Starting phenix.real_space_refine on Sat Jun 21 17:20:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yz6_39686/06_2025/8yz6_39686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yz6_39686/06_2025/8yz6_39686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yz6_39686/06_2025/8yz6_39686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yz6_39686/06_2025/8yz6_39686.map" model { file = "/net/cci-nas-00/data/ceres_data/8yz6_39686/06_2025/8yz6_39686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yz6_39686/06_2025/8yz6_39686.cif" } resolution = 4.55 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 15977 2.51 5 N 4139 2.21 5 O 4750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24972 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7521 Classifications: {'peptide': 959} Link IDs: {'PTRANS': 48, 'TRANS': 910} Chain breaks: 11 Chain: "B" Number of atoms: 7704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7704 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 48, 'TRANS': 935} Chain breaks: 10 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 7773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7773 Classifications: {'peptide': 990} Link IDs: {'PTRANS': 50, 'TRANS': 939} Chain breaks: 10 Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 888 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "E" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 837 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 100} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 15.71, per 1000 atoms: 0.63 Number of scatterers: 24972 At special positions: 0 Unit cell: (167.66, 187.58, 151.06, 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 106 16.00 O 4750 8.00 N 4139 7.00 C 15977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " 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 B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 104 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 104 " 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG L 1 " - " NAG L 2 " " NAG N 1 " - " NAG N 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 801 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A1098 " " NAG B1301 " - " ASN B 801 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 343 " " NAG C1301 " - " ASN C 801 " " NAG F 1 " - " ASN A 717 " " NAG L 1 " - " ASN B 717 " " NAG N 1 " - " ASN B1074 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C1098 " Time building additional restraints: 6.84 Conformation dependent library (CDL) restraints added in 3.4 seconds 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5912 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 50 sheets defined 24.4% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.533A pdb=" N LEU A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.870A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.948A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.741A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 891 removed outlier: 4.282A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.093A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.592A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.882A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.091A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.986A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 890 removed outlier: 4.085A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 941 removed outlier: 5.335A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.720A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.982A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.125A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.868A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.651A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 4.584A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 423 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.790A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.514A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 891 removed outlier: 4.053A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 941 removed outlier: 5.186A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.233A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'E' and resid 95 through 99 removed outlier: 3.943A pdb=" N PHE E 99 " --> pdb=" O PRO E 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 removed outlier: 4.583A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.699A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.794A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.598A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.560A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.637A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.634A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.720A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.782A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.753A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 727 removed outlier: 3.595A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A1066 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.952A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1088 through 1089 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AB8, first strand: chain 'B' and resid 52 through 55 removed outlier: 4.037A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 190 through 195 removed outlier: 4.371A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 105 through 106 removed outlier: 3.763A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 201 through 205 removed outlier: 3.579A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.498A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.571A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.887A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.487A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.644A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.604A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.888A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.959A pdb=" N THR B 716 " --> pdb=" O GLN B1071 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1047 through 1050 removed outlier: 5.969A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1086 through 1088 removed outlier: 4.179A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.829A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 52 through 55 Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.602A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.684A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 94 through 95 removed outlier: 3.704A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.445A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 