Starting phenix.real_space_refine on Fri Sep 19 10:04:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yz6_39686/09_2025/8yz6_39686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yz6_39686/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yz6_39686/09_2025/8yz6_39686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yz6_39686/09_2025/8yz6_39686.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yz6_39686/09_2025/8yz6_39686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yz6_39686/09_2025/8yz6_39686.map" } resolution = 4.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.89, per 1000 atoms: 0.20 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: 1.97 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.15 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: 6.10 Time building geometry restraints manager: 2.78 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 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 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 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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.890 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.900 ------------------------------------------------------------------------------- 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 : 18.83 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (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 ARG 0.018 0.001 ARG B1014 TYR 0.021 0.002 TYR B 655 PHE 0.029 0.002 PHE C 906 TRP 0.024 0.002 TRP C 64 HIS 0.007 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00368 (25533) covalent geometry : angle 0.67237 (34698) SS BOND : bond 0.00444 ( 36) SS BOND : angle 1.39278 ( 72) hydrogen bonds : bond 0.20086 ( 797) hydrogen bonds : angle 8.69957 ( 2199) link_BETA1-4 : bond 0.00566 ( 6) link_BETA1-4 : angle 1.57486 ( 18) link_NAG-ASN : bond 0.00295 ( 12) link_NAG-ASN : angle 4.71030 ( 36) *********************** 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 : 0.728 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: 0.7416 (m-80) REVERT: A 226 LEU cc_start: 0.8092 (mm) cc_final: 0.7698 (mp) REVERT: A 334 ASN cc_start: 0.7263 (OUTLIER) cc_final: 0.7034 (p0) REVERT: A 770 ILE cc_start: 0.9186 (mt) cc_final: 0.8904 (mt) REVERT: A 776 LYS cc_start: 0.8707 (tptp) cc_final: 0.8506 (tptm) 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: 0.8495 (t0) REVERT: A 960 ASN cc_start: 0.7661 (m110) cc_final: 0.7419 (m110) REVERT: A 1019 ARG cc_start: 0.8305 (tpt-90) cc_final: 0.8098 (tpp80) REVERT: B 387 LEU cc_start: 0.6399 (tt) cc_final: 0.6163 (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: 0.8455 (tm-30) REVERT: B 953 ASN cc_start: 0.8693 (m-40) cc_final: 0.8292 (m110) REVERT: B 957 GLN cc_start: 0.8886 (pm20) cc_final: 0.8640 (pm20) REVERT: C 45 SER cc_start: 0.8367 (p) cc_final: 0.8109 (p) REVERT: C 46 SER cc_start: 0.8435 (m) cc_final: 0.8179 (p) REVERT: C 727 LEU cc_start: 0.8814 (mt) cc_final: 0.8580 (mt) REVERT: C 970 PHE cc_start: 0.6744 (m-80) cc_final: 0.6457 (m-80) REVERT: D 66 TYR cc_start: 0.6273 (m-10) cc_final: 0.5467 (m-10) REVERT: E 105 GLN cc_start: 0.5766 (tm-30) cc_final: 0.5292 (tp-100) outliers start: 10 outliers final: 2 residues processed: 446 average time/residue: 0.1683 time to fit residues: 117.6505 Evaluate side-chains 370 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 367 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 8.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN B 417 ASN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN B1058 HIS B1088 HIS C 87 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN E 44 GLN E 106 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.209697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.159166 restraints weight = 61264.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.163023 restraints weight = 40718.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.165713 restraints weight = 30311.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.167383 restraints weight = 24661.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.168682 restraints weight = 21505.489| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25587 Z= 0.224 Angle : 0.711 16.172 34824 Z= 0.364 Chirality : 0.047 0.171 3991 Planarity : 0.006 0.074 4439 Dihedral : 6.953 59.218 3761 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.76 % Favored : 94.14 % Rotamer: Outliers : 0.18 % Allowed : 5.43 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.14), residues: 3089 helix: 0.20 (0.19), residues: 676 sheet: -0.58 (0.23), residues: 531 loop : -1.24 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 44 TYR 0.021 0.002 TYR C1047 PHE 0.022 0.002 PHE C 906 TRP 0.023 0.002 TRP A 886 HIS 0.012 0.002 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00467 (25533) covalent geometry : angle 0.70197 (34698) SS BOND : bond 