0.045 0.451 4638 Planarity : 0.004 0.063 5214 Dihedral : 5.615 58.326 4548 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.65 % Allowed : 14.57 % Favored : 83.78 % 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 aren not related in a simple way. whole: -0.22 (0.13), residues: 3627 helix: 2.48 (0.21), residues: 627 sheet: 0.28 (0.17), residues: 942 loop : -1.25 (0.12), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 498 TYR 0.018 0.001 TYR B1067 PHE 0.016 0.001 PHE E 592 TRP 0.025 0.001 TRP D 35 HIS 0.008 0.001 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00269 (29880) covalent geometry : angle 0.56296 (40629) SS BOND : bond 0.00547 ( 45) SS BOND : angle 1.76111 ( 90) hydrogen bonds : bond 0.04151 ( 1052) hydrogen bonds : angle 4.84948 ( 2859) link_NAG-ASN : bond 0.01026 ( 27) link_NAG-ASN : angle 4.79938 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 565 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7958 (m-40) cc_final: 0.7404 (t0) REVERT: A 266 TYR cc_start: 0.7453 (m-10) cc_final: 0.7071 (m-80) REVERT: A 358 ILE cc_start: 0.7643 (mp) cc_final: 0.7415 (tt) REVERT: A 465 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7158 (mt-10) REVERT: A 542 ASN cc_start: 0.7434 (t0) cc_final: 0.7171 (t0) REVERT: A 646 ARG cc_start: 0.8052 (ttt90) cc_final: 0.7737 (ttt90) REVERT: A 776 LYS cc_start: 0.8398 (ttpt) cc_final: 0.8089 (tttp) REVERT: A 779 GLN cc_start: 0.8209 (tp40) cc_final: 0.7950 (tm-30) REVERT: A 790 LYS cc_start: 0.8478 (mttt) cc_final: 0.8184 (mttp) REVERT: A 945 LEU cc_start: 0.8127 (mt) cc_final: 0.7914 (mp) REVERT: A 980 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8030 (mp) REVERT: A 1084 ASP cc_start: 0.7668 (t0) cc_final: 0.7125 (t0) REVERT: A 1139 ASP cc_start: 0.7893 (t0) cc_final: 0.7477 (t0) REVERT: H 95 TYR cc_start: 0.8363 (m-80) cc_final: 0.8124 (m-80) REVERT: K 97 MET cc_start: 0.7417 (mmm) cc_final: 0.7005 (mmm) REVERT: B 110 LEU cc_start: 0.7251 (mm) cc_final: 0.6991 (mm) REVERT: B 188 ASN cc_start: 0.7289 (p0) cc_final: 0.7025 (p0) REVERT: B 239 GLN cc_start: 0.7570 (tt0) cc_final: 0.7150 (tt0) REVERT: B 298 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7531 (mt-10) REVERT: B 305 SER cc_start: 0.8408 (t) cc_final: 0.8185 (p) REVERT: B 403 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6671 (mtt180) REVERT: B 467 ASP cc_start: 0.7604 (t0) cc_final: 0.7282 (t0) REVERT: B 498 ARG cc_start: 0.8027 (mmp80) cc_final: 0.7578 (mmp-170) REVERT: B 537 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8233 (mttp) REVERT: B 583 GLU cc_start: 0.6903 (tp30) cc_final: 0.6542 (tp30) REVERT: B 585 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7265 (pp) REVERT: B 592 PHE cc_start: 0.8658 (p90) cc_final: 0.8295 (p90) REVERT: B 646 ARG cc_start: 0.7897 (ttt90) cc_final: 0.7670 (ttt90) REVERT: B 749 CYS cc_start: 0.5823 (OUTLIER) cc_final: 0.5578 (t) REVERT: B 779 GLN cc_start: 0.8285 (tp40) cc_final: 0.8059 (tm-30) REVERT: B 804 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8075 (mm-40) REVERT: B 980 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8141 (mp) REVERT: B 1002 GLN cc_start: 0.7567 (mm110) cc_final: 0.7285 (mm-40) REVERT: B 1031 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7687 (mt-10) REVERT: B 1084 ASP cc_start: 0.7652 (t0) cc_final: 0.7094 (t0) REVERT: B 1139 ASP cc_start: 0.7721 (t0) cc_final: 0.7393 (t0) REVERT: C 39 ARG cc_start: 0.7276 (ttm-80) cc_final: 0.6751 (ttt180) REVERT: C 113 MET cc_start: 0.7549 (mmm) cc_final: 0.7280 (mmm) REVERT: D 4 MET cc_start: 0.7241 (mmm) cc_final: 0.7018 (mmm) REVERT: D 55 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6321 (tm130) REVERT: D 97 MET cc_start: 0.7765 (mmm) cc_final: 0.7376 (mmm) REVERT: E 110 LEU cc_start: 0.7280 (mm) cc_final: 0.7057 (mm) REVERT: E 118 LEU cc_start: 0.7878 (tt) cc_final: 0.7595 (tp) REVERT: E 129 LYS cc_start: 0.7970 (ptmt) cc_final: 0.7593 (ptmm) REVERT: E 239 GLN cc_start: 0.7598 (tt0) cc_final: 0.7086 (tt0) REVERT: E 353 TRP cc_start: 0.8089 (p-90) cc_final: 0.7373 (p-90) REVERT: E 355 ARG cc_start: 0.7978 (tpp80) cc_final: 0.7431 (ttt180) REVERT: E 356 LYS cc_start: 0.8079 (tptp) cc_final: 0.7831 (tptp) REVERT: E 434 ILE cc_start: 0.8009 (mt) cc_final: 0.7782 (mt) REVERT: E 465 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6898 (mt-10) REVERT: E 513 LEU cc_start: 0.7841 (mt) cc_final: 0.7430 (mt) REVERT: E 537 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8140 (mtmt) REVERT: E 675 GLN cc_start: 0.7381 (tt0) cc_final: 0.7128 (mt0) REVERT: E 690 GLN cc_start: 0.7702 (mm110) cc_final: 0.7223 (mm-40) REVERT: E 773 GLU cc_start: 0.7479 (tt0) cc_final: 0.7273 (tt0) REVERT: E 784 GLN cc_start: 0.8514 (mt0) cc_final: 0.8254 (mt0) REVERT: E 804 GLN cc_start: 0.8381 (mm-40) cc_final: 0.7762 (mm-40) REVERT: E 869 MET cc_start: 0.8300 (mtt) cc_final: 0.8016 (mtt) REVERT: E 904 TYR cc_start: 0.8225 (m-10) cc_final: 0.7603 (m-10) REVERT: E 980 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8046 (mp) REVERT: E 1084 ASP cc_start: 0.7758 (t0) cc_final: 0.7271 (t0) REVERT: E 1139 ASP cc_start: 0.7854 (t0) cc_final: 0.7482 (t0) REVERT: F 39 ARG cc_start: 0.7133 (ttm-80) cc_final: 0.6523 (ttt180) REVERT: F 59 PHE cc_start: 0.8319 (m-80) cc_final: 0.8085 (m-80) REVERT: F 83 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6375 (mtp) REVERT: G 97 MET cc_start: 0.7655 (mmm) cc_final: 0.7201 (mmm) outliers start: 53 outliers final: 30 residues processed: 599 average time/residue: 0.1753 time to fit residues: 166.3529 Evaluate side-chains 593 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 556 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 980 ILE Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 221 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 324 optimal weight: 0.7980 chunk 359 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 342 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 856 ASN K 37 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN B 32 ASN B 207 HIS B 317 ASN B 394 ASN B 774 GLN E 32 ASN E 125 ASN E 207 HIS ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.164804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.130085 restraints weight = 46178.846| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.74 r_work: 0.3581 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 29952 Z= 0.268 Angle : 0.690 14.965 40800 Z= 0.348 Chirality : 0.049 0.495 4638 Planarity : 0.005 0.061 5214 Dihedral : 5.950 55.471 4548 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.27 % Allowed : 14.69 % Favored : 83.04 % 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 aren not related in a simple way. whole: -0.49 (0.13), residues: 3627 helix: 2.04 (0.21), residues: 627 sheet: 0.17 (0.17), residues: 948 loop : -1.38 (0.12), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 498 TYR 0.024 0.002 TYR B 266 PHE 0.031 0.002 PHE A 45 TRP 0.034 0.002 TRP D 35 HIS 0.010 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00635 (29880) covalent geometry : angle 0.65472 (40629) SS BOND : bond 0.00581 ( 45) SS BOND : angle 2.30682 ( 90) hydrogen bonds : bond 0.05620 ( 1052) hydrogen bonds : angle 5.11773 ( 2859) link_NAG-ASN : bond 0.00973 ( 27) link_NAG-ASN : angle 4.30585 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 582 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7799 (mpt180) cc_final: 0.7317 (mtt90) REVERT: A 200 TYR cc_start: 0.7203 (m-80) cc_final: 0.6932 (m-80) REVERT: A 357 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7751 (ttm-80) REVERT: A 457 ARG cc_start: 0.8448 (mmm-85) cc_final: 0.8096 (tpp80) REVERT: A 465 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7211 (mt-10) REVERT: A 542 ASN cc_start: 0.7472 (t0) cc_final: 0.7228 (t0) REVERT: A 646 ARG cc_start: 0.8088 (ttt90) cc_final: 0.7792 (ttt90) REVERT: A 779 GLN cc_start: 0.8374 (tp40) cc_final: 0.8134 (tm-30) REVERT: A 790 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7890 (mtpt) REVERT: A 945 LEU cc_start: 0.8348 (mt) cc_final: 