Starting phenix.real_space_refine on Thu May 29 20:59:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1v_35934/05_2025/8j1v_35934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1v_35934/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j1v_35934/05_2025/8j1v_35934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1v_35934/05_2025/8j1v_35934.map" model { file = "/net/cci-nas-00/data/ceres_data/8j1v_35934/05_2025/8j1v_35934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1v_35934/05_2025/8j1v_35934.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: "C" 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: "D" 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: G, K, F, H, B, E Time building chain proxies: 21.82, per 1000 atoms: 0.75 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=41, 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 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: 6.57 Conformation dependent library (CDL) restraints added in 4.0 seconds 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: 4.14 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: 12.45 Time building geometry restraints manager: 7.73 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: 16680 17.20 - 34.39: 1118 34.39 - 51.59: 239 51.59 - 68.78: 50 68.78 - 85.98: 15 Dihedral angle restraints: 18102 sinusoidal: 7389 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 18099 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: 2.04 - 2.61: 247 2.61 - 3.18: 24723 3.18 - 3.75: 41172 3.75 - 4.33: 58007 4.33 - 4.90: 98724 Nonbonded interactions: 222873 Sorted by model distance: nonbonded pdb=" SG CYS C 23 " pdb=" SG CYS C 96 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS F 23 " pdb=" SG CYS F 96 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " model vdw 2.038 3.760 nonbonded pdb=" SG CYS G 23 " pdb=" SG CYS G 88 " model vdw 2.039 3.760 nonbonded pdb=" OH TYR D 36 " pdb=" OE1 GLN D 89 " model vdw 2.220 3.040 ... (remaining 222868 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: 0.18 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.030 Extract box with map and model: 1.070 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 68.970 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.090 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.440 ------------------------------------------------------------------------------- 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 29948 Z= 0.230 Angle : 0.649 12.781 40792 Z= 0.382 Chirality : 0.047 0.331 4638 Planarity : 0.009 0.302 5214 Dihedral : 12.040 75.257 11109 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP E 353 HIS 0.005 0.001 HIS F 100 PHE 0.017 0.001 PHE A 45 TYR 0.019 0.001 TYR E 396 ARG 0.005 0.000 ARG E 355 Details of bonding type rmsd link_NAG-ASN : bond 0.01034 ( 27) link_NAG-ASN : angle 3.46504 ( 81) hydrogen bonds : bond 0.22274 ( 1052) hydrogen bonds : angle 7.60740 ( 2859) SS BOND : bond 0.00389 ( 41) SS BOND : angle 1.05073 ( 82) covalent geometry : bond 0.00402 (29880) covalent geometry : angle 0.63026 (40629) *********************** 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 : 3.203 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: 0.6845 (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: 0.6908 (mt-10) REVERT: A 200 TYR cc_start: 0.6778 (m-80) cc_final: 0.6498 (m-80) REVERT: A 542 ASN cc_start: 0.7073 (t0) cc_final: 0.6840 (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: 0.7514 (mp) REVERT: A 1084 ASP cc_start: 0.6998 (t0) cc_final: 0.6548 (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: 0.7931 (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: 0.6105 (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: 0.7003 (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: 0.6438 (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: 0.7362 (t0) REVERT: E 239 GLN cc_start: 0.6917 (tt0) cc_final: 0.6489 (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: 0.7549 (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: 0.7881 (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: 0.4186 time to fit residues: 460.5158 Evaluate side-chains 592 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 591 time to evaluate : 3.501 ------------------------------------------------------------------------------- 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 306 optimal weight: 7.9990 chunk 275 optimal weight: 0.0030 chunk 152 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 284 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 173 optimal weight: 0.3980 chunk 211 optimal weight: 0.7980 chunk 329 optimal weight: 0.3980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 417 ASN 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 115 GLN E 196 ASN E 207 HIS E 417 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: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.171125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.136512 restraints weight = 46865.694| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.75 r_work: 0.3686 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 29948 Z= 0.143 Angle : 0.614 13.363 40792 Z= 0.311 Chirality : 0.046 0.443 4638 Planarity : 0.005 0.061 5214 Dihedral : 6.537 54.247 4550 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.93 % Allowed : 8.40 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3627 helix: 2.19 (0.21), residues: 651 sheet: 0.46 (0.18), residues: 885 loop : -1.26 (0.12), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 35 HIS 0.013 0.001 HIS H 100 PHE 0.030 0.001 PHE E 497 TYR 0.023 0.001 TYR E 170 ARG 0.006 0.001 ARG E1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00775 ( 27) link_NAG-ASN : angle 3.32623 ( 81) hydrogen bonds : bond 0.04931 ( 1052) hydrogen bonds : angle 5.54257 ( 2859) SS BOND : bond 0.00580 ( 41) SS BOND : angle 2.06331 ( 82) covalent geometry : bond 0.00325 (29880) covalent geometry : angle 0.58932 (40629) *********************** 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 629 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 599 time to evaluate : 2.840 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: 0.7927 (m-40) cc_final: 0.7505 (t0) REVERT: A 168 PHE cc_start: 0.7664 (t80) cc_final: 0.7417 (t80) REVERT: A 191 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7114 (mt-10) REVERT: A 200 TYR cc_start: 0.7202 (m-80) cc_final: 0.6918 (m-80) REVERT: A 229 LEU cc_start: 0.8148 (mt) cc_final: 0.7869 (mp) REVERT: A 424 LYS cc_start: 0.8494 (tptm) cc_final: 0.8220 (tptm) REVERT: A 465 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6797 (mt-10) REVERT: A 498 ARG cc_start: 0.7299 (mpt180) cc_final: 0.6991 (mpt180) REVERT: A 542 ASN cc_start: 0.7339 (t0) cc_final: 0.7123 (t0) REVERT: A 574 ASP cc_start: 0.7462 (t0) cc_final: 0.7165 (t0) REVERT: A 646 ARG cc_start: 0.8108 (ttt90) cc_final: 0.7801 (ttt90) REVERT: A 779 GLN cc_start: 0.8176 (tp40) cc_final: 0.7927 (tm-30) REVERT: A 790 LYS cc_start: 0.8658 (mtmt) cc_final: 0.7736 (mttt) REVERT: A 1031 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7635 (mt-10) REVERT: A 1084 ASP cc_start: 0.7593 (t0) cc_final: 0.7045 (t0) REVERT: A 1139 ASP cc_start: 0.7834 (t0) cc_final: 0.7631 (t0) REVERT: K 90 HIS cc_start: 0.8348 (t70) cc_final: 0.8109 (t-90) REVERT: K 97 MET cc_start: 0.7301 (mmm) cc_final: 0.7085 (mmm) REVERT: B 190 ARG cc_start: 0.7872 (mpt180) cc_final: 0.7566 (mtt90) REVERT: B 239 GLN cc_start: 0.7677 (tt0) cc_final: 0.7192 (tt0) REVERT: B 356 LYS cc_start: 0.7593 (tppt) cc_final: 0.7390 (tptp) REVERT: B 403 ARG cc_start: 0.7072 (mtt180) cc_final: 0.6646 (mtt180) REVERT: B 531 THR cc_start: 0.8183 (m) cc_final: 0.7837 (p) REVERT: B 583 GLU cc_start: 0.6868 (tp30) cc_final: 0.6562 (tp30) REVERT: B 585 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7296 (pp) REVERT: B 587 ILE cc_start: 0.8388 (mm) cc_final: 0.8167 (mt) REVERT: B 646 ARG cc_start: 0.7888 (ttt90) cc_final: 0.7680 (ttt90) REVERT: B 779 GLN cc_start: 0.8304 (tp40) cc_final: 0.8015 (tm-30) REVERT: B 804 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7893 (mm-40) REVERT: B 1084 ASP cc_start: 0.7497 (t0) cc_final: 0.7078 (t0) REVERT: B 1105 THR cc_start: 0.8289 (t) cc_final: 0.7312 (m) REVERT: B 1139 ASP cc_start: 0.7727 (t0) cc_final: 0.7331 (t0) REVERT: C 39 ARG cc_start: 0.7218 (ttm-80) cc_final: 0.6898 (ttt180) REVERT: C 48 TRP cc_start: 0.8118 (t60) cc_final: 0.7517 (t60) REVERT: D 4 MET cc_start: 0.7057 (mmm) cc_final: 0.6772 (mmm) REVERT: E 47 SER cc_start: 0.8254 (t) cc_final: 0.7996 (t) REVERT: E 121 ASN cc_start: 0.7932 (m-40) cc_final: 0.7527 (t0) REVERT: E 239 GLN cc_start: 0.7461 (tt0) cc_final: 0.6986 (tt0) REVERT: E 355 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7611 (tpp80) REVERT: E 424 LYS cc_start: 0.8343 (tptm) cc_final: 0.8118 (tptm) REVERT: E 425 LEU cc_start: 0.7905 (mt) cc_final: 0.7565 (mt) REVERT: E 465 GLU cc_start: 0.7251 (mt-10) cc_final: 0.7019 (mt-10) REVERT: E 513 LEU cc_start: 0.7759 (mt) cc_final: 0.7409 (mt) REVERT: E 559 PHE cc_start: 0.7951 (m-10) cc_final: 0.7697 (m-10) REVERT: E 567 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7872 (mtt180) REVERT: E 723 THR cc_start: 0.8323 (p) cc_final: 0.8104 (m) REVERT: E 784 GLN cc_start: 0.8517 (mt0) cc_final: 0.8292 (mt0) REVERT: E 859 THR cc_start: 0.8287 (p) cc_final: 0.8071 (t) REVERT: E 869 MET cc_start: 0.8330 (mtt) cc_final: 0.8082 (mtt) REVERT: E 904 TYR cc_start: 0.8109 (m-10) cc_final: 0.7499 (m-10) REVERT: E 1084 ASP cc_start: 0.7483 (t0) cc_final: 0.7066 (t0) REVERT: E 1114 ILE cc_start: 0.8153 (mm) cc_final: 0.7919 (mt) REVERT: E 1139 ASP cc_start: 0.7888 (t0) cc_final: 0.7514 (t0) REVERT: F 59 PHE cc_start: 0.8062 (m-80) cc_final: 0.7853 (m-80) REVERT: F 83 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6689 (mtp) REVERT: G 97 MET cc_start: 0.7462 (mmm) cc_final: 0.7060 (mmm) outliers start: 30 outliers final: 9 residues processed: 613 average time/residue: 0.4164 time to fit residues: 396.6863 Evaluate side-chains 576 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 565 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 585 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 913 GLN 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 42 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 251 optimal weight: 0.9990 chunk 298 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 B 115 GLN B 542 ASN B 774 GLN B 913 GLN D 37 GLN D 38 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS E 460 ASN E 774 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** G 92 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 = 0.4216 r_free = 0.4216 target = 0.168376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.133618 restraints weight = 46560.479| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.70 r_work: 0.3642 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 29948 Z= 0.170 Angle : 0.604 14.941 40792 Z= 0.306 Chirality : 0.045 0.318 4638 Planarity : 0.005 0.053 5214 Dihedral : 6.173 54.501 4548 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.56 % Allowed : 10.30 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3627 helix: 2.29 (0.21), residues: 627 sheet: 0.24 (0.17), residues: 957 loop : -1.27 (0.12), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 35 HIS 0.012 0.001 HIS B 207 PHE 0.019 0.002 PHE A 592 TYR 0.025 0.002 TYR B 266 ARG 0.007 0.001 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00770 ( 27) link_NAG-ASN : angle 3.22496 ( 81) hydrogen bonds : bond 0.04838 ( 1052) hydrogen bonds : angle 5.22042 ( 2859) SS BOND : bond 0.00791 ( 41) SS BOND : angle 2.25328 ( 82) covalent geometry : bond 0.00402 (29880) covalent geometry : angle 0.57927 (40629) *********************** 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 647 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 597 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.7181 (mm) cc_final: 0.6939 (mm) REVERT: A 121 ASN cc_start: 0.7908 (m-40) cc_final: 0.7422 (t0) REVERT: A 168 PHE cc_start: 0.7598 (t80) cc_final: 0.7370 (t80) REVERT: A 190 ARG cc_start: 0.7735 (mpt180) cc_final: 0.7366 (mtt90) REVERT: A 200 TYR cc_start: 0.7169 (m-80) cc_final: 0.6897 (m-80) REVERT: A 229 LEU cc_start: 0.8144 (mt) cc_final: 0.7903 (mp) REVERT: A 266 TYR cc_start: 0.7586 (m-10) cc_final: 0.7301 (m-80) REVERT: A 338 PHE cc_start: 0.8246 (m-80) cc_final: 0.8037 (m-80) REVERT: A 465 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6987 (mt-10) REVERT: A 498 ARG cc_start: 0.7620 (mpt180) cc_final: 0.7360 (mpt180) REVERT: A 513 LEU cc_start: 0.7667 (mt) cc_final: 0.7392 (mt) REVERT: A 542 ASN cc_start: 0.7391 (t0) cc_final: 0.7155 (t0) REVERT: A 567 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7554 (mtt90) REVERT: A 574 ASP cc_start: 0.7436 (t0) cc_final: 0.7207 (t0) REVERT: A 646 ARG cc_start: 0.8018 (ttt90) cc_final: 0.7707 (ttt90) REVERT: A 749 CYS cc_start: 0.6079 (OUTLIER) cc_final: 0.5754 (t) REVERT: A 779 GLN cc_start: 0.8238 (tp40) cc_final: 0.7972 (tm-30) REVERT: A 790 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8165 (mttt) REVERT: A 945 LEU cc_start: 0.8217 (mt) cc_final: 0.7937 (mp) REVERT: A 1084 ASP cc_start: 0.7601 (t0) cc_final: 0.7046 (t0) REVERT: A 1139 ASP cc_start: 0.7923 (t0) cc_final: 0.7666 (t0) REVERT: K 90 HIS cc_start: 0.8506 (t70) cc_final: 0.8136 (t-170) REVERT: K 97 MET cc_start: 0.7492 (mmm) cc_final: 0.7161 (mmm) REVERT: B 188 ASN cc_start: 0.7217 (p0) cc_final: 0.6916 (p0) REVERT: B 239 GLN cc_start: 0.7611 (tt0) cc_final: 0.7208 (tt0) REVERT: B 298 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7555 (mt-10) REVERT: B 305 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8088 (p) REVERT: B 355 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7767 (tpt-90) REVERT: B 403 ARG cc_start: 0.7404 (mtt180) cc_final: 0.6943 (mtt180) REVERT: B 424 LYS cc_start: 0.8611 (tptp) cc_final: 0.8389 (tptp) REVERT: B 425 LEU cc_start: 0.8284 (mt) cc_final: 0.7896 (mt) REVERT: B 467 ASP cc_start: 0.7707 (t0) cc_final: 0.7385 (t0) REVERT: B 567 ARG cc_start: 0.8114 (ttm170) cc_final: 0.7782 (mtt90) REVERT: B 583 GLU cc_start: 0.6919 (tp30) cc_final: 0.6508 (tp30) REVERT: B 585 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7291 (pp) REVERT: B 587 ILE cc_start: 0.8308 (mm) cc_final: 0.8082 (mt) REVERT: B 646 ARG cc_start: 0.7869 (ttt90) cc_final: 0.7643 (ttt90) REVERT: B 740 MET cc_start: 0.7670 (mmm) cc_final: 0.7273 (mmm) REVERT: B 749 CYS cc_start: 0.6170 (OUTLIER) cc_final: 0.5651 (t) REVERT: B 779 GLN cc_start: 0.8345 (tp40) cc_final: 0.8070 (tm-30) REVERT: B 804 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8023 (mm-40) REVERT: B 1002 GLN cc_start: 0.7588 (mm110) cc_final: 0.7386 (mm-40) REVERT: B 1084 ASP cc_start: 0.7578 (t0) cc_final: 0.7003 (t0) REVERT: B 1139 ASP cc_start: 0.7775 (t0) cc_final: 0.7446 (t0) REVERT: C 39 ARG cc_start: 0.7301 (ttm-80) cc_final: 0.6770 (ttt180) REVERT: D 4 MET cc_start: 0.7175 (mmm) cc_final: 0.6816 (mmm) REVERT: E 121 ASN cc_start: 0.7972 (m-40) cc_final: 0.7491 (t0) REVERT: E 129 LYS cc_start: 0.8033 (ptmt) cc_final: 0.7585 (ptmm) REVERT: E 239 GLN cc_start: 0.7587 (tt0) cc_final: 0.7099 (tt0) REVERT: E 339 ASP cc_start: 0.7911 (p0) cc_final: 0.7652 (t0) REVERT: E 355 ARG cc_start: 0.7950 (tpp80) cc_final: 0.7693 (tpp80) REVERT: E 356 LYS cc_start: 0.8070 (tptp) cc_final: 0.7867 (tptp) REVERT: E 357 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7677 (ttm-80) REVERT: E 424 LYS cc_start: 0.8540 (tptm) cc_final: 0.8238 (tptm) REVERT: E 425 LEU cc_start: 0.8073 (mt) cc_final: 0.7746 (mt) REVERT: E 434 ILE cc_start: 0.7992 (mt) cc_final: 0.7767 (mt) REVERT: E 451 TYR cc_start: 0.6203 (m-10) cc_final: 0.6003 (m-10) REVERT: E 465 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7048 (mt-10) REVERT: E 513 LEU cc_start: 0.7751 (mt) cc_final: 0.7424 (mt) REVERT: E 559 PHE cc_start: 0.8112 (m-10) cc_final: 0.7878 (m-10) REVERT: E 690 GLN cc_start: 0.7693 (mm110) cc_final: 0.7331 (mm-40) REVERT: E 749 CYS cc_start: 0.5844 (OUTLIER) cc_final: 0.5622 (t) REVERT: E 784 GLN cc_start: 0.8547 (mt0) cc_final: 0.8286 (mt0) REVERT: E 804 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7973 (mm-40) REVERT: E 859 THR cc_start: 0.8309 (p) cc_final: 0.8102 (t) REVERT: E 869 MET cc_start: 0.8397 (mtt) cc_final: 0.8134 (mtt) REVERT: E 894 LEU cc_start: 0.8766 (mt) cc_final: 0.8507 (mt) REVERT: E 904 TYR cc_start: 0.8203 (m-10) cc_final: 0.7577 (m-10) REVERT: E 1084 ASP cc_start: 0.7638 (t0) cc_final: 0.7164 (t0) REVERT: E 1102 TRP cc_start: 0.8484 (m100) cc_final: 0.8185 (m100) REVERT: E 1139 ASP cc_start: 0.7859 (t0) cc_final: 0.7501 (t0) REVERT: F 39 ARG cc_start: 0.7193 (ttm-80) cc_final: 0.6603 (ttt180) REVERT: F 59 PHE cc_start: 0.8221 (m-80) cc_final: 0.7992 (m-80) REVERT: F 83 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6943 (mtp) REVERT: F 110 GLN cc_start: 0.7682 (pm20) cc_final: 0.7246 (pm20) REVERT: G 97 MET cc_start: 0.7625 (mmm) cc_final: 0.7269 (mmm) outliers start: 50 outliers final: 25 residues processed: 622 average time/residue: 0.4281 time to fit residues: 416.6897 Evaluate side-chains 601 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 570 time to evaluate : 2.818 ------------------------------------------------------------------------------- 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 A residue 961 THR Chi-restraints excluded: chain A residue 996 LEU 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 115 GLN Chi-restraints excluded: chain B residue 305 SER 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 961 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 551 VAL Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 786 LYS 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 338 optimal weight: 0.9990 chunk 228 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 358 optimal weight: 0.0050 chunk 164 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 0.0570 overall best weight: 0.5312 ------------------------------------------------------------------------------- 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 A 774 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN B 115 GLN B 207 HIS B 542 ASN B 544 ASN ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS E 460 ASN E 564 GLN E 774 GLN E 856 ASN ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.169010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.134435 restraints weight = 47164.503| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.77 r_work: 0.3649 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29948 Z= 0.129 Angle : 0.600 15.807 40792 Z= 0.294 Chirality : 0.045 0.348 4638 Planarity : 0.004 0.051 5214 Dihedral : 6.088 59.328 4548 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.37 % Allowed : 13.01 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 3627 helix: 2.39 (0.21), residues: 627 sheet: 0.24 (0.17), residues: 930 loop : -1.27 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 35 HIS 0.004 0.001 HIS B 207 PHE 0.016 0.001 PHE A 592 TYR 0.019 0.001 TYR B1067 ARG 0.008 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00987 ( 27) link_NAG-ASN : angle 4.69850 ( 81) hydrogen bonds : bond 0.04334 ( 1052) hydrogen bonds : angle 4.97856 ( 2859) SS BOND : bond 0.00540 ( 41) SS BOND : angle 1.94964 ( 82) covalent geometry : bond 0.00297 (29880) covalent geometry : angle 0.55677 (40629) *********************** 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 618 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 574 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.7190 (mm) cc_final: 0.6933 (mm) REVERT: A 121 ASN cc_start: 0.7915 (m-40) cc_final: 0.7395 (t0) REVERT: A 190 ARG cc_start: 0.7763 (mpt180) cc_final: 0.7394 (mtt90) REVERT: A 200 TYR cc_start: 0.7173 (m-80) cc_final: 0.6893 (m-80) REVERT: A 229 LEU cc_start: 0.8074 (mt) cc_final: 0.7849 (mp) REVERT: A 266 TYR cc_start: 0.7516 (m-10) cc_final: 0.7192 (m-80) REVERT: A 338 PHE cc_start: 0.8267 (m-80) cc_final: 0.8047 (m-80) REVERT: A 465 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7015 (mt-10) REVERT: A 492 LEU cc_start: 0.9085 (pp) cc_final: 0.8652 (pp) REVERT: A 513 LEU cc_start: 0.7634 (mt) cc_final: 0.7359 (mt) REVERT: A 542 ASN cc_start: 0.7406 (t0) cc_final: 0.7164 (t0) REVERT: A 567 ARG cc_start: 0.7937 (ttm170) cc_final: 0.7692 (mtt90) REVERT: A 646 ARG cc_start: 0.8049 (ttt90) cc_final: 0.7739 (ttt90) REVERT: A 749 CYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5836 (t) REVERT: A 776 LYS cc_start: 0.8376 (ttpt) cc_final: 0.8061 (tttp) REVERT: A 779 GLN cc_start: 0.8204 (tp40) cc_final: 0.7947 (tm-30) REVERT: A 790 LYS cc_start: 0.8509 (mtmt) cc_final: 0.7844 (mttt) REVERT: A 1084 ASP cc_start: 0.7645 (t0) cc_final: 0.7088 (t0) REVERT: A 1139 ASP cc_start: 0.7891 (t0) cc_final: 0.7637 (t0) REVERT: H 5 LEU cc_start: 0.8664 (mp) cc_final: 0.8204 (mp) REVERT: K 90 HIS cc_start: 0.8467 (t70) cc_final: 0.8093 (t-170) REVERT: K 97 MET cc_start: 0.7539 (mmm) cc_final: 0.7078 (mmm) REVERT: B 110 LEU cc_start: 0.7252 (mm) cc_final: 0.6991 (mm) REVERT: B 188 ASN cc_start: 0.7175 (p0) cc_final: 0.6870 (p0) REVERT: B 239 GLN cc_start: 0.7588 (tt0) cc_final: 0.7179 (tt0) REVERT: B 298 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7504 (mt-10) REVERT: B 305 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8081 (p) REVERT: B 356 LYS cc_start: 0.7444 (tptp) cc_final: 0.7150 (tptp) REVERT: B 403 ARG cc_start: 0.7458 (mtt180) cc_final: 0.7007 (mtt180) REVERT: B 424 LYS cc_start: 0.8649 (tptp) cc_final: 0.8422 (tptp) REVERT: B 425 LEU cc_start: 0.8329 (mt) cc_final: 0.7943 (mt) REVERT: B 467 ASP cc_start: 0.7688 (t0) cc_final: 0.7351 (t0) REVERT: B 567 ARG cc_start: 0.8095 (ttm170) cc_final: 0.7847 (mtt90) REVERT: B 583 GLU cc_start: 0.6938 (tp30) cc_final: 0.6488 (tp30) REVERT: B 585 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7293 (pp) REVERT: B 646 ARG cc_start: 0.7878 (ttt90) cc_final: 0.7649 (ttt90) REVERT: B 740 MET cc_start: 0.7651 (mmm) cc_final: 0.7271 (mmm) REVERT: B 749 CYS cc_start: 0.6082 (OUTLIER) cc_final: 0.5711 (t) REVERT: B 779 GLN cc_start: 0.8308 (tp40) cc_final: 0.8039 (tm-30) REVERT: B 804 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8022 (mm-40) REVERT: B 1002 GLN cc_start: 0.7567 (mm110) cc_final: 0.7284 (mm-40) REVERT: B 1084 ASP cc_start: 0.7632 (t0) cc_final: 0.7053 (t0) REVERT: B 1139 ASP cc_start: 0.7788 (t0) cc_final: 0.7451 (t0) REVERT: C 39 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.6766 (ttt180) REVERT: D 4 MET cc_start: 0.7206 (mmm) cc_final: 0.6858 (mmm) REVERT: E 129 LYS cc_start: 0.7962 (ptmt) cc_final: 0.7600 (ptmm) REVERT: E 239 GLN cc_start: 0.7596 (tt0) cc_final: 0.7097 (tt0) REVERT: E 353 TRP cc_start: 0.8071 (p-90) cc_final: 0.7349 (p-90) REVERT: E 355 ARG cc_start: 0.7949 (tpp80) cc_final: 0.7558 (tpp80) REVERT: E 357 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7652 (ttm-80) REVERT: E 465 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6897 (mt-10) REVERT: E 513 LEU cc_start: 0.7858 (mt) cc_final: 0.7571 (mt) REVERT: E 559 PHE cc_start: 0.8135 (m-10) cc_final: 0.7895 (m-10) REVERT: E 675 GLN cc_start: 0.7258 (tt0) cc_final: 0.7019 (mt0) REVERT: E 690 GLN cc_start: 0.7688 (mm110) cc_final: 0.7308 (mm-40) REVERT: E 702 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7186 (tt0) REVERT: E 784 GLN cc_start: 0.8517 (mt0) cc_final: 0.8277 (mt0) REVERT: E 804 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7748 (mm-40) REVERT: E 869 MET cc_start: 0.8348 (mtt) cc_final: 0.8070 (mtt) REVERT: E 904 TYR cc_start: 0.8222 (m-10) cc_final: 0.7578 (m-10) REVERT: E 1084 ASP cc_start: 0.7672 (t0) cc_final: 0.7187 (t0) REVERT: E 1139 ASP cc_start: 0.7867 (t0) cc_final: 0.7494 (t0) REVERT: F 39 ARG cc_start: 0.7151 (ttm-80) cc_final: 0.6684 (ttt180) REVERT: F 83 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6933 (mtp) REVERT: F 110 GLN cc_start: 0.7609 (pm20) cc_final: 0.7315 (pm20) REVERT: G 55 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6698 (tm130) REVERT: G 97 MET cc_start: 0.7659 (mmm) cc_final: 0.7225 (mmm) outliers start: 44 outliers final: 22 residues processed: 599 average time/residue: 0.4081 time to fit residues: 380.0815 Evaluate side-chains 584 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 556 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR 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 A residue 996 LEU 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 305 SER 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 91 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 584 ILE 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 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 178 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 253 optimal weight: 0.0050 chunk 86 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 230 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 A 856 ASN B 32 ASN B 115 GLN B 125 ASN B 207 HIS B 542 ASN B 774 GLN B 853 GLN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS E 564 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.168146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.133539 restraints weight = 46268.950| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.74 r_work: 0.3639 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29948 Z= 0.142 Angle : 0.594 14.157 40792 Z= 0.292 Chirality : 0.045 0.307 4638 Planarity : 0.004 0.051 5214 Dihedral : 5.706 54.078 4548 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.68 % Allowed : 13.51 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 3627 helix: 2.38 (0.21), residues: 627 sheet: 0.30 (0.17), residues: 930 loop : -1.22 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 35 HIS 0.007 0.001 HIS D 90 PHE 0.019 0.001 PHE A 168 TYR 0.019 0.001 TYR B1067 ARG 0.008 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00958 ( 27) link_NAG-ASN : angle 4.27019 ( 81) hydrogen bonds : bond 0.04383 ( 1052) hydrogen bonds : angle 4.88436 ( 2859) SS BOND : bond 0.00533 ( 41) SS BOND : angle 1.99577 ( 82) covalent geometry : bond 0.00332 (29880) covalent geometry : angle 0.55679 (40629) *********************** 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 633 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 