0.00420 ( 36) SS BOND : angle 1.29830 ( 72) hydrogen bonds : bond 0.05325 ( 797) hydrogen bonds : angle 7.27297 ( 2199) link_BETA1-4 : bond 0.00610 ( 6) link_BETA1-4 : angle 1.84059 ( 18) link_NAG-ASN : bond 0.00414 ( 12) link_NAG-ASN : angle 3.00934 ( 36) *********************** 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: 5 poor density : 427 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8141 (mm) cc_final: 0.7833 (mp) REVERT: A 776 LYS cc_start: 0.8775 (tptp) cc_final: 0.8504 (tptm) REVERT: A 825 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8440 (mmmt) REVERT: A 872 GLN cc_start: 0.9201 (mt0) cc_final: 0.8972 (tp40) REVERT: A 950 ASP cc_start: 0.8742 (t0) cc_final: 0.8130 (t0) REVERT: A 960 ASN cc_start: 0.8214 (m110) cc_final: 0.7928 (m110) REVERT: A 1001 LEU cc_start: 0.9299 (tp) cc_final: 0.9015 (tp) REVERT: A 1002 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 1042 PHE cc_start: 0.7154 (t80) cc_final: 0.6032 (t80) REVERT: A 1047 TYR cc_start: 0.8144 (m-80) cc_final: 0.7908 (m-80) REVERT: B 49 HIS cc_start: 0.7669 (t-90) cc_final: 0.7325 (t-90) REVERT: B 740 MET cc_start: 0.7130 (tpt) cc_final: 0.6762 (tpp) REVERT: B 869 MET cc_start: 0.9220 (mtp) cc_final: 0.8728 (mtm) REVERT: B 872 GLN cc_start: 0.9384 (mt0) cc_final: 0.9079 (mt0) REVERT: B 935 GLN cc_start: 0.8942 (tt0) cc_final: 0.8569 (tm-30) REVERT: B 957 GLN cc_start: 0.9140 (pm20) cc_final: 0.8785 (pm20) REVERT: B 1009 THR cc_start: 0.9049 (m) cc_final: 0.8840 (m) REVERT: B 1017 GLU cc_start: 0.7449 (tt0) cc_final: 0.7232 (tt0) REVERT: B 1050 MET cc_start: 0.7618 (tpp) cc_final: 0.7144 (tpp) REVERT: C 44 ARG cc_start: 0.8437 (mpp80) cc_final: 0.8131 (mpp80) REVERT: C 46 SER cc_start: 0.8553 (m) cc_final: 0.8304 (p) REVERT: C 223 LEU cc_start: 0.9366 (mp) cc_final: 0.9120 (mt) REVERT: C 733 LYS cc_start: 0.9098 (pttm) cc_final: 0.8798 (pttm) REVERT: C 774 GLN cc_start: 0.8603 (tp40) cc_final: 0.8371 (tp40) REVERT: C 970 PHE cc_start: 0.7196 (m-80) cc_final: 0.6708 (m-80) REVERT: D 66 TYR cc_start: 0.7188 (m-10) cc_final: 0.6234 (m-10) REVERT: E 105 GLN cc_start: 0.6636 (tm-30) cc_final: 0.5844 (tp-100) outliers start: 5 outliers final: 0 residues processed: 430 average time/residue: 0.1589 time to fit residues: 108.3162 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 : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 236 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 280 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 204 optimal weight: 0.0270 chunk 176 optimal weight: 0.0870 chunk 247 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 overall best weight: 0.5816 ------------------------------------------------------------------------------- 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** A 928 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 777 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 949 GLN C 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.215956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.165729 restraints weight = 59563.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.169778 restraints weight = 39222.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.172712 restraints weight = 29059.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.174573 restraints weight = 23364.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.175600 restraints weight = 20166.076| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25587 Z= 0.117 Angle : 0.591 11.844 34824 Z= 0.300 Chirality : 0.045 0.196 3991 Planarity : 0.005 0.069 4439 Dihedral : 6.150 55.518 3761 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.08 % Rotamer: Outliers : 0.07 % Allowed : 2.80 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.15), residues: 3089 helix: 0.56 (0.20), residues: 677 sheet: -0.59 (0.23), residues: 525 loop : -1.13 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 44 TYR 0.018 0.001 TYR A 741 PHE 0.045 0.001 PHE A 275 TRP 0.033 0.001 TRP C 64 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00248 (25533) covalent geometry : angle 0.58034 (34698) SS BOND : bond 0.00259 ( 36) SS BOND : angle 1.02690 ( 72) hydrogen bonds : bond 0.04513 ( 797) hydrogen bonds : angle 6.69206 ( 2199) link_BETA1-4 : bond 0.00563 ( 6) link_BETA1-4 : angle 1.69858 ( 18) link_NAG-ASN : bond 0.00294 ( 12) link_NAG-ASN : angle 3.17037 ( 36) *********************** 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: 2 poor density : 431 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 ASN cc_start: 0.8204 (m110) cc_final: 0.7926 (m110) REVERT: A 962 LEU cc_start: 0.8316 (tt) cc_final: 0.7961 (tt) REVERT: A 1002 GLN cc_start: 0.8243 (tm-30) cc_final: 0.8015 (tm-30) REVERT: B 49 HIS cc_start: 0.7513 (t-90) cc_final: 0.7257 (t-90) REVERT: B 285 ILE cc_start: 0.6598 (mt) cc_final: 0.6210 (mt) REVERT: B 740 MET cc_start: 0.7041 (tpt) cc_final: 0.6602 (tpp) REVERT: B 