0.8114 (mp) REVERT: A 980 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8089 (mp) REVERT: A 1084 ASP cc_start: 0.7680 (t0) cc_final: 0.7127 (t0) REVERT: A 1114 ILE cc_start: 0.8229 (mm) cc_final: 0.8027 (mt) REVERT: A 1139 ASP cc_start: 0.7970 (t0) cc_final: 0.7544 (t0) REVERT: H 83 MET cc_start: 0.6841 (mtp) cc_final: 0.6591 (mtp) REVERT: H 93 VAL cc_start: 0.7478 (OUTLIER) cc_final: 0.7223 (p) REVERT: H 95 TYR cc_start: 0.8404 (m-80) cc_final: 0.8041 (m-80) REVERT: K 4 MET cc_start: 0.7261 (mmm) cc_final: 0.6880 (tmm) REVERT: K 97 MET cc_start: 0.7427 (mmm) cc_final: 0.7068 (mmm) REVERT: B 188 ASN cc_start: 0.7326 (p0) cc_final: 0.7066 (p0) REVERT: B 239 GLN cc_start: 0.7639 (tt0) cc_final: 0.7249 (tt0) REVERT: B 305 SER cc_start: 0.8454 (t) cc_final: 0.8237 (p) REVERT: B 453 TYR cc_start: 0.7627 (p90) cc_final: 0.7414 (p90) REVERT: B 467 ASP cc_start: 0.7639 (t0) cc_final: 0.7294 (t0) REVERT: B 498 ARG cc_start: 0.7984 (mmp80) cc_final: 0.7496 (mmp-170) REVERT: B 583 GLU cc_start: 0.6997 (tp30) cc_final: 0.6639 (tp30) REVERT: B 585 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7605 (pp) REVERT: B 646 ARG cc_start: 0.8014 (ttt90) cc_final: 0.7770 (ttt90) REVERT: B 749 CYS cc_start: 0.5744 (OUTLIER) cc_final: 0.5524 (t) REVERT: B 779 GLN cc_start: 0.8403 (tp40) cc_final: 0.8186 (tm-30) REVERT: B 804 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8178 (mm-40) REVERT: B 980 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8160 (mp) REVERT: B 1002 GLN cc_start: 0.7773 (mm110) cc_final: 0.7463 (mm-40) REVERT: B 1039 ARG cc_start: 0.8539 (mtp85) cc_final: 0.8319 (mtp180) REVERT: B 1084 ASP cc_start: 0.7759 (t0) cc_final: 0.7225 (t0) REVERT: B 1139 ASP cc_start: 0.7785 (t0) cc_final: 0.7464 (t0) REVERT: C 39 ARG cc_start: 0.7358 (ttm-80) cc_final: 0.6908 (ttm170) REVERT: C 83 MET cc_start: 0.6549 (mtm) cc_final: 0.6177 (mtp) REVERT: D 4 MET cc_start: 0.7269 (mmm) cc_final: 0.7023 (mmm) REVERT: D 55 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6471 (tm130) REVERT: D 97 MET cc_start: 0.7749 (mmm) cc_final: 0.7424 (mmm) REVERT: E 118 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7770 (tp) REVERT: E 129 LYS cc_start: 0.8143 (ptmt) cc_final: 0.7773 (ptmm) REVERT: E 239 GLN cc_start: 0.7531 (tt0) cc_final: 0.7117 (tt0) REVERT: E 305 SER cc_start: 0.8651 (t) cc_final: 0.8344 (p) REVERT: E 355 ARG cc_start: 0.8015 (tpp80) cc_final: 0.7514 (ttt180) REVERT: E 434 ILE cc_start: 0.8183 (mt) cc_final: 0.7931 (mt) REVERT: E 456 PHE cc_start: 0.8498 (m-80) cc_final: 0.8176 (m-10) REVERT: E 465 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7037 (mt-10) REVERT: E 513 LEU cc_start: 0.8042 (mt) cc_final: 0.7684 (mt) REVERT: E 675 GLN cc_start: 0.7502 (tt0) cc_final: 0.7263 (mt0) REVERT: E 690 GLN cc_start: 0.7720 (mm110) cc_final: 0.7290 (mm-40) REVERT: E 784 GLN cc_start: 0.8619 (mt0) cc_final: 0.8265 (mt0) REVERT: E 804 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7823 (mm-40) REVERT: E 869 MET cc_start: 0.8369 (mtt) cc_final: 0.8078 (mtt) REVERT: E 980 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8070 (mp) REVERT: E 1084 ASP cc_start: 0.7878 (t0) cc_final: 0.7414 (t0) REVERT: E 1139 ASP cc_start: 0.7879 (t0) cc_final: 0.7541 (t0) REVERT: F 39 ARG cc_start: 0.7205 (ttm-80) cc_final: 0.6678 (ttt180) REVERT: F 83 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6806 (mtp) REVERT: G 55 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6891 (tm130) REVERT: G 97 MET cc_start: 0.7718 (mmm) cc_final: 0.7308 (mmm) outliers start: 73 outliers final: 52 residues processed: 622 average time/residue: 0.1839 time to fit residues: 180.3325 Evaluate side-chains 620 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 557 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 464 PHE Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 641 ASN Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 961 THR Chi-restraints excluded: chain E residue 980 ILE Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain G residue 55 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 32 optimal weight: 0.7980 chunk 238 optimal weight: 9.9990 chunk 237 optimal weight: 0.3980 chunk 29 optimal weight: 0.0020 chunk 283 optimal weight: 7.9990 chunk 285 optimal weight: 3.9990 chunk 361 optimal weight: 5.9990 chunk 202 optimal weight: 0.0040 chunk 59 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 218 optimal weight: 0.3980 overall best weight: 0.