327 through 328 removed outlier: 3.740A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.798A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 552 through 554 removed outlier: 3.515A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 610 through 611 Processing sheet with id=AE5, first strand: chain 'C' and resid 655 through 656 removed outlier: 7.709A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 721 removed outlier: 4.021A pdb=" N THR C 716 " --> pdb=" O GLN C1071 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 724 through 728 removed outlier: 3.574A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1081 through 1083 removed outlier: 4.358A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.591A pdb=" N SER D 79 " --> pdb=" O TYR D 88 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 11 through 13 removed outlier: 3.612A pdb=" N THR D 122 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR D 38 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER D 54 " --> pdb=" O TRP D 41 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG D 43 " --> pdb=" O TRP D 52 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TRP D 52 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 11 through 13 removed outlier: 3.612A pdb=" N THR D 122 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE D 117 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 4 through 7 removed outlier: 11.893A pdb=" N CYS E 23 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N THR E 90 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 11.585A pdb=" N ALA E 25 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 11.163A pdb=" N THR E 88 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N GLN E 27 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASP E 86 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY E 84 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AF5, first strand: chain 'E' and resid 66 through 67 removed outlier: 6.499A pdb=" N TRP E 41 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR E 55 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU E 39 " --> pdb=" O TYR E 55 " (cutoff:3.500A) 803 hydrogen bonds defined for protein. 2199 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: 10.49 Time building geometry restraints manager: 8.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5960 1.33 - 1.46: 7197 1.46 - 1.59: 12241 1.59 - 1.71: 0 1.71 - 1.84: 135 Bond restraints: 25533 Sorted by residual: bond pdb=" N GLN A 173 " pdb=" CA GLN A 173 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.59e+01 bond pdb=" N PRO B 373 " pdb=" CD PRO B 373 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.59e+01 bond pdb=" C ARG C 815 " pdb=" N SER C 816 " ideal model delta sigma weight residual 1.329 1.383 -0.054 1.38e-02 5.25e+03 1.52e+01 bond pdb=" N ARG A 328 " pdb=" CA ARG A 328 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.27e-02 6.20e+03 9.35e+00 bond pdb=" N VAL A 171 " pdb=" CA VAL A 171 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.14e-02 7.69e+03 9.03e+00 ... (remaining 25528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 34246 2.54 - 5.07: 417 5.07 - 7.61: 28 7.61 - 10.14: 4 10.14 - 12.68: 3 Bond angle restraints: 34698 Sorted by residual: angle pdb=" CA PRO B 373 " pdb=" N PRO B 373 " pdb=" CD PRO B 373 " ideal model delta sigma weight residual 112.00 99.38 12.62 1.40e+00 5.10e-01 8.12e+01 angle pdb=" N MET A 177 " pdb=" CA MET A 177 " pdb=" C MET A 177 " ideal model delta sigma weight residual 113.97 108.79 5.18 1.28e+00 6.10e-01 1.64e+01 angle pdb=" CA PHE A 898 " pdb=" C PHE A 898 " pdb=" N ALA A 899 " ideal model delta sigma weight residual 117.07 121.61 -4.54 1.14e+00 7.69e-01 1.58e+01 angle pdb=" CB ARG B1014 " pdb=" CG ARG B1014 " pdb=" CD ARG B1014 " ideal model delta sigma weight residual 111.30 120.41 -9.11 2.30e+00 1.89e-01 1.57e+01 angle pdb=" CA ILE B 332 " pdb=" C ILE B 332 " pdb=" O ILE B 332 " ideal model delta sigma weight residual 121.97 118.10 3.87 9.80e-01 1.04e+00 1.56e+01 ... (remaining 34693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.42: 14477 21.42 - 42.85: 805 42.85 - 64.27: 106 64.27 - 85.69: 40 85.69 - 107.12: 8 Dihedral angle restraints: 15436 sinusoidal: 6257 harmonic: 9179 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -0.27 -85.73 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -20.51 -65.49 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -27.25 -58.75 1 1.00e+01 1.00e-02 4.62e+01 ... (remaining 15433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3178 0.054 - 0.107: 668 0.107 - 0.161: 130 0.161 - 0.215: 11 0.215 - 0.269: 4 Chirality restraints: 3991 Sorted by residual: chirality pdb=" C5 BMA T 3 " pdb=" C4 BMA T 3 " pdb=" C6 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE C 794 " pdb=" CA ILE C 794 " pdb=" CG1 ILE C 794 " pdb=" CG2 ILE C 794 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE C 664 " pdb=" CA ILE C 664 " pdb=" CG1 ILE C 664 " pdb=" CG2 ILE C 664 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3988 not shown) Planarity restraints: 4451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 110 " 0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO E 113 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO E 113 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO E 113 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 664 " 0.058 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO C 665 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO C 665 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 665 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 664 " 0.051 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO B 665 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 665 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 665 " 0.042 5.00e-02 4.00e+02 ... (remaining 4448 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 1 1.93 - 2.68: 603 2.68 - 3.42: 35524 3.42 - 4.16: 58226 4.16 - 4.90: 98829 Nonbonded interactions: 193183 Sorted by model distance: nonbonded pdb=" OE1 GLN A 115 " pdb=" OG1 THR A 167 " model vdw 1.194 3.040 nonbonded pdb=" OH TYR A 170 " pdb=" CG1 VAL A 227 " model vdw 1.964 3.460 nonbonded pdb=" O GLU B 309 " pdb=" OH TYR B 313 " model vdw 2.067 3.040 nonbonded pdb=" OD1 ASN C 960 " pdb=" NZ LYS C 964 " model vdw 2.077 3.120 nonbonded pdb=" O ASP E 98 " pdb=" OH TYR E 102 " model vdw 2.092 3.040 ... (remaining 193178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 61 or resid 63 through 176 or resid 185 through \ 356 or (resid 357 and (name N or name CA or name C or name O or name CB )) or r \ esid 358 through 377 or (resid 378 and (name