796 TYR cc_start: 0.5455 (t80) cc_final: 0.4830 (m-80) REVERT: B 869 MET cc_start: 0.9088 (mtp) cc_final: 0.8508 (mtm) REVERT: B 872 GLN cc_start: 0.9250 (mt0) cc_final: 0.9037 (mt0) REVERT: B 935 GLN cc_start: 0.8849 (tt0) cc_final: 0.8445 (tm-30) REVERT: B 957 GLN cc_start: 0.9014 (pm20) cc_final: 0.8678 (pm20) REVERT: B 1000 ARG cc_start: 0.7442 (mtt180) cc_final: 0.6961 (mtp180) REVERT: B 1050 MET cc_start: 0.7266 (tpp) cc_final: 0.6855 (tpp) REVERT: C 46 SER cc_start: 0.8432 (m) cc_final: 0.8073 (p) REVERT: C 223 LEU cc_start: 0.9317 (mp) cc_final: 0.9083 (mt) REVERT: C 229 LEU cc_start: 0.9108 (tp) cc_final: 0.8902 (tp) REVERT: C 733 LYS cc_start: 0.8939 (pttm) cc_final: 0.8665 (pttm) REVERT: C 772 VAL cc_start: 0.9119 (p) cc_final: 0.8901 (p) REVERT: C 869 MET cc_start: 0.9178 (mtp) cc_final: 0.8877 (mtp) REVERT: C 919 ASN cc_start: 0.8191 (t0) cc_final: 0.7586 (p0) REVERT: D 66 TYR cc_start: 0.7006 (m-10) cc_final: 0.5848 (m-10) outliers start: 2 outliers final: 1 residues processed: 433 average time/residue: 0.1638 time to fit residues: 112.8792 Evaluate side-chains 358 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 152 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 0.0050 chunk 259 optimal weight: 0.5980 chunk 221 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 262 optimal weight: 0.0370 chunk 230 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.7276 ------------------------------------------------------------------------------- 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 872 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 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 HIS 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 E 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.213545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.164098 restraints weight = 60170.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.167840 restraints weight = 40135.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.170444 restraints weight = 30278.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.172245 restraints weight = 24693.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.173006 restraints weight = 21504.873| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.1939 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= 0.131 Angle : 0.577 12.194 34824 Z= 0.294 Chirality : 0.044 0.220 3991 Planarity : 0.005 0.060 4439 Dihedral : 5.845 55.600 3761 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.76 % Favored : 95.14 % Rotamer: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.15), residues: 3089 helix: 0.60 (0.20), residues: 679 sheet: -0.67 (0.23), residues: 511 loop : -1.10 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 44 TYR 0.018 0.001 TYR C 707 PHE 0.023 0.001 PHE A 275 TRP 0.022 0.001 TRP C 64 HIS 0.014 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00275 (25533) covalent geometry : angle 0.56605 (34698) SS BOND : bond 0.00450 ( 36) SS BOND : angle 1.07654 ( 72) hydrogen bonds : bond 0.04327 ( 797) hydrogen bonds : angle 6.48011 ( 2199) link_BETA1-4 : bond 0.00515 ( 6) link_BETA1-4 : angle 1.51227 ( 18) link_NAG-ASN : bond 0.00306 ( 12) link_NAG-ASN : angle 3.04039 ( 36) *********************** 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 419 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 417 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7340 (m-10) cc_final: 0.7045 (m-80) REVERT: A 577 ARG cc_start: 0.8062 (tmm-80) cc_final: 0.7550 (tmm-80) REVERT: A 773 GLU cc_start: 0.8861 (pp20) cc_final: 0.8514 (pp20) REVERT: A 776 LYS cc_start: 0.8864 (tptm) cc_final: 0.8368 (tptm) REVERT: A 825 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8363 (mmmt) REVERT: A 960 ASN cc_start: 0.8262 (m110) cc_final: 0.7970 (m110) REVERT: A 1001 LEU cc_start: 0.9308 (tp) cc_final: 0.9099 (tp) REVERT: A 1002 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8014 (tm-30) REVERT: B 49 HIS cc_start: 0.7475 (t-90) cc_final: 0.7235 (t-90) REVERT: B 722 VAL cc_start: 0.8780 (t) cc_final: 0.8527 (t) REVERT: B 740 MET cc_start: 0.7140 (tpt) cc_final: 0.6693 (tpp) REVERT: B 796 TYR cc_start: 0.5575 (t80) cc_final: 0.4921 (m-80) REVERT: B 869 MET cc_start: 0.9090 (mtp) cc_final: 0.8605 (mtm) REVERT: B 872 GLN cc_start: 0.9246 (mt0) cc_final: 0.9006 (mt0) REVERT: B 935 GLN cc_start: 0.8827 (tt0) cc_final: 0.8540 (tm-30) REVERT: B 953 ASN cc_start: 0.8802 (m110) cc_final: 0.8528 (m110) REVERT: B 962 LEU cc_start: 0.8525 (tt) cc_final: 0.8218 (tt) REVERT: B 1000 ARG cc_start: 0.7476 (mtt180) cc_final: 0.6958 (mtp180) REVERT: B 1002 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8411 (tm-30) REVERT: B 1050 MET cc_start: 0.7377 (tpp) cc_final: 0.6906 (tpp) REVERT: C 45 SER cc_start: 0.8515 (t) cc_final: 0.8242 (t) REVERT: C 46 SER cc_start: 0.8272 (m) cc_final: 0.8032 (p) REVERT: C 229 LEU cc_start: 0.9101 (tp) cc_final: 