579 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.7259 (mm) cc_final: 0.7007 (mm) REVERT: A 121 ASN cc_start: 0.7917 (m-40) cc_final: 0.7445 (t0) REVERT: A 190 ARG cc_start: 0.7778 (mpt180) cc_final: 0.7415 (mtt90) REVERT: A 266 TYR cc_start: 0.7497 (m-10) cc_final: 0.7087 (m-80) REVERT: A 358 ILE cc_start: 0.7661 (mp) cc_final: 0.7379 (tt) REVERT: A 465 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6970 (mt-10) REVERT: A 513 LEU cc_start: 0.7687 (mt) cc_final: 0.7449 (mt) REVERT: A 542 ASN cc_start: 0.7431 (t0) cc_final: 0.7186 (t0) REVERT: A 567 ARG cc_start: 0.7926 (ttm170) cc_final: 0.7710 (mtt90) REVERT: A 646 ARG cc_start: 0.8046 (ttt90) cc_final: 0.7731 (ttt90) REVERT: A 749 CYS cc_start: 0.5994 (OUTLIER) cc_final: 0.5748 (t) REVERT: A 776 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8106 (tttp) REVERT: A 779 GLN cc_start: 0.8223 (tp40) cc_final: 0.7960 (tm-30) REVERT: A 790 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8260 (mttt) REVERT: A 1084 ASP cc_start: 0.7664 (t0) cc_final: 0.7112 (t0) REVERT: A 1139 ASP cc_start: 0.7896 (t0) cc_final: 0.7492 (t0) REVERT: H 113 MET cc_start: 0.7631 (mmm) cc_final: 0.7389 (mmm) REVERT: K 90 HIS cc_start: 0.8505 (t70) cc_final: 0.8140 (t-170) REVERT: K 97 MET cc_start: 0.7569 (mmm) cc_final: 0.7077 (mmm) REVERT: B 110 LEU cc_start: 0.7252 (mm) cc_final: 0.6997 (mm) REVERT: B 188 ASN cc_start: 0.7249 (p0) cc_final: 0.6960 (p0) REVERT: B 239 GLN cc_start: 0.7577 (tt0) cc_final: 0.7159 (tt0) REVERT: B 298 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7466 (mt-10) REVERT: B 305 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8087 (p) REVERT: B 356 LYS cc_start: 0.7561 (tptp) cc_final: 0.7180 (tptp) REVERT: B 403 ARG cc_start: 0.7522 (mtt180) cc_final: 0.6996 (mtt180) REVERT: B 453 TYR cc_start: 0.7807 (p90) cc_final: 0.7402 (p90) REVERT: B 467 ASP cc_start: 0.7654 (t0) cc_final: 0.7317 (t0) REVERT: B 583 GLU cc_start: 0.6930 (tp30) cc_final: 0.6498 (tp30) REVERT: B 585 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7404 (pp) REVERT: B 646 ARG cc_start: 0.7897 (ttt90) cc_final: 0.7672 (ttt90) REVERT: B 740 MET cc_start: 0.7614 (mmm) cc_final: 0.7273 (mmm) REVERT: B 749 CYS cc_start: 0.5952 (OUTLIER) cc_final: 0.5668 (t) REVERT: B 779 GLN cc_start: 0.8319 (tp40) cc_final: 0.8072 (tm-30) REVERT: B 804 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8077 (mm-40) REVERT: B 1002 GLN cc_start: 0.7598 (mm110) cc_final: 0.7313 (mm-40) REVERT: B 1031 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 1084 ASP cc_start: 0.7654 (t0) cc_final: 0.7095 (t0) REVERT: B 1139 ASP cc_start: 0.7753 (t0) cc_final: 0.7408 (t0) REVERT: C 39 ARG cc_start: 0.7374 (ttm-80) cc_final: 0.6834 (ttt180) REVERT: D 4 MET cc_start: 0.7214 (mmm) cc_final: 0.6865 (mmm) REVERT: D 55 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6317 (tm130) REVERT: D 97 MET cc_start: 0.7815 (mmm) cc_final: 0.7431 (mmm) REVERT: E 129 LYS cc_start: 0.8004 (ptmt) cc_final: 0.7633 (ptmm) REVERT: E 239 GLN cc_start: 0.7619 (tt0) cc_final: 0.7110 (tt0) REVERT: E 353 TRP cc_start: 0.8077 (p-90) cc_final: 0.7336 (p-90) REVERT: E 355 ARG cc_start: 0.7971 (tpp80) cc_final: 0.7403 (ttt180) REVERT: E 434 ILE cc_start: 0.7992 (mt) cc_final: 0.7780 (mt) REVERT: E 465 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6890 (mt-10) REVERT: E 513 LEU cc_start: 0.7796 (mt) cc_final: 0.7467 (mt) REVERT: E 675 GLN cc_start: 0.7333 (tt0) cc_final: 0.7089 (mt0) REVERT: E 690 GLN cc_start: 0.7692 (mm110) cc_final: 0.7295 (mm-40) REVERT: E 735 SER cc_start: 0.8564 (t) cc_final: 0.8073 (p) REVERT: E 784 GLN cc_start: 0.8507 (mt0) cc_final: 0.8247 (mt0) REVERT: E 804 GLN cc_start: 0.8376 (mm-40) cc_final: 0.7722 (mm-40) REVERT: E 869 MET cc_start: 0.8354 (mtt) cc_final: 0.8079 (mtt) REVERT: E 904 TYR cc_start: 0.8249 (m-10) cc_final: 0.7529 (m-10) REVERT: E 1084 ASP cc_start: 0.7731 (t0) cc_final: 0.7248 (t0) REVERT: E 1139 ASP cc_start: 0.7862 (t0) cc_final: 0.7497 (t0) REVERT: F 23 CYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6747 (t) REVERT: F 39 ARG cc_start: 0.7145 (ttm-80) cc_final: 0.6657 (ttt180) REVERT: F 83 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6387 (mtp) REVERT: F 110 GLN cc_start: 0.7537 (pm20) cc_final: 0.7233 (pm20) REVERT: G 97 MET cc_start: 0.7632 (mmm) cc_final: 0.7245 (mmm) outliers start: 54 outliers final: 31 residues processed: 612 average time/residue: 0.4022 time to fit residues: 387.1443 Evaluate side-chains 595 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 557 time to evaluate : 3.203 ------------------------------------------------------------------------------- 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 749 CYS 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 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 129 LYS Chi-restraints excluded: chain B residue 305 SER 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 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 233 ILE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU 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 961 THR Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain F residue 23 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 234 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 54 optimal weight: 0.0370 chunk 84 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- 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 A 853 GLN A1010 GLN K 37 GLN B 32 ASN B 115 GLN B 207 HIS B 317 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN E 207 HIS E 450 ASN E 564 GLN E 774 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.164367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.129556 restraints weight = 46411.959| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.73 r_work: 0.3587 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 29948 Z= 0.272 Angle : 0.687 13.910 40792 Z= 0.344 Chirality : 0.049 0.454 4638 Planarity : 0.005 0.054 5214 Dihedral : 5.949 55.349 4548 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.27 % Allowed : 14.04 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.13), residues: 3627 helix: 2.02 (0.21), residues: 627 sheet: 0.27 (0.17), residues: 909 loop : -1.34 (0.12), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 35 HIS 0.011 0.001 HIS A1058 PHE 0.030 0.002 PHE A 45 TYR 0.025 0.002 TYR B 266 ARG 0.007 0.001 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.01006 ( 27) link_NAG-ASN : angle 4.44760 ( 81) hydrogen bonds : bond 0.05529 ( 1052) hydrogen bonds : angle 5.10280 ( 2859) SS BOND : bond 0.00683 ( 41) SS BOND : angle 2.43095 ( 82) covalent geometry : bond 0.00648 (29880) covalent geometry : angle 0.64958 (40629) *********************** 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 648 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 575 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7803 (mpt180) cc_final: 0.7425 (mtt90) REVERT: A 200 TYR cc_start: 0.7197 (m-80) cc_final: 0.6922 (m-80) REVERT: A 377 PHE cc_start: 0.6960 (t80) cc_final: 0.6552 (t80) REVERT: A 465 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7040 (mt-10) REVERT: A 493 GLN cc_start: 0.7766 (tt0) cc_final: 0.7475 (tt0) REVERT: A 513 LEU cc_start: 0.7901 (mt) cc_final: 0.7615 (mt) REVERT: A 542 ASN cc_start: 0.7455 (t0) cc_final: 0.7233 (t0) REVERT: A 646 ARG cc_start: 0.8107 (ttt90) cc_final: 0.7814 (ttt90) REVERT: A 749 CYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5656 (t) REVERT: A 779 GLN cc_start: 0.8361 (tp40) cc_final: 0.8108 (tm-30) REVERT: A 790 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8220 (mttt) REVERT: A 980 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8083 (mp) REVERT: A 1084 ASP cc_start: 0.7712 (t0) cc_final: 0.7168 (t0) REVERT: A 1114 ILE cc_start: 0.8224 (mm) cc_final: 0.8016 (mt) REVERT: A 1139 ASP cc_start: 0.7949 (t0) cc_final: 0.7510 (t0) REVERT: H 95 TYR cc_start: 0.8343 (m-80) cc_final: 0.8086 (m-80) REVERT: H 113 MET cc_start: 0.7724 (mmm) cc_final: 0.7309 (mmm) REVERT: K 97 MET cc_start: 0.7629 (mmm) cc_final: 0.7148 (mmm) REVERT: B 115 GLN cc_start: 0.7052 (tp-100) cc_final: 0.6810 (mm-40) REVERT: B 188 ASN cc_start: 0.7270 (p0) cc_final: 0.7017 (p0) REVERT: B 239 GLN cc_start: 0.7632 (tt0) cc_final: 0.7241 (tt0) REVERT: B 305 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8124 (p) REVERT: B 453 TYR cc_start: 0.7811 (p90) cc_final: 0.7611 (p90) REVERT: B 467 ASP cc_start: 0.7652 (t0) cc_final: 0.7313 (t0) REVERT: B 583 GLU cc_start: 0.6999 (tp30) cc_final: 0.6600 (tp30) REVERT: B 585 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7609 (pp) REVERT: B 646 ARG cc_start: 0.8059 (ttt90) cc_final: 0.7825 (ttt90) REVERT: B 740 MET cc_start: 0.7911 (mmm) cc_final: 0.7612 (mmm) REVERT: B 749 CYS cc_start: 0.5871 (OUTLIER) cc_final: 0.5543 (t) REVERT: B 779 GLN cc_start: 0.8384 (tp40) cc_final: 0.8178 (tm-30) REVERT: B 804 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8158 (mm-40) REVERT: B 980 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8159 (mp) REVERT: B 1002 GLN cc_start: 0.7763 (mm110) cc_final: 0.7452 (mm-40) REVERT: B 1084 ASP cc_start: 0.7749 (t0) cc_final: 0.7206 (t0) REVERT: B 1139 ASP cc_start: 0.7818 (t0) cc_final: 0.7481 (t0) REVERT: C 39 ARG cc_start: 0.7352 (ttm-80) cc_final: 0.6780 (ttt180) REVERT: C 83 MET cc_start: 0.6470 (mtm) cc_final: 0.6069 (mtp) REVERT: C 113 MET cc_start: 0.7499 (mmm) cc_final: 0.7251 (mmm) REVERT: D 4 MET cc_start: 0.7209 (mmm) cc_final: 0.6935 (mmm) REVERT: D 55 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6440 (tm130) REVERT: D 97 MET cc_start: 0.7850 (mmm) cc_final: 0.7465 (mmm) REVERT: E 129 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7763 (ptmm) REVERT: E 239 GLN cc_start: 0.7617 (tt0) cc_final: 0.7173 (tt0) REVERT: E 305 SER cc_start: 0.8667 (t) cc_final: 0.8343 (p) REVERT: E 342 PHE cc_start: 0.8279 (m-80) cc_final: 0.7977 (m-80) REVERT: E 355 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7527 (ttt180) REVERT: E 357 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7472 (ttm-80) REVERT: E 434 ILE cc_start: 0.8070 (mt) cc_final: 0.7819 (mt) REVERT: E 456 PHE cc_start: 0.8494 (m-80) cc_final: 0.8168 (m-10) REVERT: E 465 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7041 (mt-10) REVERT: E 513 LEU cc_start: 0.7970 (mt) cc_final: 0.7660 (mt) REVERT: E 675 GLN cc_start: 0.7455 (tt0) cc_final: 0.7220 (mt0) REVERT: E 690 GLN cc_start: 0.7709 (mm110) cc_final: 0.7309 (mm-40) REVERT: E 735 SER cc_start: 0.8594 (t) cc_final: 0.8088 (p) REVERT: E 784 GLN cc_start: 0.8583 (mt0) cc_final: 0.8267 (mt0) REVERT: E 804 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7791 (mm-40) REVERT: E 869 MET cc_start: 0.8350 (mtt) cc_final: 0.8058 (mtt) REVERT: E 980 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8059 (mp) REVERT: E 1084 ASP cc_start: 0.7867 (t0) cc_final: 0.7331 (t0) REVERT: E 1139 ASP cc_start: 0.7896 (t0) cc_final: 0.7584 (t0) REVERT: F 23 CYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6834 (t) REVERT: F 39 ARG cc_start: 0.7244 (ttm-80) cc_final: 0.6719 (ttt180) REVERT: F 65 ARG cc_start: 0.7375 (mtt180) cc_final: 0.7059 (mtt-85) REVERT: F 83 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6695 (mtp) REVERT: F 95 TYR cc_start: 0.8331 (m-80) cc_final: 0.7888 (m-80) REVERT: G 55 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6879 (tm130) REVERT: G 90 HIS cc_start: 0.8887 (t70) cc_final: 0.8553 (t70) REVERT: G 97 MET cc_start: 0.7707 (mmm) cc_final: 0.7316 (mmm) outliers start: 73 outliers final: 41 residues processed: 620 average time/residue: 0.4039 time to fit residues: 393.4976 Evaluate side-chains 608 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 556 time to evaluate : 2.982 ------------------------------------------------------------------------------- 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 115 GLN 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 749 CYS 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 B residue 49 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 305 SER 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 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 90 VAL Chi-restraints excluded: chain E residue 233 ILE 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 723 THR Chi-restraints excluded: chain E residue 961 THR 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 E residue 1096 VAL Chi-restraints excluded: chain F residue 23 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 240 optimal weight: 0.2980 chunk 278 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 213 optimal weight: 0.0980 chunk 122 optimal weight: 0.4980 chunk 133 optimal weight: 8.9990 chunk 348 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 355 optimal weight: 2.9990 chunk 263 optimal weight: 0.0970 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 B 207 HIS B 317 ASN B 542 ASN B 774 GLN E 115 GLN E 207 HIS E 564 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.167771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133137 restraints weight = 46188.304| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.74 r_work: 0.3641 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 29948 Z= 0.117 Angle : 0.600 16.327 40792 Z= 0.293 Chirality : 0.045 0.318 4638 Planarity : 0.004 0.053 5214 Dihedral : 5.675 59.596 4548 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.96 % Allowed : 15.03 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.13), residues: 3627 helix: 2.38 (0.21), residues: 627 sheet: 0.31 (0.17), residues: 915 loop : -1.26 (0.12), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 35 HIS 0.007 0.001 HIS D 90 PHE 0.022 0.001 PHE A 168 TYR 0.021 0.001 TYR A 495 ARG 0.004 0.000 ARG E 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00961 ( 27) link_NAG-ASN : angle 4.62425 ( 81) hydrogen bonds : bond 0.04272 ( 1052) hydrogen bonds : angle 4.83412 ( 2859) SS BOND : bond 0.00534 ( 41) SS BOND : angle 1.84494 ( 82) covalent geometry : bond 0.00265 (29880) covalent geometry : angle 0.55871 (40629) *********************** 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 623 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 560 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7940 (m-40) cc_final: 0.7375 (t0) REVERT: A 190 ARG cc_start: 0.7774 (mpt180) cc_final: 0.7400 (mtt90) REVERT: A 358 ILE cc_start: 0.7602 (mp) cc_final: 0.7365 (tt) REVERT: A 377 PHE cc_start: 0.6984 (t80) cc_final: 0.6526 (t80) REVERT: A 465 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6910 (mt-10) REVERT: A 466 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7067 (ttp80) REVERT: A 493 GLN cc_start: 0.7653 (tt0) cc_final: 0.7344 (tt0) REVERT: A 513 LEU cc_start: 0.7905 (mt) cc_final: 0.7563 (mt) REVERT: A 542 ASN cc_start: 0.7432 (t0) cc_final: 0.7170 (t0) REVERT: A 564 GLN cc_start: 0.7880 (mt0) cc_final: 0.7585 (mm-40) REVERT: A 646 ARG cc_start: 0.8040 (ttt90) cc_final: 0.7729 (ttt90) REVERT: A 779 GLN cc_start: 0.8215 (tp40) cc_final: 0.7946 (tm-30) REVERT: A 790 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8256 (mtmt) REVERT: A 980 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8076 (mp) REVERT: A 1084 ASP cc_start: 0.7692 (t0) cc_final: 0.7151 (t0) REVERT: A 1114 ILE cc_start: 0.8204 (mm) cc_final: 0.7987 (mt) REVERT: A 1139 ASP cc_start: 0.7896 (t0) cc_final: 0.7472 (t0) REVERT: H 83 MET cc_start: 0.6596 (mtp) cc_final: 0.6393 (mtp) REVERT: H 95 TYR cc_start: 0.8266 (m-80) cc_final: 0.8023 (m-80) REVERT: H 113 MET cc_start: 0.7681 (mmm) cc_final: 0.7325 (mmm) REVERT: K 4 MET cc_start: 0.7261 (mmm) cc_final: 0.6956 (tmm) REVERT: K 97 MET cc_start: 0.7450 (mmm) cc_final: 0.7009 (mmm) REVERT: B 110 LEU cc_start: 0.7418 (mm) cc_final: 0.7179 (mm) REVERT: B 188 ASN cc_start: 0.7272 (p0) cc_final: 0.7024 (p0) REVERT: B 239 GLN cc_start: 0.7579 (tt0) cc_final: 0.7180 (tt0) REVERT: B 305 SER cc_start: 0.8468 (t) cc_final: 0.8088 (p) REVERT: B 403 ARG cc_start: 0.7490 (mtt180) cc_final: 0.7035 (mtt180) REVERT: B 453 TYR cc_start: 0.7802 (p90) cc_final: 0.7503 (p90) REVERT: B 467 ASP cc_start: 0.7619 (t0) cc_final: 0.7311 (t0) REVERT: B 583 GLU cc_start: 0.6944 (tp30) cc_final: 0.6498 (tp30) REVERT: B 585 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7426 (pp) REVERT: B 592 PHE cc_start: 0.8665 (p90) cc_final: 0.8266 (p90) REVERT: B 646 ARG cc_start: 0.7893 (ttt90) cc_final: 0.7661 (ttt90) REVERT: B 740 MET cc_start: 0.7678 (mmm) cc_final: 0.7414 (mmm) REVERT: B 779 GLN cc_start: 0.8333 (tp40) cc_final: 0.8126 (tm-30) REVERT: B 804 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8118 (mm-40) REVERT: B 868 GLU cc_start: 0.7003 (mp0) cc_final: 0.6709 (mp0) REVERT: B 980 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8135 (mp) REVERT: B 1084 ASP cc_start: 0.7688 (t0) cc_final: 0.7145 (t0) REVERT: B 1139 ASP cc_start: 0.7799 (t0) cc_final: 0.7451 (t0) REVERT: C 39 ARG cc_start: 0.7253 (ttm-80) cc_final: 0.6830 (ttt180) REVERT: C 82 GLN cc_start: 0.8098 (tp40) cc_final: 0.7873 (tp40) REVERT: D 4 MET cc_start: 0.7152 (mmm) cc_final: 0.6891 (mmm) REVERT: D 55 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6476 (tm130) REVERT: D 97 MET cc_start: 0.7681 (mmm) cc_final: 0.7468 (mmm) REVERT: E 129 LYS cc_start: 0.7999 (ptmt) cc_final: 0.7472 (ptmm) REVERT: E 239 GLN cc_start: 0.7637 (tt0) cc_final: 0.7194 (tt0) REVERT: E 305 SER cc_start: 0.8648 (t) cc_final: 0.8319 (p) REVERT: E 353 TRP cc_start: 0.8065 (p-90) cc_final: 0.7409 (p-90) REVERT: E 355 ARG cc_start: 