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 207 HIS A 544 ASN K 55 GLN B 207 HIS B 542 ASN E 32 ASN E 207 HIS E 774 GLN ** E 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.168096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.133449 restraints weight = 46418.881| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.76 r_work: 0.3631 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29952 Z= 0.118 Angle : 0.616 18.309 40800 Z= 0.301 Chirality : 0.045 0.328 4638 Planarity : 0.004 0.053 5214 Dihedral : 5.655 58.247 4548 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.96 % Allowed : 15.90 % Favored : 82.14 % 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 aren not related in a simple way. whole: -0.27 (0.13), residues: 3627 helix: 2.42 (0.21), residues: 627 sheet: 0.24 (0.16), residues: 969 loop : -1.29 (0.12), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 158 TYR 0.019 0.001 TYR E 380 PHE 0.018 0.001 PHE E 592 TRP 0.043 0.002 TRP G 35 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00261 (29880) covalent geometry : angle 0.57247 (40629) SS BOND : bond 0.00515 ( 45) SS BOND : angle 1.80423 ( 90) hydrogen bonds : bond 0.04301 ( 1052) hydrogen bonds : angle 4.85320 ( 2859) link_NAG-ASN : bond 0.01112 ( 27) link_NAG-ASN : angle 4.81878 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 560 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7774 (mpt180) cc_final: 0.7533 (mtt-85) REVERT: A 358 ILE cc_start: 0.7731 (mp) cc_final: 0.7442 (tt) REVERT: A 377 PHE cc_start: 0.7042 (t80) cc_final: 0.6571 (t80) REVERT: A 465 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7064 (mt-10) REVERT: A 542 ASN cc_start: 0.7442 (t0) cc_final: 0.7186 (t0) REVERT: A 564 GLN cc_start: 0.7925 (mt0) cc_final: 0.7638 (mm-40) REVERT: A 646 ARG cc_start: 0.8073 (ttt90) cc_final: 0.7771 (ttt90) REVERT: A 776 LYS cc_start: 0.8407 (ttpt) cc_final: 0.8143 (tttt) REVERT: A 779 GLN cc_start: 0.8228 (tp40) cc_final: 0.7964 (tm-30) REVERT: A 980 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 1084 ASP cc_start: 0.7698 (t0) cc_final: 0.7162 (t0) REVERT: A 1114 ILE cc_start: 0.8229 (mm) cc_final: 0.8019 (mt) REVERT: A 1139 ASP cc_start: 0.7922 (t0) cc_final: 0.7509 (t0) REVERT: H 47 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7375 (tm-30) REVERT: H 83 MET cc_start: 0.6708 (mtp) cc_final: 0.6502 (mtp) REVERT: H 93 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7156 (p) REVERT: H 95 TYR cc_start: 0.8304 (m-80) cc_final: 0.7969 (m-80) REVERT: K 4 MET cc_start: 0.7286 (mmm) cc_final: 0.6864 (tmm) REVERT: K 55 GLN cc_start: 0.5139 (OUTLIER) cc_final: 0.4802 (pm20) REVERT: B 110 LEU cc_start: 0.7291 (mm) cc_final: 0.7081 (mm) REVERT: B 188 ASN cc_start: 0.7323 (p0) cc_final: 0.7071 (p0) REVERT: B 239 GLN cc_start: 0.7625 (tt0) cc_final: 0.7218 (tt0) REVERT: B 305 SER cc_start: 0.8402 (t) cc_final: 0.8183 (p) REVERT: B 403 ARG cc_start: 0.7379 (mtt180) cc_final: 0.6862 (mtt180) REVERT: B 467 ASP cc_start: 0.7548 (t0) cc_final: 0.7202 (t0) REVERT: B 498 ARG cc_start: 0.7934 (mmp80) cc_final: 0.7497 (mmp-170) REVERT: B 583 GLU cc_start: 0.6977 (tp30) cc_final: 0.6639 (tp30) REVERT: B 585 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7357 (pp) REVERT: B 592 PHE cc_start: 0.8684 (p90) cc_final: 0.8276 (p90) REVERT: B 646 ARG cc_start: 0.7915 (ttt90) cc_final: 0.7681 (ttt90) REVERT: B 804 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8120 (mm-40) REVERT: B 980 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8124 (mp) REVERT: B 1084 ASP cc_start: 