0.8899 (tp) REVERT: C 699 LEU cc_start: 0.8005 (mt) cc_final: 0.7731 (mt) REVERT: C 733 LYS cc_start: 0.9005 (pttm) cc_final: 0.8763 (pttm) REVERT: C 869 MET cc_start: 0.9146 (mtp) cc_final: 0.8854 (mtp) REVERT: C 872 GLN cc_start: 0.9051 (pm20) cc_final: 0.8474 (pm20) REVERT: D 66 TYR cc_start: 0.7140 (m-10) cc_final: 0.6485 (m-10) REVERT: E 105 GLN cc_start: 0.6505 (tm-30) cc_final: 0.5581 (tp-100) outliers start: 2 outliers final: 0 residues processed: 417 average time/residue: 0.1638 time to fit residues: 109.2673 Evaluate side-chains 345 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 311 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** 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 777 ASN B 954 HIS B1023 ASN C 87 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN E 106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.212899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.163842 restraints weight = 60376.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.167579 restraints weight = 40947.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.170144 restraints weight = 30834.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.171544 restraints weight = 25210.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.172931 restraints weight = 22241.587| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25587 Z= 0.137 Angle : 0.590 12.238 34824 Z= 0.300 Chirality : 0.045 0.178 3991 Planarity : 0.005 0.087 4439 Dihedral : 5.734 55.967 3761 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 0.04 % Allowed : 1.78 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.15), residues: 3089 helix: 0.58 (0.20), residues: 678 sheet: -0.60 (0.23), residues: 497 loop : -1.12 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 43 TYR 0.013 0.001 TYR A1047 PHE 0.033 0.001 PHE A 275 TRP 0.023 0.001 TRP C 64 HIS 0.016 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00288 (25533) covalent geometry : angle 0.57917 (34698) SS BOND : bond 0.00314 ( 36) SS BOND : angle 1.32345 ( 72) hydrogen bonds : bond 0.04357 ( 797) hydrogen bonds : angle 6.39701 ( 2199) link_BETA1-4 : bond 0.00545 ( 6) link_BETA1-4 : angle 1.31738 ( 18) link_NAG-ASN : bond 0.00287 ( 12) link_NAG-ASN : angle 2.94726 ( 36) *********************** 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 415 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 1.011 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: 0.7311 (m-10) cc_final: 0.7054 (m-80) REVERT: A 577 ARG cc_start: 0.7980 (tmm-80) cc_final: 0.7345 (tmm-80) REVERT: A 773 GLU cc_start: 0.8928 (pp20) cc_final: 0.8667 (pp20) REVERT: A 780 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7762 (mt-10) REVERT: A 861 LEU cc_start: 0.9081 (mm) cc_final: 0.8881 (mm) REVERT: A 960 ASN cc_start: 0.8232 (m110) cc_final: 0.7960 (m110) REVERT: A 1000 ARG cc_start: 0.8355 (mmm160) cc_final: 0.7314 (mmm160) REVERT: A 1002 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8049 (tm-30) REVERT: B 740 MET cc_start: 0.7098 (tpt) cc_final: 0.6626 (tpp) REVERT: B 796 TYR cc_start: 0.5480 (t80) cc_final: 0.4763 (m-80) REVERT: B 869 MET cc_start: 0.9123 (mtp) cc_final: 0.8798 (mtm) REVERT: B 872 GLN cc_start: 0.9268 (mt0) cc_final: 0.9022 (mt0) REVERT: B 935 GLN cc_start: 0.8939 (tt0) cc_final: 0.8650 (tm-30) REVERT: B 936 ASP cc_start: 0.8754 (t0) cc_final: 0.8401 (t0) REVERT: B 957 GLN cc_start: 0.9071 (pm20) cc_final: 0.8806 (pm20) REVERT: B 962 LEU cc_start: 0.8550 (tt) cc_final: 0.8218 (tt) REVERT: B 1000 ARG cc_start: 0.7436 (mtt180) cc_final: 0.6909 (mtp180) REVERT: B 1002 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8381 (tm-30) REVERT: B 1014 ARG cc_start: 0.8245 (mtt90) cc_final: 0.7969 (tpp80) REVERT: B 1017 GLU cc_start: 0.7692 (pt0) cc_final: 0.7364 (pt0) REVERT: B 1050 MET cc_start: 0.7251 (tpp) cc_final: 0.6740 (tpp) REVERT: C 201 PHE cc_start: 0.8143 (t80) cc_final: 0.7883 (t80) REVERT: C 727 LEU cc_start: 0.8864 (mt) cc_final: 0.8656 (mt) REVERT: C 733 LYS cc_start: 0.9016 (pttm) cc_final: 0.8808 (pttm) REVERT: C 869 MET cc_start: 0.9090 (mtp) cc_final: 0.8796 (mtp) REVERT: C 872 GLN cc_start: 0.9114 (pm20) cc_final: 0.8612 (pm20) REVERT: C 970 PHE cc_start: 0.6742 (m-80) cc_final: 0.6399 (m-80) REVERT: D 66 TYR cc_start: 0.7137 (m-10) cc_final: 0.6463 (m-10) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.1650 time to fit residues: 109.1772 Evaluate side-chains 346 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 77 optimal weight: 0.7980 chunk 238 optimal weight: 8.9990 chunk 311 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 233 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN A1036 GLN A1106 GLN B 414 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 954 HIS B 965 GLN B1023 ASN ** B1088 HIS ** 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 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN E 44 GLN E 106 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.211848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.162796 restraints weight = 60521.