N or name CA or name C or name O or \ name CB )) or resid 379 through 390 or (resid 391 and (name N or name CA or nam \ e C or name O or name CB )) or resid 392 through 518 or resid 521 through 527 or \ (resid 528 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 1 through 703 or resid 705 through 1135 or resid 1301)) selection = (chain 'B' and (resid 27 through 61 or resid 63 through 108 or resid 115 through \ 131 or resid 167 through 469 or resid 491 through 528 or resid 531 through 1135 \ or resid 1301)) selection = (chain 'C' and (resid 27 through 108 or resid 115 through 131 or resid 167 throu \ gh 356 or (resid 357 and (name N or name CA or name C or name O or name CB )) or \ resid 358 through 377 or (resid 378 and (name N or name CA or name C or name O \ or name CB )) or resid 379 through 390 or (resid 391 and (name N or name CA or n \ ame C or name O or name CB )) or resid 392 through 518 or resid 521 through 527 \ or (resid 528 and (name N or name CA or name C or name O or name CB )) or resid \ 531 through 703 or resid 705 through 1135 or resid 1301)) } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'N' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.240 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 60.810 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 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 0.086 25587 Z= 0.196 Angle : 0.692 17.114 34824 Z= 0.372 Chirality : 0.046 0.269 3991 Planarity : 0.005 0.100 4439 Dihedral : 13.464 107.115 9416 Min Nonbonded Distance : 1.194 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.76 % Favored : 96.02 % Rotamer: Outliers : 0.36 % Allowed : 0.29 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % 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: -0.97 (0.15), residues: 3089 helix: 0.41 (0.20), residues: 677 sheet: -0.32 (0.24), residues: 480 loop : -1.15 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 64 HIS 0.007 0.001 HIS C 49 PHE 0.029 0.002 PHE C 906 TYR 0.021 0.002 TYR B 655 ARG 0.018 0.001 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 12) link_NAG-ASN : angle 4.71030 ( 36) link_BETA1-4 : bond 0.00566 ( 6) link_BETA1-4 : angle 1.57486 ( 18) hydrogen bonds : bond 0.20086 ( 797) hydrogen bonds : angle 8.69957 ( 2199) SS BOND : bond 0.00444 ( 36) SS BOND : angle 1.39278 ( 72) covalent geometry : bond 0.00368 (25533) covalent geometry : angle 0.67237 (34698) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 438 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7627 (m-10) cc_final: 0.7406 (m-10) REVERT: A 334 ASN cc_start: 0.7263 (OUTLIER) cc_final: 0.7019 (p0) REVERT: A 770 ILE cc_start: 0.9186 (mt) cc_final: 0.8902 (mt) REVERT: A 861 LEU cc_start: 0.9131 (mm) cc_final: 0.8864 (mm) REVERT: A 950 ASP cc_start: 0.8755 (t0) cc_final: 0.8437 (t0) REVERT: A 960 ASN cc_start: 0.7661 (m110) cc_final: 0.7391 (m110) REVERT: A 1019 ARG cc_start: 0.8305 (tpt-90) cc_final: 0.8104 (tpp80) REVERT: B 387 LEU cc_start: 0.6399 (tt) cc_final: 0.6169 (tt) REVERT: B 740 MET cc_start: 0.7283 (tpt) cc_final: 0.6732 (tpp) REVERT: B 935 GLN cc_start: 0.8793 (tt0) cc_final: 0.8459 (tm-30) REVERT: B 953 ASN cc_start: 0.8693 (m-40) cc_final: 0.8305 (m110) REVERT: B 957 GLN cc_start: 0.8886 (pm20) cc_final: 0.8632 (pm20) REVERT: B 1023 ASN cc_start: 0.9003 (m110) cc_final: 0.8153 (m110) REVERT: C 45 SER cc_start: 0.8367 (p) cc_final: 0.8107 (p) REVERT: C 46 SER cc_start: 0.8435 (m) cc_final: 0.8177 (p) REVERT: C 727 LEU cc_start: 0.8814 (mt) cc_final: 0.8578 (mt) REVERT: C 970 PHE cc_start: 0.6744 (m-80) cc_final: 0.6462 (m-80) REVERT: D 66 TYR cc_start: 0.6273 (m-10) cc_final: 0.5472 (m-10) REVERT: E 105 GLN cc_start: 0.5766 (tm-30) cc_final: 0.5289 (tp-100) outliers start: 10 outliers final: 2 residues processed: 446 average time/residue: 0.3659 time to fit residues: 255.2344 Evaluate side-chains 369 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 366 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 0.9990 chunk 237 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 246 optimal weight: 0.0270 chunk 95 optimal weight: 0.5980 chunk 149 optimal weight: 8.9990 chunk 183 optimal weight: 0.4980 chunk 285 optimal weight: 4.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A 957 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN B 417 ASN B 505 HIS ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 953 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS B1088 HIS C 87 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.217735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.167110 restraints weight = 59230.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.171039 restraints weight = 38847.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.173776 restraints weight = 28942.894| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25587 Z= 0.124 Angle : 0.595 10.697 34824 Z= 0.307 Chirality : 0.045 0.181 3991 Planarity : 0.005 0.067 4439 Dihedral : 6.693 66.296 3761 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 0.04 % Allowed : 3.57 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % 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: -0.80 (0.15), residues: 3089 helix: 0.69 (0.20), residues: 683 sheet: -0.33 (0.24), residues: 494 loop : -1.07 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.008 0.001 HIS B1048 PHE 0.015 0.001 PHE B 906 TYR 0.024 0.001 TYR C 756 ARG 0.011 0.001 ARG C 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 12) link_NAG-ASN : angle 2.68734 ( 36) link_BETA1-4 : bond 0.00606 ( 6) link_BETA1-4 : angle 1.68845 ( 18) hydrogen bonds : bond 0.04528 ( 797) hydrogen bonds : angle 6.90066 ( 2199) SS BOND : bond 0.00307 ( 36) SS BOND : angle 1.09547 ( 72) covalent geometry : bond 0.00271 (25533) covalent geometry : angle 0.58608 (34698) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 431 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7375 (m-10) cc_final: 0.7114 (m-80) REVERT: A 226 LEU cc_start: 0.8126 (mm) cc_final: 0.7869 (mp) REVERT: A 825 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8422 (mmmt) REVERT: A 872 GLN cc_start: 0.9119 (mt0) cc_final: 0.8857 (tp40) REVERT: A 926 GLN cc_start: 0.8783 (mp10) cc_final: 0.8563 (mp10) REVERT: A 950 ASP cc_start: 0.8616 (t0) cc_final: 0.8094 (t0) REVERT: A 1001 LEU cc_start: 0.9311 (tp) cc_final: 0.9031 (tp) REVERT: A 1002 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 1054 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8069 (mm-40) REVERT: B 387 LEU cc_start: 0.6300 (tt) cc_final: 0.5873 (tt) REVERT: B 740 MET cc_start: 0.7089 (tpt) cc_final: 0.6688 (tpp) REVERT: B 796 TYR cc_start: 0.5575 (t80) cc_final: 0.5172 (m-80) REVERT: B 869 MET cc_start: 0.9052 (mtp) cc_final: 