0.7711 (t0) cc_final: 0.7168 (t0) REVERT: B 1139 ASP cc_start: 0.7798 (t0) cc_final: 0.7470 (t0) REVERT: C 39 ARG cc_start: 0.7232 (ttm-80) cc_final: 0.6831 (ttm170) REVERT: C 82 GLN cc_start: 0.8103 (tp40) cc_final: 0.7890 (tp40) REVERT: D 55 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6365 (tm130) REVERT: D 97 MET cc_start: 0.7723 (mmm) cc_final: 0.7465 (mmm) REVERT: E 118 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7619 (tp) REVERT: E 129 LYS cc_start: 0.8038 (ptmt) cc_final: 0.7665 (ptmm) REVERT: E 239 GLN cc_start: 0.7541 (tt0) cc_final: 0.7124 (tt0) REVERT: E 305 SER cc_start: 0.8636 (t) cc_final: 0.8326 (p) REVERT: E 353 TRP cc_start: 0.8082 (p-90) cc_final: 0.7408 (p-90) REVERT: E 355 ARG cc_start: 0.8005 (tpp80) cc_final: 0.7399 (ttt180) REVERT: E 434 ILE cc_start: 0.8193 (mt) cc_final: 0.7949 (mt) REVERT: E 456 PHE cc_start: 0.8477 (m-80) cc_final: 0.8146 (m-10) REVERT: E 465 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6883 (mt-10) REVERT: E 498 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.8065 (mmm-85) REVERT: E 513 LEU cc_start: 0.7954 (mt) cc_final: 0.7608 (mt) REVERT: E 537 LYS cc_start: 0.8404 (mtpt) cc_final: 0.8188 (mtmt) REVERT: E 675 GLN cc_start: 0.7416 (tt0) cc_final: 0.7181 (mt0) REVERT: E 784 GLN cc_start: 0.8510 (mt0) cc_final: 0.8241 (mt0) REVERT: E 804 GLN cc_start: 0.8364 (mm-40) cc_final: 0.7753 (mt0) REVERT: E 869 MET cc_start: 0.8290 (mtt) cc_final: 0.7983 (mtt) REVERT: E 904 TYR cc_start: 0.8280 (m-10) cc_final: 0.7604 (m-10) REVERT: E 980 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8059 (mp) REVERT: E 1084 ASP cc_start: 0.7884 (t0) cc_final: 0.7409 (t0) REVERT: E 1139 ASP cc_start: 0.7856 (t0) cc_final: 0.7483 (t0) REVERT: F 39 ARG cc_start: 0.7131 (ttm-80) cc_final: 0.6615 (ttt180) REVERT: F 83 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6372 (mtp) REVERT: G 55 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6849 (tm130) REVERT: G 97 MET cc_start: 0.7627 (mmm) cc_final: 0.7209 (mmm) outliers start: 63 outliers final: 43 residues processed: 592 average time/residue: 0.1946 time to fit residues: 180.3396 Evaluate side-chains 604 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 551 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain K residue 55 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 980 ILE Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain G residue 55 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 233 optimal weight: 10.0000 chunk 251 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 360 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 274 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 280 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 544 ASN A1002 GLN A1119 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN B 207 HIS B 774 GLN B 853 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 207 HIS E 690 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.167561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.132908 restraints weight = 46155.016| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.75 r_work: 0.3630 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29952 Z= 0.132 Angle : 0.620 16.830 40800 Z= 0.303 Chirality : 0.045 0.305 4638 Planarity : 0.004 0.053 5214 Dihedral : 5.538 56.936 4548 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.12 % Allowed : 16.40 % Favored : 81.48 % 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 aren not related in a simple way. whole: -0.23 (0.13), residues: 3627 helix: 2.43 (0.21), residues: 627 sheet: 0.28 (0.16), residues: 969 loop : -1.26 (0.12), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 158 TYR 0.024 0.001 TYR B 380 PHE 0.022 0.001 PHE E 168 TRP 0.032 0.002 TRP K 35 HIS 0.006 0.001 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00306 (29880) covalent geometry : angle 0.57934 (40629) SS BOND : bond 0.00516 ( 45) SS BOND : angle 2.00092 ( 90) hydrogen bonds : bond 0.04333 ( 1052) hydrogen