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.166397 restraints weight = 40437.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.169090 restraints weight = 30701.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.170628 restraints weight = 25022.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.171906 restraints weight = 21953.315| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25587 Z= 0.149 Angle : 0.593 12.521 34824 Z= 0.302 Chirality : 0.044 0.157 3991 Planarity : 0.005 0.057 4439 Dihedral : 5.690 56.452 3761 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.24 % Favored : 94.66 % Rotamer: Outliers : 0.07 % Allowed : 2.18 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.15), residues: 3089 helix: 0.47 (0.20), residues: 679 sheet: -0.61 (0.23), residues: 497 loop : -1.14 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1019 TYR 0.017 0.001 TYR A 655 PHE 0.023 0.001 PHE A 275 TRP 0.024 0.001 TRP C 64 HIS 0.015 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00315 (25533) covalent geometry : angle 0.58307 (34698) SS BOND : bond 0.00339 ( 36) SS BOND : angle 1.15492 ( 72) hydrogen bonds : bond 0.04361 ( 797) hydrogen bonds : angle 6.38392 ( 2199) link_BETA1-4 : bond 0.00525 ( 6) link_BETA1-4 : angle 1.24538 ( 18) link_NAG-ASN : bond 0.00267 ( 12) link_NAG-ASN : angle 3.02121 ( 36) *********************** 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 420 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 418 time to evaluate : 0.963 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: A 104 TRP cc_start: 0.2995 (m-10) cc_final: 0.2789 (m100) REVERT: A 658 ASN cc_start: 0.7473 (t0) cc_final: 0.7229 (t0) REVERT: A 773 GLU cc_start: 0.8937 (pp20) cc_final: 0.8699 (pp20) REVERT: A 802 PHE cc_start: 0.7997 (m-10) cc_final: 0.7670 (m-10) REVERT: A 960 ASN cc_start: 0.8303 (m110) cc_final: 0.8041 (m110) REVERT: A 1000 ARG cc_start: 0.8382 (mmm160) cc_final: 0.7753 (mmm160) REVERT: A 1002 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 1005 GLN cc_start: 0.8799 (mt0) cc_final: 0.8583 (mt0) REVERT: B 49 HIS cc_start: 0.7444 (t-90) cc_final: 0.7230 (t-90) REVERT: B 740 MET cc_start: 0.7092 (tpt) cc_final: 0.6655 (tpp) REVERT: B 796 TYR cc_start: 0.5537 (t80) cc_final: 0.4769 (m-80) REVERT: B 869 MET cc_start: 0.9155 (mtp) cc_final: 0.8763 (mtp) REVERT: B 872 GLN cc_start: 0.9258 (mt0) cc_final: 0.8930 (mt0) REVERT: B 935 GLN cc_start: 0.9001 (tt0) cc_final: 0.8715 (tm-30) REVERT: B 936 ASP cc_start: 0.8745 (t0) cc_final: 0.8406 (t0) REVERT: B 953 ASN cc_start: 0.8848 (m110) cc_final: 0.8561 (m-40) REVERT: B 962 LEU cc_start: 0.8531 (tt) cc_final: 0.8204 (tt) REVERT: B 977 LEU cc_start: 0.7920 (mt) cc_final: 0.7646 (pp) REVERT: B 996 LEU cc_start: 0.8328 (mt) cc_final: 0.8107 (mt) REVERT: B 1000 ARG cc_start: 0.7498 (mtt180) cc_final: 0.6787 (ttm110) REVERT: B 1002 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8722 (tm-30) REVERT: B 1014 ARG cc_start: 0.8280 (mtt90) cc_final: 0.8052 (tpp80) REVERT: B 1017 GLU cc_start: 0.7678 (pt0) cc_final: 0.7373 (pt0) REVERT: B 1050 MET cc_start: 0.7456 (tpp) cc_final: 0.6891 (tpp) REVERT: C 201 PHE cc_start: 0.8218 (t80) cc_final: 0.7985 (t80) REVERT: C 557 LYS cc_start: 0.7878 (tmtt) cc_final: 0.7074 (mmtm) REVERT: C 727 LEU cc_start: 0.8801 (mt) cc_final: 0.8579 (mt) REVERT: C 761 THR cc_start: 0.8662 (p) cc_final: 0.8449 (p) REVERT: C 869 MET cc_start: 0.9105 (mtp) cc_final: 0.8761 (mtp) REVERT: C 970 PHE cc_start: 0.6866 (m-80) cc_final: 0.6284 (m-80) REVERT: C 995 ARG cc_start: 0.8401 (mmp80) cc_final: 0.8195 (mmp80) REVERT: C 1028 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7707 (tppt) REVERT: D 66 TYR cc_start: 0.7269 (m-10) cc_final: 0.6603 (m-10) REVERT: D 87 LEU cc_start: 0.8530 (mp) cc_final: 0.8022 (tp) REVERT: E 105 GLN cc_start: 0.6615 (tm-30) cc_final: 0.5900 (tp-100) outliers start: 2 outliers final: 0 residues processed: 419 average time/residue: 0.1628 time to fit residues: 108.9952 Evaluate side-chains 351 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 193 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 273 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 872 GLN A 925 ASN ** A 957 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 762 GLN B 954 HIS B1023 ASN ** B1088 HIS ** 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 388 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.210621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.161591 restraints weight = 60693.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.165360 restraints weight = 40193.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.168119 restraints weight = 30067.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.169674 restraints weight = 24421.