0.8698 (mtp) REVERT: B 935 GLN cc_start: 0.8886 (tt0) cc_final: 0.8578 (tm-30) REVERT: B 957 GLN cc_start: 0.8970 (pm20) cc_final: 0.8658 (pm20) REVERT: B 962 LEU cc_start: 0.8429 (tt) cc_final: 0.8032 (tt) REVERT: B 1050 MET cc_start: 0.7373 (tpp) cc_final: 0.6907 (tpp) REVERT: C 46 SER cc_start: 0.8449 (m) cc_final: 0.8237 (p) REVERT: C 727 LEU cc_start: 0.8870 (mt) cc_final: 0.8615 (mt) REVERT: C 733 LYS cc_start: 0.8958 (pttm) cc_final: 0.8496 (pttm) REVERT: C 740 MET cc_start: 0.7973 (tpp) cc_final: 0.7185 (tpp) REVERT: C 773 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8006 (mt-10) REVERT: C 970 PHE cc_start: 0.6800 (m-80) cc_final: 0.6064 (m-80) REVERT: D 66 TYR cc_start: 0.6821 (m-10) cc_final: 0.5744 (m-10) REVERT: E 105 GLN cc_start: 0.6510 (tm-30) cc_final: 0.5728 (tp-100) REVERT: E 109 VAL cc_start: 0.4857 (t) cc_final: 0.4496 (p) outliers start: 1 outliers final: 0 residues processed: 432 average time/residue: 0.3485 time to fit residues: 237.4405 Evaluate side-chains 354 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 210 optimal weight: 4.9990 chunk 292 optimal weight: 30.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN B 394 ASN B 564 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN E 106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.211412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.160694 restraints weight = 60912.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.164373 restraints weight = 40937.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.167126 restraints weight = 30858.701| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25587 Z= 0.193 Angle : 0.653 14.529 34824 Z= 0.334 Chirality : 0.046 0.207 3991 Planarity : 0.005 0.074 4439 Dihedral : 6.246 56.172 3761 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.46 % Rotamer: Outliers : 0.15 % Allowed : 4.12 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % 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: -1.06 (0.14), residues: 3089 helix: 0.36 (0.19), residues: 674 sheet: -0.63 (0.23), residues: 505 loop : -1.13 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 886 HIS 0.012 0.002 HIS C 49 PHE 0.020 0.002 PHE B1062 TYR 0.019 0.002 TYR C1047 ARG 0.008 0.001 ARG C 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 12) link_NAG-ASN : angle 3.30278 ( 36) link_BETA1-4 : bond 0.00499 ( 6) link_BETA1-4 : angle 1.79186 ( 18) hydrogen bonds : bond 0.05049 ( 797) hydrogen bonds : angle 6.85837 ( 2199) SS BOND : bond 0.00346 ( 36) SS BOND : angle 1.08558 ( 72) covalent geometry : bond 0.00401 (25533) covalent geometry : angle 0.64210 (34698) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 429 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 LYS cc_start: 0.8785 (tptp) cc_final: 0.8441 (tptm) REVERT: A 825 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8478 (mmmt) REVERT: A 950 ASP cc_start: 0.8915 (t0) cc_final: 0.8650 (t0) REVERT: A 960 ASN cc_start: 0.8235 (m110) cc_final: 0.8000 (m110) REVERT: A 1001 LEU cc_start: 0.9243 (tp) cc_final: 0.9042 (tp) REVERT: A 1002 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8070 (tm-30) REVERT: B 49 HIS cc_start: 0.7576 (t-90) cc_final: 0.7359 (t-90) REVERT: B 722 VAL cc_start: 0.8922 (t) cc_final: 0.8683 (t) REVERT: B 740 MET cc_start: 0.7106 (tpt) cc_final: 0.6755 (tpp) REVERT: B 796 TYR cc_start: 0.5686 (t80) cc_final: 0.5212 (m-80) REVERT: B 869 MET cc_start: 0.9129 (mtp) cc_final: 0.8679 (mtm) REVERT: B 872 GLN cc_start: 0.9333 (mt0) cc_final: 0.9099 (mt0) REVERT: B 935 GLN cc_start: 0.8955 (tt0) cc_final: 0.8648 (tm-30) REVERT: B 957 GLN cc_start: 0.9126 (pm20) cc_final: 0.8712 (pm20) REVERT: B 1000 ARG cc_start: 0.7498 (mtt180) cc_final: 0.7057 (mtp180) REVERT: B 1002 GLN cc_start: 0.9160 (tp40) cc_final: 0.8870 (tm-30) REVERT: B 1009 THR cc_start: 0.9036 (m) cc_final: 0.8679 (m) REVERT: B 1050 MET cc_start: 0.7473 (tpp) cc_final: 0.6941 (tpp) REVERT: C 46 SER cc_start: 0.8525 (m) cc_final: 0.8128 (p) REVERT: C 557 LYS cc_start: 0.8080 (tmmt) cc_final: 0.7863 (tmtt) REVERT: C 740 MET cc_start: 0.7962 (tpp) cc_final: 0.7170 (tpp) REVERT: C 970 PHE cc_start: 0.7077 (m-80) cc_final: 0.6325 (m-80) REVERT: D 66 TYR cc_start: 0.7195 (m-10) cc_final: 0.6098 (m-10) outliers start: 4 outliers final: 1 residues processed: 431 average time/residue: 0.3658 time to fit residues: 249.0751 Evaluate side-chains 352 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 351 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 43 optimal weight: 4.9990 chunk 161 optimal weight: 0.4980 chunk 249 optimal weight: 0.3980 chunk 165 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 251 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 184 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN C 87 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1054 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.213971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.164497 restraints weight = 60445.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.168258 restraints weight = 40234.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.170951 restraints weight = 30287.680| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25587 Z= 0.125 Angle : 0.581 11.763 34824 Z= 0.297 Chirality : 0.044 0.215 3991 Planarity : 0.005 0.061 4439 Dihedral : 5.818 55.935 3761 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Rotamer: Outliers : 0.11 % Allowed : 2.69 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % 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: -0.93 (0.15), residues: 3089 helix: 0.60 (0.20), residues: 676 sheet: -0.65 (0.23), residues: 517 loop : -1.08 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 41 HIS 0.009 0.001 HIS A 954 PHE 0.024 0.001 PHE A 275 TYR 0.015 0.001 TYR C 655 ARG 0.005 0.000 ARG C 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 12) link_NAG-ASN : angle 2.77204 ( 36) link_BETA1-4 : bond 0.00633 ( 6) link_BETA1-4 : angle 1.48531 ( 18) hydrogen bonds : bond 0.04297 ( 797) hydrogen bonds : angle 6.55162 ( 2199) SS BOND : bond 0.00345 ( 36) SS BOND : angle 1.22439 ( 72) covalent geometry : bond 0.00268 (25533) covalent geometry : angle 0.57128 (34698) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 412 time to evaluate : 2.805 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: A 28 TYR cc_start: 0.7320 (m-10) cc_final: 0.7117 (m-10) REVERT: A 577 ARG cc_start: 0.8079 (tmm-80) cc_final: 0.7596 (tmm-80) REVERT: A 773 GLU cc_start: 0.8885 (pp20) cc_final: 0.8654 (pp20) REVERT: A 776 LYS cc_start: 0.8750 (tptp) cc_final: 0.8524 (tptp) REVERT: A 825 LYS cc_start: 0.8594 (mtpt) cc_final: 0.8351 (mmmt) REVERT: A 861 LEU cc_start: 0.9017 (mm) cc_final: 0.8814 (mm) REVERT: A 926 GLN cc_start: 0.8725 (mp10) cc_final: 0.8508 (mp10) REVERT: A 950 ASP cc_start: 0.8824 (t0) cc_final: 0.8470 (t0) REVERT: A 954 HIS cc_start: 0.7742 (m-70) cc_final: 0.7488 (m-70) REVERT: A 960 ASN cc_start: 0.8143 (m110) cc_final: 0.7873 (m110) REVERT: A 1002 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8002 (tm-30) REVERT: B 49 HIS cc_start: 0.7535 (t-90) cc_final: 0.7322 (t-90) REVERT: B 740 MET cc_start: 0.7116 (tpt) cc_final: 0.6647 (tpp) REVERT: B 796 TYR cc_start: 0.5503 (t80) cc_final: 0.5110 (m-80) REVERT: B 869 MET cc_start: 0.9068 (mtp) cc_final: 0.8531 (mtm) REVERT: B 872 GLN cc_start: 0.9261 (mt0) cc_final: 0.9027 (mt0) REVERT: B 935 GLN cc_start: 0.8951 (tt0) cc_final: 0.8619 (tm-30) REVERT: B 950 ASP cc_start: 0.8808 (p0) cc_final: 0.8557 (p0) REVERT: B 957 GLN cc_start: 0.8983 (pm20) cc_final: 0.8650 (pm20) REVERT: B 962 LEU cc_start: 0.8473 (tt) cc_final: 0.8136 (tt) REVERT: B 1000 ARG cc_start: 0.7479 (mtt180) cc_final: 0.7064 (mtp180) REVERT: B 1002 GLN cc_start: 0.9128 (tp40) cc_final: 0.8792 (tp40) REVERT: B 1050 MET cc_start: 0.7298 (tpp) cc_final: 0.6741 (tpp) REVERT: B 1053 PRO cc_start: 0.9569 (Cg_endo) cc_final: 0.9267 (Cg_exo) REVERT: C 45 SER cc_start: 0.8563 (t) cc_final: 0.8282 (t) REVERT: C 46 SER cc_start: 0.8370 (m) cc_final: 0.8139 (p) REVERT: C 201 PHE cc_start: 0.8167 (t80) cc_final: 0.7933 (t80) REVERT: C 229 LEU cc_start: 0.9064 (tp) cc_final: 0.8859 (tp) REVERT: C 729 VAL cc_start: 0.8029 (t) cc_final: 0.7826 (t) REVERT: C 733 LYS cc_start: 0.8881 (pttm) cc_final: 0.8539 (pttm) REVERT: D 39 MET cc_start: 0.5794 (tpt) cc_final: 0.5561 (tpt) REVERT: D 66 TYR cc_start: 0.7114 (m-10) cc_final: 0.6445 (m-10) REVERT: E 105 GLN cc_start: 0.6437 (tm-30) cc_final: 0.5526 (tp-100) outliers start: 3 outliers final: 0 residues processed: 414 average time/residue: 0.3499 time to fit residues: 230.1443 Evaluate side-chains 352 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 253 optimal weight: 7.9990 chunk 52 optimal weight: 0.0170 chunk 140 optimal weight: 7.9990 chunk 286 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 210 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 297 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 overall best weight: 4.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 321 GLN A 331 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN A 928 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN B 414 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 895 GLN B 965 GLN B1023 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.207823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.158294 restraints weight = 61947.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.161227 restraints weight = 45245.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.165304 restraints weight = 33647.188| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 25587 Z= 0.233 Angle : 0.704 15.654 34824 Z= 0.360 Chirality : 0.047 0.199 3991 Planarity : 0.005 0.062 4439 Dihedral : 6.174 57.396 3761 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.22 % Favored : 93.65 % Rotamer: Outliers : 0.15 % Allowed : 2.84 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % 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: -1.30 (0.14), residues: 3089 helix: 0.04 (0.19), residues: 677 sheet: -0.75 (0.23), residues: 503 loop : -1.25 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 886 HIS 0.015 0.002 HIS C 49 PHE 0.024 0.002 PHE A 275 TYR 0.021 0.002 TYR C 707 ARG 0.007 0.001 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 12) link_NAG-ASN : angle 3.48142 ( 36) link_BETA1-4 : bond 0.00616 ( 6) link_BETA1-4 : angle 1.55060 ( 18) hydrogen bonds : bond 0.05199 ( 797) hydrogen bonds : angle 6.90407 ( 2199) SS BOND : bond 0.00649 ( 36) SS BOND : angle 1.48750 ( 72) covalent geometry : bond 0.00485 (25533) covalent geometry : angle 0.69246 (34698) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 410 time to evaluate : 2.994 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 776 LYS cc_start: 0.8765 (tptp) cc_final: 0.8375 (tptm) REVERT: A 960 ASN cc_start: 0.8353 (m110) cc_final: 0.8053 (m110) REVERT: A 1002 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 1042 PHE cc_start: 0.7049 (t80) cc_final: 0.6500 (t80) REVERT: B 49 HIS cc_start: 0.7606 (t-90) cc_final: 0.7388 (t-90) REVERT: B 740 MET cc_start: 0.7117 (tpt) cc_final: 0.6732 (tpp) REVERT: B 796 TYR cc_start: 0.5474 (t80) cc_final: 0.4790 (m-80) REVERT: B 869 MET cc_start: 0.9224 (mtp) cc_final: 0.9002 (mtm) REVERT: B 872 GLN cc_start: 0.9363 (mt0) cc_final: 0.8962 (mt0) REVERT: B 935 GLN cc_start: 0.9065 (tt0) cc_final: 0.8730 (tm-30) REVERT: B 957 GLN cc_start: 0.9170 (pm20) cc_final: 0.8869 (pm20) REVERT: B 977 LEU cc_start: 0.8038 (mt) cc_final: 0.7733 (pp) REVERT: B 1002 GLN cc_start: 0.9209 (tp40) cc_final: 0.8899 (tp40) REVERT: B 1050 MET cc_start: 0.7564 (tpp) cc_final: 0.6920 (tpp) REVERT: C 740 MET cc_start: 0.7841 (tpp) cc_final: 0.7333 (tpp) REVERT: C 995 ARG cc_start: 0.8393 (mmp80) cc_final: 0.8190 (mmp80) REVERT: C 1111 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8608 (mt-10) REVERT: D 66 TYR cc_start: 0.7379 (m-10) cc_final: 0.6318 (m-10) outliers start: 4 outliers final: 2 residues processed: 412 average time/residue: 0.3745 time to fit residues: 248.0277 Evaluate side-chains 354 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 352 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 60 optimal weight: 0.9980 chunk 157 optimal weight: 20.0000 chunk 262 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 131 optimal weight: 30.0000 chunk 297 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 313 optimal weight: 40.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 955 ASN B1023 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 87 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS E 106 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.206979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.157885 restraints weight = 61479.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.161544 restraints weight = 41553.