bonds : angle 4.79234 ( 2859) link_NAG-ASN : bond 0.00962 ( 27) link_NAG-ASN : angle 4.55456 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 555 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.7817 (mp) cc_final: 0.7511 (tt) REVERT: A 377 PHE cc_start: 0.7089 (t80) cc_final: 0.6571 (t80) REVERT: A 457 ARG cc_start: 0.8412 (mmm-85) cc_final: 0.7945 (tpp80) REVERT: A 542 ASN cc_start: 0.7453 (t0) cc_final: 0.7186 (t0) REVERT: A 564 GLN cc_start: 0.8000 (mt0) cc_final: 0.7691 (mm-40) REVERT: A 776 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8121 (tttt) REVERT: A 779 GLN cc_start: 0.8226 (tp40) cc_final: 0.7974 (tm-30) REVERT: A 980 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8037 (mp) REVERT: A 1084 ASP cc_start: 0.7709 (t0) cc_final: 0.7174 (t0) REVERT: A 1139 ASP cc_start: 0.7908 (t0) cc_final: 0.7479 (t0) REVERT: H 47 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7265 (tm-30) REVERT: H 83 MET cc_start: 0.6695 (mtp) cc_final: 0.6459 (mtp) REVERT: H 93 VAL cc_start: 0.7493 (OUTLIER) cc_final: 0.7183 (p) REVERT: H 95 TYR cc_start: 0.8287 (m-80) cc_final: 0.7955 (m-80) REVERT: K 4 MET cc_start: 0.7275 (mmm) cc_final: 0.6837 (tmm) REVERT: B 110 LEU cc_start: 0.7266 (mm) cc_final: 0.7046 (mm) REVERT: B 188 ASN cc_start: 0.7317 (p0) cc_final: 0.7052 (p0) REVERT: B 239 GLN cc_start: 0.7650 (tt0) cc_final: 0.7228 (tt0) REVERT: B 305 SER cc_start: 0.8400 (t) cc_final: 0.8179 (p) REVERT: B 403 ARG cc_start: 0.7361 (mtt180) cc_final: 0.6869 (mtt180) REVERT: B 467 ASP cc_start: 0.7550 (t0) cc_final: 0.7233 (t0) REVERT: B 498 ARG cc_start: 0.7921 (mmp80) cc_final: 0.7510 (mmp-170) REVERT: B 583 GLU cc_start: 0.6974 (tp30) cc_final: 0.6635 (tp30) REVERT: B 585 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7432 (pp) REVERT: B 646 ARG cc_start: 0.7942 (ttt90) cc_final: 0.7720 (ttt90) REVERT: B 804 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8131 (mm-40) REVERT: B 980 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8110 (mp) REVERT: B 1084 ASP cc_start: 0.7723 (t0) cc_final: 0.7184 (t0) REVERT: B 1139 ASP cc_start: 0.7807 (t0) cc_final: 0.7467 (t0) REVERT: C 39 ARG cc_start: 0.7295 (ttm-80) cc_final: 0.6876 (ttm170) REVERT: C 83 MET cc_start: 0.6381 (mtm) cc_final: 0.5925 (mtp) REVERT: D 55 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6360 (tm130) REVERT: D 97 MET cc_start: 0.7696 (mmm) cc_final: 0.7397 (mmm) REVERT: E 118 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7642 (tp) REVERT: E 129 LYS cc_start: 0.8036 (ptmt) cc_final: 0.7663 (ptmm) REVERT: E 239 GLN cc_start: 0.7565 (tt0) cc_final: 0.7137 (tt0) REVERT: E 305 SER cc_start: 0.8632 (t) cc_final: 0.8294 (p) REVERT: E 355 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7516 (ttt180) REVERT: E 434 ILE cc_start: 0.8231 (mt) cc_final: 0.7976 (mt) REVERT: E 456 PHE cc_start: 0.8498 (m-80) cc_final: 0.8142 (m-10) REVERT: E 465 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6936 (mt-10) REVERT: E 498 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.8065 (mmm-85) REVERT: E 513 LEU cc_start: 0.7930 (mt) cc_final: 0.7595 (mt) REVERT: E 675 GLN cc_start: 0.7430 (tt0) cc_final: 0.7196 (mt0) REVERT: E 784 GLN cc_start: 0.8540 (mt0) cc_final: 0.8243 (mt0) REVERT: E 804 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7737 (mt0) REVERT: E 869 MET cc_start: 0.8308 (mtt) cc_final: 0.8009 (mtt) REVERT: E 904 TYR cc_start: 0.8252 (m-10) cc_final: 0.7651 (m-10) REVERT: E 980 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8007 (mp) REVERT: E 1084 ASP cc_start: 0.7922 (t0) cc_final: 0.7433 (t0) REVERT: E 1139 ASP cc_start: 0.7853 (t0) cc_final: 0.7473 (t0) REVERT: F 39 ARG cc_start: 0.7151 (ttm-80) cc_final: 0.6618 (ttt180) REVERT: F 83 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6414 (mtp) REVERT: G 55 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6844 (tm130) REVERT: G 97 MET cc_start: 0.7677 (mmm) cc_final: 0.7247 (mmm) outliers start: 68 outliers final: 46 residues processed: 593 average time/residue: 