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.171018 restraints weight = 21354.598| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.2607 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= 0.165 Angle : 0.617 13.119 34824 Z= 0.316 Chirality : 0.045 0.270 3991 Planarity : 0.005 0.074 4439 Dihedral : 5.720 56.838 3761 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.11 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.15), residues: 3089 helix: 0.40 (0.19), residues: 677 sheet: -0.66 (0.23), residues: 493 loop : -1.16 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 44 TYR 0.025 0.001 TYR A 873 PHE 0.032 0.002 PHE A 275 TRP 0.026 0.002 TRP C 64 HIS 0.018 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00343 (25533) covalent geometry : angle 0.60908 (34698) SS BOND : bond 0.00420 ( 36) SS BOND : angle 1.29426 ( 72) hydrogen bonds : bond 0.04538 ( 797) hydrogen bonds : angle 6.45620 ( 2199) link_BETA1-4 : bond 0.00538 ( 6) link_BETA1-4 : angle 1.20804 ( 18) link_NAG-ASN : bond 0.00460 ( 12) link_NAG-ASN : angle 2.57684 ( 36) *********************** 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 411 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.944 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: A 28 TYR cc_start: 0.7337 (m-10) cc_final: 0.7100 (m-10) REVERT: A 104 TRP cc_start: 0.3173 (m-10) cc_final: 0.2940 (m100) REVERT: A 319 ARG cc_start: 0.8109 (mmt-90) cc_final: 0.7616 (ptp90) REVERT: A 658 ASN cc_start: 0.7416 (t0) cc_final: 0.7161 (t0) REVERT: A 776 LYS cc_start: 0.8801 (tptm) cc_final: 0.8471 (tptm) REVERT: A 802 PHE cc_start: 0.8105 (m-10) cc_final: 0.7901 (m-10) REVERT: A 861 LEU cc_start: 0.9123 (mm) cc_final: 0.8917 (mm) REVERT: A 960 ASN cc_start: 0.8308 (m110) cc_final: 0.8024 (m110) REVERT: A 1000 ARG cc_start: 0.8416 (mmm160) cc_final: 0.7891 (mmm160) REVERT: A 1001 LEU cc_start: 0.9351 (tp) cc_final: 0.9117 (tp) REVERT: A 1002 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8083 (tm-30) REVERT: B 740 MET cc_start: 0.7124 (tpt) cc_final: 0.6575 (tpp) REVERT: B 796 TYR cc_start: 0.5604 (t80) cc_final: 0.4728 (m-80) REVERT: B 869 MET cc_start: 0.9205 (mtp) cc_final: 0.8802 (mtp) REVERT: B 872 GLN cc_start: 0.9303 (mt0) cc_final: 0.8948 (mt0) REVERT: B 935 GLN cc_start: 0.9013 (tt0) cc_final: 0.8724 (tm-30) REVERT: B 936 ASP cc_start: 0.8802 (t0) cc_final: 0.8270 (p0) REVERT: B 953 ASN cc_start: 0.8820 (m110) cc_final: 0.8575 (m110) REVERT: B 962 LEU cc_start: 0.8623 (tt) cc_final: 0.8309 (tt) REVERT: B 977 LEU cc_start: 0.7952 (mt) cc_final: 0.7735 (pp) REVERT: B 996 LEU cc_start: 0.8359 (mt) cc_final: 0.8154 (mt) REVERT: B 1000 ARG cc_start: 0.7471 (mtt180) cc_final: 0.6670 (ttm110) REVERT: B 1002 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8755 (tm-30) REVERT: B 1050 MET cc_start: 0.7494 (tpp) cc_final: 0.6938 (tpp) REVERT: C 201 PHE cc_start: 0.8205 (t80) cc_final: 0.7974 (t80) REVERT: C 733 LYS cc_start: 0.8987 (pttm) cc_final: 0.8581 (pttm) REVERT: C 869 MET cc_start: 0.9183 (mtp) cc_final: 0.8867 (mtp) REVERT: C 872 GLN cc_start: 0.9135 (pm20) cc_final: 0.8684 (pm20) REVERT: C 970 PHE cc_start: 0.6958 (m-80) cc_final: 0.6327 (m-80) REVERT: C 995 ARG cc_start: 0.8490 (mmp80) cc_final: 0.8230 (mmp80) REVERT: C 1028 LYS cc_start: 0.7946 (ttmt) cc_final: 0.7680 (tppt) REVERT: D 66 TYR cc_start: 0.7355 (m-10) cc_final: 0.6213 (m-10) REVERT: D 87 LEU cc_start: 0.8557 (mp) cc_final: 0.8131 (tp) REVERT: E 105 GLN cc_start: 0.6513 (tm-30) cc_final: 0.6088 (tp-100) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.1663 time to fit residues: 109.3227 Evaluate side-chains 351 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 77 optimal weight: 0.9980 chunk 298 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 271 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 223 optimal weight: 0.9990 chunk 218 optimal weight: 0.6980 chunk 242 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** A 957 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 762 GLN B 777 ASN B 954 HIS B1023 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN C 87 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 872 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 = 0.4701 r_free = 0.4701 target = 0.214284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.164479 restraints weight = 59829.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.168285 restraints weight = 39526.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.171047 restraints weight = 29700.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.172602 restraints weight = 24121.