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.164133 restraints weight = 31000.915| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25587 Z= 0.215 Angle : 0.688 15.676 34824 Z= 0.352 Chirality : 0.047 0.264 3991 Planarity : 0.005 0.074 4439 Dihedral : 6.243 58.078 3761 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.63 % Favored : 94.27 % Rotamer: Outliers : 0.07 % Allowed : 2.40 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % 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: -1.48 (0.14), residues: 3089 helix: -0.06 (0.19), residues: 675 sheet: -0.92 (0.23), residues: 513 loop : -1.38 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 64 HIS 0.018 0.002 HIS C 954 PHE 0.029 0.002 PHE C 906 TYR 0.017 0.002 TYR E 102 ARG 0.010 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 12) link_NAG-ASN : angle 3.31210 ( 36) link_BETA1-4 : bond 0.00495 ( 6) link_BETA1-4 : angle 1.40974 ( 18) hydrogen bonds : bond 0.05128 ( 797) hydrogen bonds : angle 6.96805 ( 2199) SS BOND : bond 0.00540 ( 36) SS BOND : angle 1.30137 ( 72) covalent geometry : bond 0.00444 (25533) covalent geometry : angle 0.67807 (34698) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 416 time to evaluate : 2.652 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 28 TYR cc_start: 0.7385 (m-10) cc_final: 0.7163 (m-10) REVERT: A 237 ARG cc_start: 0.8084 (mtp180) cc_final: 0.7640 (mmt180) REVERT: A 658 ASN cc_start: 0.7535 (t0) cc_final: 0.7275 (t0) REVERT: A 776 LYS cc_start: 0.8764 (tptp) cc_final: 0.8354 (tptm) REVERT: A 861 LEU cc_start: 0.9146 (mm) cc_final: 0.8946 (mm) REVERT: A 960 ASN cc_start: 0.8213 (m110) cc_final: 0.7939 (m110) REVERT: A 1000 ARG cc_start: 0.8307 (mmm160) cc_final: 0.7681 (mmm160) REVERT: A 1002 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8028 (tm-30) REVERT: B 49 HIS cc_start: 0.7585 (t-90) cc_final: 0.7384 (t-90) REVERT: B 722 VAL cc_start: 0.8845 (m) cc_final: 0.8639 (m) REVERT: B 740 MET cc_start: 0.7045 (tpt) cc_final: 0.6624 (tpp) REVERT: B 869 MET cc_start: 0.9277 (mtp) cc_final: 0.8845 (mtm) REVERT: B 872 GLN cc_start: 0.9339 (mt0) cc_final: 0.8983 (mt0) REVERT: B 935 GLN cc_start: 0.9013 (tt0) cc_final: 0.8685 (tm-30) REVERT: B 953 ASN cc_start: 0.8830 (m110) cc_final: 0.8538 (m110) REVERT: B 1002 GLN cc_start: 0.9244 (tp40) cc_final: 0.8736 (tm-30) REVERT: B 1050 MET cc_start: 0.7621 (tpp) cc_final: 0.7088 (tpp) REVERT: C 733 LYS cc_start: 0.8980 (pttm) cc_final: 0.8771 (pttm) REVERT: C 970 PHE cc_start: 0.7454 (m-80) cc_final: 0.6997 (m-80) REVERT: C 995 ARG cc_start: 0.8385 (mmp80) cc_final: 0.8151 (mmp80) REVERT: D 66 TYR cc_start: 0.7452 (m-10) cc_final: 0.6480 (m-10) REVERT: D 87 LEU cc_start: 0.8503 (mp) cc_final: 0.8003 (tp) REVERT: E 41 TRP cc_start: 0.5271 (t-100) cc_final: 0.4996 (t-100) REVERT: E 105 GLN cc_start: 0.6678 (tm-30) cc_final: 0.5894 (tp-100) outliers start: 2 outliers final: 0 residues processed: 417 average time/residue: 0.3633 time to fit residues: 241.1656 Evaluate side-chains 357 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 210 optimal weight: 0.7980 chunk 238 optimal weight: 5.9990 chunk 267 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 160 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 224 optimal weight: 20.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 955 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 87 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN E 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.209570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.160871 restraints weight = 61009.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.164825 restraints weight = 40058.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.167381 restraints weight = 29602.379| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25587 Z= 0.154 Angle : 0.629 13.421 34824 Z= 0.319 Chirality : 0.045 0.190 3991 Planarity : 0.005 0.062 4439 Dihedral : 5.979 58.301 3761 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.37 % Favored : 94.53 % Rotamer: Outliers : 0.07 % Allowed : 1.68 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % 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: -1.37 (0.14), residues: 3089 helix: 0.08 (0.19), residues: 675 sheet: -0.89 (0.23), residues: 484 loop : -1.30 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 64 HIS 0.008 0.001 HIS A 954 PHE 0.027 0.001 PHE A 275 TYR 0.015 0.001 TYR C 655 ARG 0.007 0.001 ARG E 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 12) link_NAG-ASN : angle 3.12081 ( 36) link_BETA1-4 : bond 0.00523 ( 6) link_BETA1-4 : angle 1.22179 ( 18) hydrogen bonds : bond 0.04610 ( 797) hydrogen bonds : angle 6.63598 ( 2199) SS BOND : bond 0.00338 ( 36) SS BOND : angle 1.13466 ( 72) covalent geometry : bond 0.00326 (25533) covalent geometry : angle 0.61898 (34698) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 412 time to evaluate : 2.803 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 104 TRP cc_start: 0.3249 (m-10) cc_final: 0.2457 (m-10) REVERT: A 237 ARG cc_start: 0.8056 (mtp180) cc_final: 0.7641 (mmt180) REVERT: A 319 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7599 (mtm110) REVERT: A 658 ASN cc_start: 0.7565 (t0) cc_final: 0.7293 (t0) REVERT: A 773 GLU cc_start: 0.9031 (pp20) cc_final: 0.8817 (pp20) REVERT: A 776 LYS cc_start: 0.8895 (tptp) cc_final: 0.8501 (tptm) REVERT: A 861 LEU cc_start: 0.9140 (mm) cc_final: 0.8923 (mm) REVERT: A 960 ASN cc_start: 0.8300 (m110) cc_final: 0.8008 (m110) REVERT: A 1000 ARG cc_start: 0.8436 (mmm160) cc_final: 0.7987 (mmm160) REVERT: A 1002 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8084 (tm-30) REVERT: B 722 VAL cc_start: 0.8880 (m) cc_final: 0.8649 (m) REVERT: B 740 MET cc_start: 0.7108 (tpt) cc_final: 0.6577 (tpp) REVERT: B 869 MET cc_start: 0.9277 (mtp) cc_final: 0.8834 (mtm) REVERT: B 872 GLN cc_start: 0.9274 (mt0) cc_final: 0.8916 (mt0) REVERT: B 935 GLN cc_start: 0.9048 (tt0) cc_final: 0.8700 (tm-30) REVERT: B 953 ASN cc_start: 0.8793 (m110) cc_final: 0.8421 (m110) REVERT: B 1002 GLN cc_start: 0.9230 (tp40) cc_final: 0.8780 (tm-30) REVERT: B 1009 THR cc_start: 0.8790 (m) cc_final: 0.8569 (m) REVERT: B 1050 MET cc_start: 0.7572 (tpp) cc_final: 0.7106 (tpp) REVERT: C 223 LEU cc_start: 0.9312 (mp) cc_final: 0.9106 (mt) REVERT: C 995 ARG cc_start: 0.8448 (mmp80) cc_final: 0.8158 (mmp80) REVERT: C 1072 GLU cc_start: 0.6841 (pp20) cc_final: 0.6619 (pm20) REVERT: C 1111 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8436 (mt-10) REVERT: D 66 TYR cc_start: 0.7395 (m-10) cc_final: 0.6445 (m-10) REVERT: D 87 LEU cc_start: 0.8691 (mp) cc_final: 0.8287 (tp) REVERT: E 105 GLN cc_start: 0.6616 (tm-30) cc_final: 0.5821 (tp-100) outliers start: 2 outliers final: 0 residues processed: 413 average time/residue: 0.3582 time to fit residues: 233.6761 Evaluate side-chains 362 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 225 optimal weight: 7.9990 chunk 137 optimal weight: 20.0000 chunk 112 optimal weight: 50.0000 chunk 147 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.1980 chunk 271 optimal weight: 8.9990 chunk 258 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 895 GLN B1023 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 87 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.209810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.161319 restraints weight = 60172.