0.1745 time to fit residues: 162.7410 Evaluate side-chains 610 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 555 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 980 ILE Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain G residue 55 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 250 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 290 optimal weight: 0.6980 chunk 326 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 299 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 207 HIS B 207 HIS B 542 ASN B 774 GLN B 856 ASN E 32 ASN E 207 HIS E 774 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.167118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.132572 restraints weight = 46270.032| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.75 r_work: 0.3623 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29952 Z= 0.143 Angle : 0.633 14.497 40800 Z= 0.309 Chirality : 0.046 0.304 4638 Planarity : 0.004 0.052 5214 Dihedral : 5.512 57.395 4548 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.90 % Allowed : 16.50 % Favored : 81.61 % 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 aren not related in a simple way. whole: -0.23 (0.13), residues: 3627 helix: 2.41 (0.21), residues: 627 sheet: 0.27 (0.16), residues: 969 loop : -1.26 (0.12), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 466 TYR 0.022 0.001 TYR B 423 PHE 0.017 0.001 PHE E 592 TRP 0.034 0.002 TRP G 35 HIS 0.006 0.001 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00333 (29880) covalent geometry : angle 0.59565 (40629) SS BOND : bond 0.00533 ( 45) SS BOND : angle 2.01701 ( 90) hydrogen bonds : bond 0.04374 ( 1052) hydrogen bonds : angle 4.80268 ( 2859) link_NAG-ASN : bond 0.00992 ( 27) link_NAG-ASN : angle 4.36519 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 550 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7142 (m-80) cc_final: 0.6864 (m-80) REVERT: A 235 ILE cc_start: 0.7966 (mm) cc_final: 0.7702 (tp) REVERT: A 358 ILE cc_start: 0.7850 (mp) cc_final: 0.7563 (tt) REVERT: A 377 PHE cc_start: 0.7049 (t80) cc_final: 0.6497 (t80) REVERT: A 542 ASN cc_start: 0.7440 (t0) cc_final: 0.7177 (t0) REVERT: A 564 GLN cc_start: 0.8004 (mt0) cc_final: 0.7696 (mm-40) REVERT: A 776 LYS cc_start: 0.8375 (ttpt) cc_final: 0.8120 (tttt) REVERT: A 779 GLN cc_start: 0.8238 (tp40) cc_final: 0.7978 (tm-30) REVERT: A 980 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8032 (mp) REVERT: A 1084 ASP cc_start: 0.7716 (t0) cc_final: 0.7194 (t0) REVERT: A 1139 ASP cc_start: 0.7914 (t0) cc_final: 0.7709 (t0) REVERT: H 47 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7249 (tm-30) REVERT: H 83 MET cc_start: 0.6614 (mtp) cc_final: 0.6361 (mtp) REVERT: H 93 VAL cc_start: 0.7508 (OUTLIER) cc_final: 0.7210 (p) REVERT: H 95 TYR cc_start: 0.8284 (m-80) cc_final: 0.7955 (m-80) REVERT: K 4 MET cc_start: 0.7253 (mmm) cc_final: 0.6802 (tmm) REVERT: B 110 LEU cc_start: 0.7265 (mm) cc_final: 0.7051 (mm) REVERT: B 188 ASN cc_start: 0.7325 (p0) cc_final: 0.7050 (p0) REVERT: B 239 GLN cc_start: 0.7608 (tt0) cc_final: 0.7203 (tt0) REVERT: B 305 SER cc_start: 0.8418 (t) cc_final: 0.8187 (p) REVERT: B 358 ILE cc_start: 0.7130 (tp) cc_final: 0.6916 (tt) REVERT: B 403 ARG cc_start: 0.7384 (mtt180) cc_final: 0.6888 (mtt180) REVERT: B 467 ASP cc_start: 0.7489 (t0) cc_final: 0.7177 (t0) REVERT: B 583 GLU cc_start: 0.6980 (tp30) cc_final: 0.6637 (tp30) REVERT: B 585 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7484 (pp) REVERT: B 592 PHE cc_start: 0.8674 (p90) cc_final: 0.8244 (p90) REVERT: B 646 ARG cc_start: 0.7943 (ttt90) cc_final: 0.7714 (ttt90) REVERT: B 804 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8137 (mm-40) REVERT: B 980 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8099 (mp) REVERT: B 1084 ASP cc_start: 0.7732 (t0) cc_final: 0.7196 (t0) REVERT: B 1139 ASP cc_start: 0.7797 (t0) cc_final: 0.7450 (t0) REVERT: C 39 ARG cc_start: 0.7241 (ttm-80) cc_final: 0.6813 (ttm170) REVERT: C 83 MET cc_start: 