0.8005 (tpp80) cc_final: 0.7451 (ttt180) REVERT: E 357 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7620 (ttm-80) REVERT: E 434 ILE cc_start: 0.8058 (mt) cc_final: 0.7835 (mt) REVERT: E 456 PHE cc_start: 0.8458 (m-80) cc_final: 0.8131 (m-10) REVERT: E 465 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6869 (mt-10) REVERT: E 537 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8169 (mtmt) REVERT: E 675 GLN cc_start: 0.7424 (tt0) cc_final: 0.7182 (mt0) REVERT: E 690 GLN cc_start: 0.7694 (mm110) cc_final: 0.7341 (mm-40) REVERT: E 784 GLN cc_start: 0.8497 (mt0) cc_final: 0.8231 (mt0) REVERT: E 804 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7732 (mt0) REVERT: E 869 MET cc_start: 0.8295 (mtt) cc_final: 0.7982 (mtt) REVERT: E 904 TYR cc_start: 0.8256 (m-10) cc_final: 0.7592 (m-10) REVERT: E 980 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8059 (mp) REVERT: E 1084 ASP cc_start: 0.7880 (t0) cc_final: 0.7328 (t0) REVERT: E 1139 ASP cc_start: 0.7854 (t0) cc_final: 0.7502 (t0) REVERT: F 23 CYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6770 (t) REVERT: F 39 ARG cc_start: 0.7146 (ttm-80) cc_final: 0.6730 (ttt180) REVERT: F 65 ARG cc_start: 0.7360 (mtt180) cc_final: 0.7135 (mtt180) REVERT: F 83 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6591 (mtp) REVERT: F 95 TYR cc_start: 0.8239 (m-80) cc_final: 0.7831 (m-80) REVERT: F 110 GLN cc_start: 0.7664 (pm20) cc_final: 0.7426 (pm20) REVERT: G 55 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6923 (tm130) REVERT: G 97 MET cc_start: 0.7487 (mmm) cc_final: 0.7200 (mmm) outliers start: 63 outliers final: 36 residues processed: 595 average time/residue: 0.4161 time to fit residues: 388.7940 Evaluate side-chains 596 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 552 time to evaluate : 2.975 ------------------------------------------------------------------------------- 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 115 GLN Chi-restraints excluded: chain A residue 205 SER 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 702 GLU Chi-restraints excluded: chain A residue 913 GLN 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 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 274 THR 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 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 55 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 966 LEU 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 23 CYS 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 197 optimal weight: 0.5980 chunk 188 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 227 optimal weight: 0.2980 chunk 196 optimal weight: 0.7980 chunk 343 optimal weight: 0.7980 chunk 299 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 280 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 544 ASN A 774 GLN K 89 GLN B 32 ASN B 207 HIS B 394 ASN B 774 GLN E 207 HIS E 564 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.167157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.132506 restraints weight = 46609.036| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.77 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: 0.7371 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 29948 Z= 0.137 Angle : 0.607 15.296 40792 Z= 0.296 Chirality : 0.045 0.308 4638 Planarity : 0.004 0.063 5214 Dihedral : 5.566 55.410 4548 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.99 % Allowed : 16.22 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 3627 helix: 2.39 (0.21), residues: 627 sheet: 0.38 (0.17), residues: 924 loop : -1.23 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 35 HIS 0.005 0.001 HIS D 90 PHE 0.020 0.001 PHE A 168 TYR 0.019 0.001 TYR A 495 ARG 0.007 0.000 ARG G 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00900 ( 27) link_NAG-ASN : angle 4.21156 ( 81) hydrogen bonds : bond 0.04349 ( 1052) hydrogen bonds : angle 4.77724 ( 2859) SS BOND : bond 0.00597 ( 41) SS BOND : angle 1.92592 ( 82) covalent geometry : bond 0.00319 (29880) covalent geometry : angle 0.57138 (40629) *********************** 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 616 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 552 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7943 (m-40) cc_final: 0.7362 (t0) REVERT: A 190 ARG cc_start: 0.7791 (mpt180) cc_final: 0.7415 (mtt90) REVERT: A 357 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8018 (mmp80) REVERT: A 358 ILE cc_start: 0.7728 (mp) cc_final: 0.7399 (tt) REVERT: A 377 PHE cc_start: 0.6995 (t80) cc_final: 0.6520 (t80) REVERT: A 493 GLN cc_start: 0.7733 (tt0) cc_final: 0.7375 (tt0) REVERT: A 542 ASN cc_start: 0.7435 (t0) cc_final: 0.7166 (t0) REVERT: A 564 GLN cc_start: 0.7901 (mt0) cc_final: 0.7604 (mm-40) REVERT: A 646 ARG cc_start: 0.8042 (ttt90) cc_final: 0.7728 (ttt90) REVERT: A 776 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8161 (tttt) REVERT: A 779 GLN cc_start: 0.8236 (tp40) cc_final: 0.7977 (tm-30) REVERT: A 790 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8318 (mtpt) REVERT: A 980 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8093 (mp) REVERT: A 1084 ASP cc_start: 0.7708 (t0) cc_final: 0.7165 (t0) REVERT: A 1139 ASP cc_start: 0.7902 (t0) cc_final: 0.7473 (t0) REVERT: H 83 MET cc_start: 0.6667 (mtp) cc_final: 0.6466 (mtp) REVERT: H 95 TYR cc_start: 0.8226 (m-80) cc_final: 0.7994 (m-80) REVERT: H 113 MET cc_start: 0.7692 (mmm) cc_final: 0.7431 (mmm) REVERT: K 4 MET cc_start: 0.7301 (mmm) cc_final: 0.6963 (tmm) REVERT: K 97 MET cc_start: 0.7497 (mmm) cc_final: 0.7272 (mmm) REVERT: B 110 LEU cc_start: 0.7303 (mm) cc_final: 0.7080 (mm) REVERT: B 188 ASN cc_start: 0.7348 (p0) cc_final: 0.7092 (p0) REVERT: B 239 GLN cc_start: 0.7684 (tt0) cc_final: 0.7265 (tt0) REVERT: B 305 SER cc_start: 0.8474 (t) cc_final: 0.8095 (p) REVERT: B 403 ARG cc_start: 0.7542 (mtt180) cc_final: 0.7090 (mtt180) REVERT: B 453 TYR cc_start: 0.7815 (p90) cc_final: 0.7531 (p90) REVERT: B 467 ASP cc_start: 0.7621 (t0) cc_final: 0.7357 (t0) REVERT: B 583 GLU cc_start: 0.6979 (tp30) cc_final: 0.6631 (tp30) REVERT: B 585 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7571 (pp) REVERT: B 646 ARG cc_start: 0.7894 (ttt90) cc_final: 0.7671 (ttt90) REVERT: B 740 MET cc_start: 0.7687 (mmm) cc_final: 0.7400 (mmm) REVERT: B 779 GLN cc_start: 0.8353 (tp40) cc_final: 0.8131 (tm-30) REVERT: B 804 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8135 (mm-40) REVERT: B 980 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8140 (mp) REVERT: B 1084 ASP cc_start: 0.7698 (t0) cc_final: 0.7156 (t0) REVERT: B 1139 ASP cc_start: 0.7808 (t0) cc_final: 0.7449 (t0) REVERT: C 39 ARG cc_start: 0.7240 (ttm-80) cc_final: 0.6805 (ttt180) REVERT: C 83 MET cc_start: 0.6314 (mtm) cc_final: 0.6062 (mtm) REVERT: D 4 MET cc_start: 0.7155 (mmm) cc_final: 0.6901 (mmm) REVERT: D 55 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6376 (tm130) REVERT: D 97 MET cc_start: 0.7653 (mmm) cc_final: 0.7412 (mmm) REVERT: E 115 GLN cc_start: 0.6918 (tp-100) cc_final: 0.6640 (mm-40) REVERT: E 129 LYS cc_start: 0.8013 (ptmt) cc_final: 0.7495 (ptmm) REVERT: E 239 GLN cc_start: 0.7647 (tt0) cc_final: 0.7220 (tt0) REVERT: E 305 SER cc_start: 0.8646 (t) cc_final: 0.8310 (p) REVERT: E 355 ARG cc_start: 0.8031 (tpp80) cc_final: 0.7567 (ttt180) REVERT: E 357 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7599 (ttm-80) REVERT: E 434 ILE cc_start: 0.8085 (mt) cc_final: 0.7868 (mt) REVERT: E 453 TYR cc_start: 0.7723 (p90) cc_final: 0.7509 (p90) REVERT: E 456 PHE cc_start: 0.8462 (m-80) cc_final: 0.8128 (m-10) REVERT: E 465 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6962 (mt-10) REVERT: E 537 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8194 (mtmt) REVERT: E 675 GLN cc_start: 0.7437 (tt0) cc_final: 0.7186 (mt0) REVERT: E 690 GLN cc_start: 0.7702 (mm110) cc_final: 0.7318 (mm-40) REVERT: E 776 LYS cc_start: 0.8371 (ttmt) cc_final: 0.8109 (tttp) REVERT: E 784 GLN cc_start: 0.8519 (mt0) cc_final: 0.8237 (mt0) REVERT: E 790 LYS cc_start: 0.8617 (mttm) cc_final: 0.8381 (mttm) REVERT: E 804 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7752 (mt0) REVERT: E 869 MET cc_start: 0.8313 (mtt) cc_final: 0.8003 (mtt) REVERT: E 904 TYR cc_start: 0.8266 (m-10) cc_final: 0.7642 (m-10) REVERT: E 980 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8030 (mp) REVERT: E 1084 ASP cc_start: 0.7902 (t0) cc_final: 0.7352 (t0) REVERT: E 1139 ASP cc_start: 0.7852 (t0) cc_final: 0.7492 (t0) REVERT: F 23 CYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6798 (t) REVERT: F 39 ARG cc_start: 0.7164 (ttm-80) cc_final: 0.6730 (ttt180) REVERT: F 65 ARG cc_start: 0.7395 (mtt180) cc_final: 0.7163 (mtt-85) REVERT: F 83 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6427 (mtp) REVERT: F 95 TYR cc_start: 0.8223 (m-80) cc_final: 0.7822 (m-80) REVERT: F 110 GLN cc_start: 0.7580 (pm20) cc_final: 0.7322 (pm20) REVERT: G 55 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6829 (tm130) REVERT: G 97 MET cc_start: 0.7585 (mmm) cc_final: 0.7284 (mmm) outliers start: 64 outliers final: 42 residues processed: 590 average time/residue: 0.4167 time to fit residues: 383.5632 Evaluate side-chains 599 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 549 time to evaluate : 3.117 ------------------------------------------------------------------------------- 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 115 GLN Chi-restraints excluded: chain A residue 127 VAL 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 702 GLU 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 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 274 THR 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 980 ILE Chi-restraints excluded: chain B residue 996 LEU 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 127 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 551 VAL 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 966 LEU 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 E residue 1096 VAL Chi-restraints excluded: chain F residue 23 CYS 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 146 optimal weight: 0.9990 chunk 185 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 307 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 333 optimal weight: 0.0570 chunk 142 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 227 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 207 HIS B 542 ASN B 774 GLN E 207 HIS ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.167976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.133423 restraints weight = 46283.461| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.75 r_work: 0.3641 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 29948 Z= 0.120 Angle : 0.597 14.171 40792 Z= 0.291 Chirality : 0.045 0.309 4638 Planarity : 0.004 0.054 5214 Dihedral : 5.443 57.561 4548 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.87 % Allowed : 16.50 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3627 helix: 2.46 (0.21), residues: 627 sheet: 0.35 (0.17), residues: 954 loop : -1.18 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP K 35 HIS 0.006 0.001 HIS D 90 PHE 0.022 0.001 PHE A 168 TYR 0.019 0.001 TYR B 380 ARG 0.005 0.000 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00893 ( 27) link_NAG-ASN : angle 3.95899 ( 81) hydrogen bonds : bond 0.04112 ( 1052) hydrogen bonds : angle 4.69155 ( 2859) SS BOND : bond 0.00576 ( 41) SS BOND : angle 1.82287 ( 82) covalent geometry : bond 0.00274 (29880) covalent geometry : angle 0.56533 (40629) *********************** 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 609 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 549 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.7688 (tp) cc_final: 0.7452 (tt) REVERT: A 357 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.8038 (mmp80) REVERT: A 358 ILE cc_start: 0.7750 (mp) cc_final: 0.7420 (tt) REVERT: A 377 PHE cc_start: 0.6999 (t80) cc_final: 0.6465 (t80) REVERT: A 457 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.7975 (tpp80) REVERT: A 493 GLN cc_start: 0.7731 (tt0) cc_final: 0.7330 (tt0) REVERT: A 498 ARG cc_start: 0.7645 (mmm160) cc_final: 0.7439 (mmm160) REVERT: A 542 ASN cc_start: 0.7442 (t0) cc_final: 0.7179 (t0) REVERT: A 564 GLN cc_start: 0.7895 (mt0) cc_final: 0.7615 (mm-40) REVERT: A 776 LYS cc_start: 0.8416 (ttpt) cc_final: 0.8135 (tttp) REVERT: A 779 GLN cc_start: 0.8205 (tp40) cc_final: 0.7947 (tm-30) REVERT: A 980 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8056 (mp) REVERT: A 1084 ASP cc_start: 0.7704 (t0) cc_final: 0.7169 (t0) REVERT: A 1139 ASP cc_start: 0.7903 (t0) cc_final: 0.7487 (t0) REVERT: H 83 MET cc_start: 0.6349 (mtp) cc_final: 0.6109 (mtp) REVERT: H 95 TYR cc_start: 0.8245 (m-80) cc_final: 0.8019 (m-80) REVERT: H 113 MET cc_start: 0.7737 (mmm) cc_final: 0.7459 (mmm) REVERT: K 4 MET cc_start: 0.7327 (mmm) cc_final: 0.6927 (tmm) REVERT: K 97 MET cc_start: 0.7567 (mmm) cc_final: 0.7308 (mmm) REVERT: B 110 LEU cc_start: 0.7233 (mm) cc_final: 0.7002 (mm) REVERT: B 188 ASN cc_start: 0.7334 (p0) cc_final: 0.7071 (p0) REVERT: B 239 GLN cc_start: 0.7640 (tt0) cc_final: 0.7230 (tt0) REVERT: B 298 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7657 (mt-10) REVERT: B 305 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.8250 (t) REVERT: B 403 ARG cc_start: 0.7536 (mtt180) cc_final: 0.7081 (mtt180) REVERT: B 453 TYR cc_start: 0.7855 (p90) cc_final: 0.7565 (p90) REVERT: B 467 ASP cc_start: 0.7633 (t0) cc_final: 0.7312 (t0) REVERT: B 583 GLU cc_start: 0.6955 (tp30) cc_final: 0.6542 (tp30) REVERT: B 585 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7570 (pp) REVERT: B 592 PHE cc_start: 0.8649 (p90) cc_final: 0.8254 (p90) REVERT: B 646 ARG cc_start: 0.7907 (ttt90) cc_final: 0.7676 (ttt90) REVERT: B 740 MET cc_start: 0.7596 (mmm) cc_final: 0.7289 (mmm) REVERT: B 779 GLN cc_start: 0.8293 (tp40) cc_final: 0.8063 (tm-30) REVERT: B 804 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8121 (mm-40) REVERT: B 980 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8103 (mp) REVERT: B 1084 ASP cc_start: 0.7692 (t0) cc_final: 0.7161 (t0) REVERT: B 1139 ASP cc_start: 0.7808 (t0) cc_final: 0.7462 (t0) REVERT: C 39 ARG cc_start: 0.7200 (ttm-80) cc_final: 0.6746 (ttt180) REVERT: C 83 MET cc_start: 0.6209 (mtm) cc_final: 0.5910 (mtm) REVERT: D 4 MET cc_start: 0.7185 (mmm) cc_final: 0.6922 (mmm) REVERT: D 55 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6364 (tm130) REVERT: D 97 MET cc_start: 0.7689 (mmm) cc_final: 0.7375 (mmm) REVERT: E 115 GLN cc_start: 0.6895 (tp-100) cc_final: 0.6670 (mm-40) REVERT: E 129 LYS cc_start: 0.7931 (ptmt) cc_final: 0.7400 (ptmm) REVERT: E 239 GLN cc_start: 0.7567 (tt0) cc_final: 0.7134 (tt0) REVERT: E 355 ARG cc_start: 0.8027 (tpp80) cc_final: 0.7552 (ttt180) REVERT: E 357 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7508 (ttm-80) REVERT: E 453 TYR cc_start: 0.7704 (p90) cc_final: 0.7430 (p90) REVERT: E 456 PHE cc_start: 0.8478 (m-80) cc_final: 0.8109 (m-10) REVERT: E 465 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6970 (mt-10) REVERT: E 537 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8177 (mtmt) REVERT: E 675 GLN cc_start: 0.7416 (tt0) cc_final: 0.7168 (mt0) REVERT: E 690 GLN cc_start: 0.7698 (mm110) cc_final: 0.7321 (mm-40) REVERT: E 776 LYS cc_start: 0.8375 (ttmt) cc_final: 0.8114 (tttp) REVERT: E 784 GLN cc_start: 0.8492 (mt0) cc_final: 0.8212 (mt0) REVERT: E 790 LYS cc_start: 0.8565 (mttm) cc_final: 0.8317 (mttm) REVERT: E 804 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7744 (mt0) REVERT: E 869 MET cc_start: 0.8304 (mtt) cc_final: 0.8009 (mtt) REVERT: E 904 TYR cc_start: 0.8258 (m-10) cc_final: 0.7588 (m-10) REVERT: E 980 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7998 (mp) REVERT: E 1084 ASP cc_start: 0.7884 (t0) cc_final: 0.7340 (t0) REVERT: E 1139 ASP cc_start: 0.7828 (t0) cc_final: 0.7468 (t0) REVERT: F 23 CYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6865 (t) REVERT: F 39 ARG cc_start: 0.7168 (ttm-80) cc_final: 0.6706 (ttt180) REVERT: F 65 ARG cc_start: 0.7429 (mtt180) cc_final: 0.7168 (mtt-85) REVERT: F 83 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6460 (mtp) REVERT: F 95 TYR cc_start: 0.8206 (m-80) cc_final: 0.7804 (m-80) REVERT: F 110 GLN cc_start: 0.7682 (pm20) cc_final: 0.7392 (pm20) REVERT: G 55 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.6954 (tm130) REVERT: G 97 MET cc_start: 0.7617 (mmm) cc_final: 0.7274 (mmm) outliers start: 60 outliers final: 40 residues processed: 583 average time/residue: 0.4272 time to fit residues: 390.4288 Evaluate side-chains 591 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 542 time to evaluate : 3.179 ------------------------------------------------------------------------------- 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 127 VAL 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 702 GLU 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 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 274 THR Chi-restraints excluded: chain B residue 305 SER 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 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 55 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 233 ILE 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 723 THR Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 966 LEU 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 23 CYS 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 90 optimal weight: 0.9990 chunk 174 optimal