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.165027 restraints weight = 40773.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.167608 restraints weight = 30373.334| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25587 Z= 0.145 Angle : 0.618 12.634 34824 Z= 0.315 Chirality : 0.045 0.165 3991 Planarity : 0.005 0.082 4439 Dihedral : 5.859 57.780 3761 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.34 % Favored : 94.56 % Rotamer: Outliers : 0.07 % Allowed : 1.02 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % 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: -1.31 (0.14), residues: 3089 helix: 0.16 (0.20), residues: 679 sheet: -0.86 (0.23), residues: 490 loop : -1.28 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 64 HIS 0.008 0.001 HIS A 954 PHE 0.028 0.001 PHE A 275 TYR 0.020 0.001 TYR A 655 ARG 0.015 0.001 ARG C 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 12) link_NAG-ASN : angle 2.84855 ( 36) link_BETA1-4 : bond 0.00504 ( 6) link_BETA1-4 : angle 1.16239 ( 18) hydrogen bonds : bond 0.04496 ( 797) hydrogen bonds : angle 6.55551 ( 2199) SS BOND : bond 0.00331 ( 36) SS BOND : angle 1.32782 ( 72) covalent geometry : bond 0.00307 (25533) covalent geometry : angle 0.60822 (34698) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 415 time to evaluate : 2.553 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 104 TRP cc_start: 0.3372 (m-10) cc_final: 0.3108 (m100) REVERT: A 237 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7682 (mmt180) REVERT: A 319 ARG cc_start: 0.8205 (mmt-90) cc_final: 0.7605 (mtm110) REVERT: A 658 ASN cc_start: 0.7482 (t0) cc_final: 0.7217 (t0) REVERT: A 773 GLU cc_start: 0.9033 (pp20) cc_final: 0.8816 (pp20) REVERT: A 776 LYS cc_start: 0.8802 (tptp) cc_final: 0.8333 (tptm) REVERT: A 861 LEU cc_start: 0.9110 (mm) cc_final: 0.8900 (mm) REVERT: A 960 ASN cc_start: 0.8227 (m110) cc_final: 0.7957 (m110) REVERT: A 1000 ARG cc_start: 0.8508 (mmm160) cc_final: 0.8157 (tpt90) REVERT: A 1002 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8017 (tm-30) REVERT: A 1029 MET cc_start: 0.8501 (tpp) cc_final: 0.7949 (tpp) REVERT: A 1110 TYR cc_start: 0.7248 (t80) cc_final: 0.6910 (t80) REVERT: B 309 GLU cc_start: 0.8532 (tp30) cc_final: 0.8263 (tp30) REVERT: B 740 MET cc_start: 0.7158 (tpt) cc_final: 0.6635 (tpp) REVERT: B 869 MET cc_start: 0.9219 (mtp) cc_final: 0.8914 (mtm) REVERT: B 872 GLN cc_start: 0.9274 (mt0) cc_final: 0.8977 (mt0) REVERT: B 935 GLN cc_start: 0.9000 (tt0) cc_final: 0.8683 (tm-30) REVERT: B 936 ASP cc_start: 0.8927 (t0) cc_final: 0.8229 (p0) REVERT: B 953 ASN cc_start: 0.8707 (m110) cc_final: 0.8502 (m110) REVERT: B 957 GLN cc_start: 0.9128 (pm20) cc_final: 0.8663 (pm20) REVERT: B 1002 GLN cc_start: 0.9277 (tp40) cc_final: 0.8753 (tm-30) REVERT: B 1029 MET cc_start: 0.7461 (tpp) cc_final: 0.7187 (tpp) REVERT: B 1050 MET cc_start: 0.7509 (tpp) cc_final: 0.7078 (tpp) REVERT: C 733 LYS cc_start: 0.8887 (pttm) cc_final: 0.8666 (pttm) REVERT: C 995 ARG cc_start: 0.8427 (mmp80) cc_final: 0.8128 (mmp80) REVERT: C 1072 GLU cc_start: 0.6889 (pp20) cc_final: 0.6605 (pm20) REVERT: D 66 TYR cc_start: 0.7418 (m-10) cc_final: 0.6420 (m-10) REVERT: D 87 LEU cc_start: 0.8680 (mp) cc_final: 0.8286 (tp) REVERT: E 105 GLN cc_start: 0.6567 (tm-30) cc_final: 0.5872 (tp-100) outliers start: 2 outliers final: 0 residues processed: 416 average time/residue: 0.3361 time to fit residues: 222.7656 Evaluate side-chains 360 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 161 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 211 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN B1023 ASN C 49 HIS C 87 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 784 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.209466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.161307 restraints weight = 60964.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.165070 restraints weight = 40794.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.167670 restraints weight = 30487.016| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25587 Z= 0.156 Angle : 0.632 12.268 34824 Z= 0.323 Chirality : 0.045 0.163 3991 Planarity : 0.005 0.088 4439 Dihedral : 5.822 58.033 3761 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.50 % Favored : 94.40 % Rotamer: Outliers : 0.04 % Allowed : 0.73 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % 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: -1.31 (0.14), residues: 3089 helix: 0.16 (0.19), residues: 681 sheet: -0.88 (0.23), residues: 487 loop : -1.28 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 64 HIS 0.014 0.001 HIS A1048 PHE 0.019 0.001 PHE C 559 TYR 0.028 0.002 TYR A 756 ARG 0.009 0.001 ARG C 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 12) link_NAG-ASN : angle 2.78237 ( 36) link_BETA1-4 : bond 0.00479 ( 6) link_BETA1-4 : angle 1.15371 ( 18) hydrogen bonds : bond 0.04528 ( 797) hydrogen bonds : angle 6.53961 ( 2199) SS BOND : bond 0.00376 ( 36) SS BOND : angle 1.34061 ( 72) covalent geometry : bond 0.00328 (25533) covalent geometry : angle 0.62365 (34698) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 424 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7326 (m-10) cc_final: 0.7097 (m-10) REVERT: A 104 TRP cc_start: 0.3362 (m-10) cc_final: 0.3075 (m100) REVERT: A 237 ARG cc_start: 0.8046 (mtp180) cc_final: 0.7635 (mmt180) REVERT: A 319 ARG cc_start: 0.8264 (mmt-90) cc_final: 0.7648 (mtm110) REVERT: A 620 VAL cc_start: 0.5574 (m) cc_final: 0.5330 (m) REVERT: A 658 ASN cc_start: 0.7578 (t0) cc_final: 0.7304 (t0) REVERT: A 773 GLU cc_start: 0.9016 (pp20) cc_final: 0.8690 (pp20) REVERT: A 776 LYS cc_start: 0.8798 (tptp) cc_final: 0.8357 (tptm) REVERT: A 861 LEU cc_start: 0.9092 (mm) cc_final: 0.8884 (mm) REVERT: A 960 ASN cc_start: 0.8276 (m110) cc_final: 0.8010 (m110) REVERT: A 1000 ARG cc_start: 0.8487 (mmm160) cc_final: 0.8123 (tpt90) REVERT: A 1002 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8061 (tm-30) REVERT: A 1110 TYR cc_start: 0.7283 (t80) cc_final: 0.6951 (t80) REVERT: B 309 GLU cc_start: 0.8545 (tp30) cc_final: 0.8260 (tp30) REVERT: B 316 SER cc_start: 0.8467 (t) cc_final: 0.8226 (p) REVERT: B 740 MET cc_start: 0.7169 (tpt) cc_final: 0.6544 (tpp) REVERT: B 869 MET cc_start: 0.9216 (mtp) cc_final: 0.8888 (mtm) REVERT: B 872 GLN cc_start: 0.9258 (mt0) cc_final: 0.8987 (mt0) REVERT: B 935 GLN cc_start: 0.9025 (tt0) cc_final: 0.8692 (tm-30) REVERT: B 936 ASP cc_start: 0.8940 (t0) cc_final: 0.8257 (p0) REVERT: B 953 ASN cc_start: 0.8737 (m110) cc_final: 0.8519 (m110) REVERT: B 957 GLN cc_start: 0.9151 (pm20) cc_final: 0.8709 (pm20) REVERT: B 962 LEU cc_start: 0.8613 (tt) cc_final: 0.8187 (tt) REVERT: B 996 LEU cc_start: 0.8454 (mt) cc_final: 0.8192 (mt) REVERT: B 1002 GLN cc_start: 0.9273 (tp40) cc_final: 0.8711 (tm-30) REVERT: B 1050 MET cc_start: 0.7595 (tpp) cc_final: 0.7169 (tpp) REVERT: C 557 LYS cc_start: 0.7768 (tmtt) cc_final: 0.6889 (mmtm) REVERT: C 733 LYS cc_start: 0.8927 (pttm) cc_final: 0.8705 (pttm) REVERT: C 995 ARG cc_start: 0.8451 (mmp80) cc_final: 0.8146 (mmp80) REVERT: C 1072 GLU cc_start: 0.6939 (pp20) cc_final: 0.6633 (pm20) REVERT: D 66 TYR cc_start: 0.7453 (m-10) cc_final: 0.6469 (m-10) REVERT: D 87 LEU cc_start: 0.8659 (mp) cc_final: 0.8283 (tp) REVERT: E 105 GLN cc_start: 0.6513 (tm-30) cc_final: 0.6073 (tp-100) outliers start: 1 outliers final: 0 residues processed: 425 average time/residue: 0.3539 time to fit residues: 241.1657 Evaluate side-chains 368 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 81 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 201 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 236 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 192 optimal weight: 0.0170 chunk 101 optimal weight: 20.0000 chunk 306 optimal weight: 2.9990 overall best weight: 1.6824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B1023 ASN B1088 HIS C 49 HIS C 87 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 784 GLN ** C 949 GLN ** 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 = 0.4673 r_free = 0.4673 target = 0.211031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.162459 restraints weight = 60795.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.166189 restraints weight = 40404.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.168841 restraints weight = 30239.316| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25587 Z= 0.136 Angle : 0.619 10.938 34824 Z= 0.316 Chirality : 0.045 0.205 3991 Planarity : 0.005 0.078 4439 Dihedral : 5.693 57.960 3761 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % 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: -1.27 (0.15), residues: 3089 helix: 0.17 (0.19), residues: 681 sheet: -0.90 (0.23), residues: 494 loop : -1.23 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 41 HIS 0.009 0.001 HIS A1048 PHE 0.028 0.001 PHE C 906 TYR 0.014 0.001 TYR A 873 ARG 0.008 0.001 ARG B 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 12) link_NAG-ASN : angle 2.97126 ( 36) link_BETA1-4 : bond 0.00580 ( 6) link_BETA1-4 : angle 1.10779 ( 18) hydrogen bonds : bond 0.04416 ( 797) hydrogen bonds : angle 6.44016 ( 2199) SS BOND : bond 0.00333 ( 36) SS BOND : angle 1.34252 ( 72) covalent geometry : bond 0.00290 (25533) covalent geometry : angle 0.60952 (34698) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 432 time to evaluate : 2.786 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: A 28 TYR cc_start: 0.7347 (m-10) cc_final: 0.7079 (m-10) REVERT: A 104 TRP cc_start: 0.3468 (m-10) cc_final: 0.3176 (m100) REVERT: A 237 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7665 (mmt180) REVERT: A 319 ARG cc_start: 0.8258 (mmt-90) cc_final: 0.7625 (mtm110) REVERT: A 658 ASN cc_start: 0.7617 (t0) cc_final: 0.7352 (t0) REVERT: A 776 LYS cc_start: 0.8758 (tptp) cc_final: 0.8291 (tptm) REVERT: A 820 ASP cc_start: 0.8004 (m-30) cc_final: 0.7720 (m-30) REVERT: A 960 ASN cc_start: 0.8236 (m110) cc_final: 0.8017 (m110) REVERT: A 1000 ARG cc_start: 0.8444 (mmm160) cc_final: 0.8149 (tpt90) REVERT: A 1002 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 1110 TYR cc_start: 0.7308 (t80) cc_final: 0.6951 (t80) REVERT: B 309 GLU cc_start: 0.8513 (tp30) cc_final: 0.8247 (tp30) REVERT: B 869 MET cc_start: 0.9143 (mtp) cc_final: 0.8752 (mtm) REVERT: B 872 GLN cc_start: 0.9242 (mt0) cc_final: 0.8791 (mt0) REVERT: B 925 ASN cc_start: 0.8978 (m-40) cc_final: 0.8764 (m-40) REVERT: B 935 GLN cc_start: 0.8979 (tt0) cc_final: 0.8638 (tm-30) REVERT: B 936 ASP cc_start: 0.8935 (t0) cc_final: 0.8225 (p0) REVERT: B 953 ASN cc_start: 0.8860 (m110) cc_final: 0.8636 (m110) REVERT: B 957 GLN cc_start: 0.9088 (pm20) cc_final: 0.8815 (pm20) REVERT: B 962 LEU cc_start: 0.8606 (tt) cc_final: 0.8008 (tt) REVERT: B 1000 ARG cc_start: 0.7435 (mtt180) cc_final: 0.6839 (mtp180) REVERT: B 1002 GLN cc_start: 0.9225 (tp40) cc_final: 0.8676 (tm-30) REVERT: B 1017 GLU cc_start: 0.7705 (pt0) cc_final: 0.5601 (pt0) REVERT: B 1050 MET cc_start: 0.7424 (tpp) cc_final: 0.7063 (tpp) REVERT: C 651 ILE cc_start: 0.5781 (mm) cc_final: 0.5570 (mm) REVERT: C 729 VAL cc_start: 0.7988 (t) cc_final: 0.7757 (t) REVERT: C 733 LYS cc_start: 0.8890 (pttm) cc_final: 0.8659 (pttm) REVERT: C 1072 GLU cc_start: 0.6800 (pp20) cc_final: 0.6573 (pm20) REVERT: D 66 TYR cc_start: 0.7400 (m-10) cc_final: 0.6397 (m-10) REVERT: D 81 ASP cc_start: 0.5380 (t0) cc_final: 0.5170 (t0) REVERT: D 87 LEU cc_start: 0.8666 (mp) cc_final: 0.8283 (tp) REVERT: E 105 GLN cc_start: 0.6602 (tm-30) cc_final: 0.6170 (tp-100) outliers start: 1 outliers final: 0 residues processed: 433 average time/residue: 0.3688 time to fit residues: 254.0394 Evaluate side-chains 358 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 285 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 212 optimal weight: 20.0000 chunk 271 optimal weight: 0.7980 chunk 266 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1023 ASN B1088 HIS C 49 HIS C 87 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.205777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.156878 restraints weight = 61484.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.160553 restraints weight = 40913.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.162623 restraints weight = 30675.411| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25587 Z= 0.228 Angle : 0.720 12.830 34824 Z= 0.369 Chirality : 0.048 0.187 3991 Planarity : 0.006 0.129 4439 Dihedral : 6.140 59.351 3761 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.09 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % 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: -1.55 (0.14), residues: 3089 helix: -0.19 (0.19), residues: 678 sheet: -1.10 (0.22), residues: 483 loop : -1.34 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 64 HIS 0.013 0.002 HIS A1048 PHE 0.035 0.002 PHE C 906 TYR 0.028 0.002 TYR A 756 ARG 0.023 0.001 ARG D 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 12) link_NAG-ASN : angle 3.32027 ( 36) link_BETA1-4 : bond 0.00450 ( 6) link_BETA1-4 : angle 1.31030 ( 18) hydrogen bonds : bond 0.05216 ( 797) hydrogen bonds : angle 6.83054 ( 2199) SS BOND : bond 0.00442 ( 36) SS BOND : angle 1.39270 ( 72) covalent geometry : bond 0.00473 (25533) covalent geometry : angle 0.71039 (34698) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8789.61 seconds wall clock time: 153 minutes 12.71 seconds (9192.71 seconds total)