0.6371 (mtm) cc_final: 0.6082 (mtm) REVERT: D 4 MET cc_start: 0.7055 (mmm) cc_final: 0.6812 (mmm) REVERT: D 55 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6397 (tm130) REVERT: D 97 MET cc_start: 0.7692 (mmm) cc_final: 0.7414 (mmm) REVERT: E 118 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7654 (tp) REVERT: E 129 LYS cc_start: 0.8034 (ptmt) cc_final: 0.7658 (ptmm) REVERT: E 239 GLN cc_start: 0.7570 (tt0) cc_final: 0.7136 (tt0) REVERT: E 305 SER cc_start: 0.8639 (t) cc_final: 0.8295 (p) REVERT: E 355 ARG cc_start: 0.8019 (tpp80) cc_final: 0.7510 (ttt180) REVERT: E 434 ILE cc_start: 0.8262 (mt) cc_final: 0.8001 (mt) REVERT: E 456 PHE cc_start: 0.8516 (m-80) cc_final: 0.8145 (m-10) REVERT: E 465 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7003 (mt-10) REVERT: E 498 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.8081 (mmm-85) REVERT: E 513 LEU cc_start: 0.7910 (mt) cc_final: 0.7577 (mt) REVERT: E 675 GLN cc_start: 0.7459 (tt0) cc_final: 0.7223 (mt0) REVERT: E 784 GLN cc_start: 0.8550 (mt0) cc_final: 0.8252 (mt0) REVERT: E 804 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7730 (mt0) REVERT: E 869 MET cc_start: 0.8306 (mtt) cc_final: 0.7999 (mtt) REVERT: E 904 TYR cc_start: 0.8255 (m-10) cc_final: 0.7645 (m-10) REVERT: E 980 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7987 (mp) REVERT: E 1084 ASP cc_start: 0.7898 (t0) cc_final: 0.7415 (t0) REVERT: E 1139 ASP cc_start: 0.7854 (t0) cc_final: 0.7474 (t0) REVERT: F 39 ARG cc_start: 0.7153 (ttm-80) cc_final: 0.6619 (ttt180) REVERT: F 83 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6469 (mtp) REVERT: G 55 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6916 (tm130) REVERT: G 89 GLN cc_start: 0.7631 (pt0) cc_final: 0.7269 (pt0) REVERT: G 97 MET cc_start: 0.7702 (mmm) cc_final: 0.7258 (mmm) outliers start: 61 outliers final: 47 residues processed: 587 average time/residue: 0.1839 time to fit residues: 170.0198 Evaluate side-chains 599 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 543 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 980 ILE Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain G residue 55 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 147 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 216 optimal weight: 0.5980 chunk 188 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 181 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 304 optimal weight: 0.8980 chunk 234 optimal weight: 0.0570 chunk 315 optimal weight: 0.0870 chunk 49 optimal weight: 0.9980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 207 HIS A 544 ASN B 207 HIS B 542 ASN B 774 GLN B 853 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS E 853 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.169187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.134756 restraints weight = 46626.440| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.77 r_work: 0.3661 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 29952 Z= 0.108 Angle : 0.607 13.483 40800 Z= 0.293 Chirality : 0.045 0.305 4638 Planarity : 0.004 0.062 5214 Dihedral : 5.305 58.214 4548 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.59 % Allowed : 17.12 % Favored : 81.29 % 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 aren not related in a simple way. whole: -0.08 (0.14), residues: 3627 helix: 2.55 (0.21), residues: 627 sheet: 0.44 (0.17), residues: 939 loop : -1.18 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 61 TYR 0.019 0.001 TYR B 380 PHE 0.027 0.001 PHE E 168 TRP 0.047 0.002 TRP G 35 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00241 (29880) covalent geometry : angle 0.57520 (40629) SS BOND : bond 0.00476 ( 45) SS BOND : angle 1.72115 ( 90) hydrogen bonds : bond 0.03778 ( 1052) hydrogen bonds : angle 4.69591 ( 2859) link_NAG-ASN : bond 0.00959 ( 27) link_NAG-ASN : angle 4.01559 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7579.63 seconds wall clock time: 130 minutes 31.19 seconds (7831.19 seconds total)