weight: 0.3980 chunk 222 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 279 optimal weight: 10.0000 chunk 267 optimal weight: 0.0060 chunk 181 optimal weight: 0.3980 chunk 347 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 A 544 ASN B 207 HIS B 542 ASN B 774 GLN D 92 ASN E 207 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.167774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133198 restraints weight = 46266.861| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.75 r_work: 0.3636 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29948 Z= 0.128 Angle : 0.605 14.232 40792 Z= 0.295 Chirality : 0.045 0.304 4638 Planarity : 0.004 0.053 5214 Dihedral : 5.393 58.163 4548 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.53 % Allowed : 17.09 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3627 helix: 2.45 (0.21), residues: 627 sheet: 0.39 (0.17), residues: 954 loop : -1.17 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 353 HIS 0.018 0.001 HIS G 90 PHE 0.022 0.001 PHE E 168 TYR 0.018 0.001 TYR B1067 ARG 0.007 0.000 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00886 ( 27) link_NAG-ASN : angle 3.79983 ( 81) hydrogen bonds : bond 0.04162 ( 1052) hydrogen bonds : angle 4.68742 ( 2859) SS BOND : bond 0.00531 ( 41) SS BOND : angle 1.75826 ( 82) covalent geometry : bond 0.00295 (29880) covalent geometry : angle 0.57668 (40629) ********************** 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 599 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 550 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7820 (mpt180) cc_final: 0.7421 (mtt90) REVERT: A 357 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.7912 (mmp80) REVERT: A 377 PHE cc_start: 0.7051 (t80) cc_final: 0.6525 (t80) REVERT: A 492 LEU cc_start: 0.9039 (pp) cc_final: 0.8786 (pt) REVERT: A 542 ASN cc_start: 0.7442 (t0) cc_final: 0.7170 (t0) REVERT: A 564 GLN cc_start: 0.7907 (mt0) cc_final: 0.7618 (mm-40) REVERT: A 776 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8130 (tttp) REVERT: A 779 GLN cc_start: 0.8222 (tp40) cc_final: 0.7964 (tm-30) REVERT: A 980 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8042 (mp) REVERT: A 1031 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7597 (mt-10) REVERT: A 1084 ASP cc_start: 0.7704 (t0) cc_final: 0.7167 (t0) REVERT: A 1139 ASP cc_start: 0.7901 (t0) cc_final: 0.7479 (t0) REVERT: H 83 MET cc_start: 0.6357 (mtp) cc_final: 0.6124 (mtp) REVERT: H 95 TYR cc_start: 0.8226 (m-80) cc_final: 0.8002 (m-80) REVERT: H 113 MET cc_start: 0.7736 (mmm) cc_final: 0.7455 (mmm) REVERT: K 4 MET cc_start: 0.7321 (mmm) cc_final: 0.6902 (tmm) REVERT: K 97 MET cc_start: 0.7572 (mmm) cc_final: 0.7316 (mmm) REVERT: B 110 LEU cc_start: 0.7231 (mm) cc_final: 0.7007 (mm) REVERT: B 188 ASN cc_start: 0.7359 (p0) cc_final: 0.7095 (p0) REVERT: B 239 GLN cc_start: 0.7652 (tt0) cc_final: 0.7237 (tt0) REVERT: B 298 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7661 (mt-10) REVERT: B 305 SER cc_start: 0.8508 (t) cc_final: 0.8275 (t) REVERT: B 403 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7126 (mtt180) REVERT: B 453 TYR cc_start: 0.7875 (p90) cc_final: 0.7600 (p90) REVERT: B 467 ASP cc_start: 0.7590 (t0) cc_final: 0.7268 (t0) REVERT: B 583 GLU cc_start: 0.6972 (tp30) cc_final: 0.6556 (tp30) REVERT: B 585 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7626 (pp) REVERT: B 592 PHE cc_start: 0.8651 (p90) cc_final: 0.8388 (p90) REVERT: B 616 ASN cc_start: 0.8054 (m-40) cc_final: 0.7797 (m110) REVERT: B 646 ARG cc_start: 0.7932 (ttt90) cc_final: 0.7701 (ttt90) REVERT: B 740 MET cc_start: 0.7625 (mmm) cc_final: 0.7278 (mmm) REVERT: B 779 GLN cc_start: 0.8300 (tp40) cc_final: 0.8071 (tm-30) REVERT: B 804 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7729 (mt0) REVERT: B 980 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8120 (mp) REVERT: B 1084 ASP cc_start: 0.7698 (t0) cc_final: 0.7179 (t0) REVERT: B 1139 ASP cc_start: 0.7762 (t0) cc_final: 0.7430 (t0) REVERT: C 39 ARG cc_start: 0.7222 (ttm-80) cc_final: 0.6735 (ttt180) REVERT: C 83 MET cc_start: 0.6222 (mtm) cc_final: 0.5915 (mtm) REVERT: D 4 MET cc_start: 0.7172 (mmm) cc_final: 0.6936 (mmm) REVERT: D 55 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6382 (tm130) REVERT: D 97 MET cc_start: 0.7682 (mmm) cc_final: 0.7369 (mmm) REVERT: E 115 GLN cc_start: 0.6891 (tp-100) cc_final: 0.6655 (mm-40) REVERT: E 129 LYS cc_start: 0.7934 (ptmt) cc_final: 0.7402 (ptmm) REVERT: E 239 GLN cc_start: 0.7576 (tt0) cc_final: 0.7141 (tt0) REVERT: E 355 ARG cc_start: 0.8022 (tpp80) cc_final: 0.7535 (ttt180) REVERT: E 357 ARG cc_start: 0.8050 (ttm-80) cc_final: 0.7496 (ttm-80) REVERT: E 453 TYR cc_start: 0.7651 (p90) cc_final: 0.7326 (p90) REVERT: E 456 PHE cc_start: 0.8483 (m-80) cc_final: 0.8107 (m-10) REVERT: E 465 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6981 (mt-10) REVERT: E 559 PHE cc_start: 0.8150 (m-10) cc_final: 0.7908 (m-10) REVERT: E 675 GLN cc_start: 0.7417 (tt0) cc_final: 0.7176 (mt0) REVERT: E 690 GLN cc_start: 0.7697 (mm110) cc_final: 0.7310 (mm-40) REVERT: E 776 LYS cc_start: 0.8393 (ttmt) cc_final: 0.8117 (tttp) REVERT: E 784 GLN cc_start: 0.8507 (mt0) cc_final: 0.8221 (mt0) REVERT: E 804 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7746 (mt0) REVERT: E 869 MET cc_start: 0.8296 (mtt) cc_final: 0.7962 (mtt) REVERT: E 904 TYR cc_start: 0.8249 (m-10) cc_final: 0.7635 (m-10) REVERT: E 980 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8003 (mp) REVERT: E 1084 ASP cc_start: 0.7904 (t0) cc_final: 0.7360 (t0) REVERT: E 1139 ASP cc_start: 0.7840 (t0) cc_final: 0.7475 (t0) REVERT: F 23 CYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6882 (t) REVERT: F 39 ARG cc_start: 0.7177 (ttm-80) cc_final: 0.6712 (ttt180) REVERT: F 65 ARG cc_start: 0.7452 (mtt180) cc_final: 0.7234 (mtt-85) REVERT: F 83 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6459 (mtp) REVERT: F 95 TYR cc_start: 0.8191 (m-80) cc_final: 0.7798 (m-80) REVERT: F 110 GLN cc_start: 0.7673 (pm20) cc_final: 0.7377 (pm20) REVERT: G 55 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6874 (tm130) REVERT: G 97 MET cc_start: 0.7641 (mmm) cc_final: 0.7308 (mmm) outliers start: 49 outliers final: 40 residues processed: 580 average time/residue: 0.4117 time to fit residues: 372.8360 Evaluate side-chains 589 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 541 time to evaluate : 2.977 ------------------------------------------------------------------------------- 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 127 VAL 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 702 GLU 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 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 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 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 55 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 433 VAL 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 723 THR Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 966 LEU Chi-restraints excluded: chain E residue 980 ILE Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain F residue 23 CYS 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 184 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 292 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 251 optimal weight: 0.0980 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 68 HIS A 207 HIS A 544 ASN B 207 HIS B 542 ASN B 774 GLN B1088 HIS ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS E 853 GLN ** 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 = 0.167297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.132659 restraints weight = 46128.629| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.74 r_work: 0.3625 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 29948 Z= 0.139 Angle : 0.608 14.525 40792 Z= 0.298 Chirality : 0.045 0.301 4638 Planarity : 0.005 0.101 5214 Dihedral : 5.378 57.947 4548 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.62 % Allowed : 17.15 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3627 helix: 2.44 (0.21), residues: 627 sheet: 0.40 (0.17), residues: 954 loop : -1.16 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 35 HIS 0.005 0.001 HIS A 207 PHE 0.019 0.001 PHE A 168 TYR 0.020 0.001 TYR A 266 ARG 0.007 0.000 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00871 ( 27) link_NAG-ASN : angle 3.74626 ( 81) hydrogen bonds : bond 0.04270 ( 1052) hydrogen bonds : angle 4.69992 ( 2859) SS BOND : bond 0.00546 ( 41) SS BOND : angle 1.74946 ( 82) covalent geometry : bond 0.00324 (29880) covalent geometry : angle 0.58013 (40629) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15782.34 seconds wall clock time: 274 minutes 59.19 seconds (16499.19 seconds total)