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.173938 restraints weight = 21133.387| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25587 Z= 0.112 Angle : 0.594 13.298 34824 Z= 0.299 Chirality : 0.045 0.213 3991 Planarity : 0.005 0.054 4439 Dihedral : 5.528 56.097 3761 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.15), residues: 3089 helix: 0.55 (0.20), residues: 680 sheet: -0.59 (0.23), residues: 490 loop : -1.10 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 905 TYR 0.033 0.001 TYR A 873 PHE 0.019 0.001 PHE A 275 TRP 0.024 0.001 TRP C 64 HIS 0.018 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00240 (25533) covalent geometry : angle 0.58036 (34698) SS BOND : bond 0.00314 ( 36) SS BOND : angle 1.11472 ( 72) hydrogen bonds : bond 0.04022 ( 797) hydrogen bonds : angle 6.14047 ( 2199) link_BETA1-4 : bond 0.00624 ( 6) link_BETA1-4 : angle 1.17604 ( 18) link_NAG-ASN : bond 0.00357 ( 12) link_NAG-ASN : angle 3.61854 ( 36) *********************** 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 419 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 0.956 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: A 28 TYR cc_start: 0.7321 (m-10) cc_final: 0.7090 (m-10) REVERT: A 104 TRP cc_start: 0.3118 (m-10) cc_final: 0.2851 (m100) REVERT: A 319 ARG cc_start: 0.8141 (mmt-90) cc_final: 0.7576 (ptp90) REVERT: A 658 ASN cc_start: 0.7615 (t0) cc_final: 0.7310 (t0) REVERT: A 773 GLU cc_start: 0.8912 (pp20) cc_final: 0.8664 (pp20) REVERT: A 776 LYS cc_start: 0.8834 (tptm) cc_final: 0.8613 (tptp) REVERT: A 802 PHE cc_start: 0.8022 (m-10) cc_final: 0.7744 (m-10) REVERT: A 872 GLN cc_start: 0.9166 (pt0) cc_final: 0.8047 (tm-30) REVERT: A 953 ASN cc_start: 0.8371 (m110) cc_final: 0.8142 (m110) REVERT: A 960 ASN cc_start: 0.8256 (m110) cc_final: 0.7951 (m110) REVERT: A 1000 ARG cc_start: 0.8391 (mmm160) cc_final: 0.7878 (mmm160) REVERT: A 1002 GLN cc_start: 0.8332 (tm-30) cc_final: 0.8029 (tm-30) REVERT: B 740 MET cc_start: 0.7106 (tpt) cc_final: 0.6407 (tpp) REVERT: B 796 TYR cc_start: 0.5400 (t80) cc_final: 0.4610 (m-80) REVERT: B 869 MET cc_start: 0.9166 (mtp) cc_final: 0.8744 (mtm) REVERT: B 872 GLN cc_start: 0.9217 (mt0) cc_final: 0.8919 (mt0) REVERT: B 935 GLN cc_start: 0.8992 (tt0) cc_final: 0.8717 (tm-30) REVERT: B 936 ASP cc_start: 0.8760 (t0) cc_final: 0.8416 (t0) REVERT: B 953 ASN cc_start: 0.8757 (m110) cc_final: 0.8502 (m110) REVERT: B 957 GLN cc_start: 0.9118 (pm20) cc_final: 0.8699 (pm20) REVERT: B 962 LEU cc_start: 0.8566 (tt) cc_final: 0.8144 (tt) REVERT: B 1000 ARG cc_start: 0.7334 (mtt180) cc_final: 0.6501 (ttm110) REVERT: B 1002 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8497 (tm-30) REVERT: B 1014 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7970 (tpp80) REVERT: B 1050 MET cc_start: 0.7282 (tpp) cc_final: 0.6997 (tpp) REVERT: C 557 LYS cc_start: 0.7644 (tmtt) cc_final: 0.7013 (mmtm) REVERT: C 733 LYS cc_start: 0.8923 (pttm) cc_final: 0.8576 (pttm) REVERT: C 869 MET cc_start: 0.9174 (mtp) cc_final: 0.8880 (mtp) REVERT: C 970 PHE cc_start: 0.6696 (m-80) cc_final: 0.6331 (m-80) REVERT: C 995 ARG cc_start: 0.8459 (mmp80) cc_final: 0.8190 (mmp80) REVERT: C 1028 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7700 (tppt) REVERT: D 66 TYR cc_start: 0.7157 (m-10) cc_final: 0.6544 (m-10) REVERT: D 87 LEU cc_start: 0.8683 (mp) cc_final: 0.8312 (tp) REVERT: E 105 GLN cc_start: 0.6534 (tm-30) cc_final: 0.6044 (tp-100) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.1706 time to fit residues: 113.6691 Evaluate side-chains 354 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 256 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 192 optimal weight: 0.4980 chunk 275 optimal weight: 0.7980 chunk 221 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN A1106 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 954 HIS 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 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C 960 ASN ** 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 = 0.4690 r_free = 0.4690 target = 0.213030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.164125 restraints weight = 60203.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.167538 restraints weight = 40546.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.170446 restraints weight = 30655.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.171948 restraints weight = 24803.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.173197 restraints weight = 21737.947| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25587 Z= 0.129 Angle : 0.600 10.942 34824 Z= 0.304 Chirality : 0.045 0.222 3991 Planarity : 0.005 0.084 4439 Dihedral : 5.439 58.002 3761 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.89 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.15), residues: 3089 helix: 0.52 (0.20), residues: 682 sheet: -0.64 (0.23), residues: 487 loop : -1.06 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B1039 TYR 0.030 0.001 TYR A 873 PHE 0.029 0.001 PHE A 275 TRP 0.025 0.001 TRP C 64 HIS 0.018 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00279 (25533) covalent geometry : angle 0.58598 (34698) SS BOND : bond 0.00390 ( 36) SS BOND : angle 1.36035 ( 72) hydrogen bonds : bond 0.04139 ( 797) hydrogen bonds : angle 6.12568 ( 2199) link_BETA1-4 : bond 0.00495 ( 6) link_BETA1-4 : angle 1.10911 ( 18) link_NAG-ASN : bond 0.00365 ( 12) link_NAG-ASN : angle 3.61753 ( 36) *********************** 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 405 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7301 (m-10) cc_final: 0.7065 (m-10) REVERT: A 104 TRP cc_start: 0.3192 (m-10) cc_final: 0.2880 (m100) REVERT: A 319 ARG cc_start: 0.8225 (mmt-90) cc_final: 0.7633 (mtm110) REVERT: A 577 ARG cc_start: 0.7894 (tmm-80) cc_final: 0.7536 (tmm-80) REVERT: A 658 ASN cc_start: 0.7519 (t0) cc_final: 0.7305 (t0) REVERT: A 960 ASN cc_start: 0.8220 (m110) cc_final: 0.7948 (m110) REVERT: A 1000 ARG cc_start: 0.8399 (mmm160) cc_final: 0.7904 (mmm160) REVERT: A 1002 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8097 (tm-30) REVERT: B 309 GLU cc_start: 0.8566 (tp30) cc_final: 0.8232 (tp30) REVERT: B 740 MET cc_start: 0.7100 (tpt) cc_final: 0.6273 (tpp) REVERT: B 796 TYR cc_start: 0.5404 (t80) cc_final: 0.4599 (m-80) REVERT: B 869 MET cc_start: 0.9153 (mtp) cc_final: 0.8740 (mtm) REVERT: B 872 GLN cc_start: 0.9262 (mt0) cc_final: 0.8954 (mt0) REVERT: B 935 GLN cc_start: 0.8911 (tt0) cc_final: 0.8670 (tm-30) REVERT: B 936 ASP cc_start: 0.8743 (t0) cc_final: 0.8367 (t0) REVERT: B 953 ASN cc_start: 0.8758 (m110) cc_final: 0.8488 (m-40) REVERT: B 957 GLN cc_start: 0.9137 (pm20) cc_final: 0.8667 (pm20) REVERT: B 962 LEU cc_start: 0.8568 (tt) cc_final: 0.8160 (tt) REVERT: B 996 LEU cc_start: 0.8322 (mt) cc_final: 0.8118 (mt) REVERT: B 1000 ARG cc_start: 0.7366 (mtt180) cc_final: 0.6562 (ttm110) REVERT: B 1002 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8676 (tm-30) REVERT: B 1014 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7958 (tpp80) REVERT: B 1050 MET cc_start: 0.7413 (tpp) cc_final: 0.6897 (tpp) REVERT: C 64 TRP cc_start: 0.4482 (t60) cc_final: 0.4238 (t60) REVERT: C 557 LYS cc_start: 0.7847 (tmmt) cc_final: 0.7110 (mmtm) REVERT: C 733 LYS cc_start: 0.8950 (pttm) cc_final: 0.8613 (pttm) REVERT: C 869 MET cc_start: 0.9149 (mtp) cc_final: 0.8867 (mtp) REVERT: C 995 ARG cc_start: 0.8427 (mmp80) cc_final: 0.8175 (mmp80) REVERT: C 1028 LYS cc_start: 0.8025 (ttmt) cc_final: 0.7698 (tppt) REVERT: D 66 TYR cc_start: 0.7244 (m-10) cc_final: 0.6134 (m-10) REVERT: D 87 LEU cc_start: 0.8672 (mp) cc_final: 0.8275 (tp) REVERT: E 105 GLN cc_start: 0.6627 (tm-30) cc_final: 0.6023 (tp-100) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.1721 time to fit residues: 110.9524 Evaluate side-chains 345 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 244 optimal weight: 5.9990 chunk 280 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 268 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 774 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 762 GLN B 954 HIS 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 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 872 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 = 0.4674 r_free = 0.4674 target = 0.211264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.162392 restraints weight = 60683.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.166243 restraints weight = 40747.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.168093 restraints weight = 30470.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.170198 restraints weight = 25779.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.171135 restraints weight = 22353.571| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25587 Z= 0.143 Angle : 0.612 9.858 34824 Z= 0.312 Chirality : 0.045 0.245 3991 Planarity : 0.005 0.068 4439 Dihedral : 5.527 59.432 3761 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.15), residues: 3089 helix: 0.38 (0.19), residues: 688 sheet: -0.72 (0.23), residues: 489 loop : -1.09 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1039 TYR 0.031 0.001 TYR A 873 PHE 0.021 0.001 PHE C 906 TRP 0.025 0.002 TRP C 64 HIS 0.022 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00302 (25533) covalent geometry : angle 0.60032 (34698) SS BOND : bond 0.00325 ( 36) SS BOND : angle 1.29372 ( 72) hydrogen bonds : bond 0.04292 ( 797) hydrogen bonds : angle 6.23361 ( 2199) link_BETA1-4 : bond 0.00490 ( 6) link_BETA1-4 : angle 1.11076 ( 18) link_NAG-ASN : bond 0.00342 ( 12) link_NAG-ASN : angle 3.34256 ( 36) ********************** 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 407 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.903 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: A 28 TYR cc_start: 0.7290 (m-10) cc_final: 0.7080 (m-10) REVERT: A 104 TRP cc_start: 0.3375 (m-10) cc_final: 0.3071 (m100) REVERT: A 319 ARG cc_start: 0.8294 (mmt-90) cc_final: 0.7631 (mtm110) REVERT: A 577 ARG cc_start: 0.7931 (tmm-80) cc_final: 0.7563 (tmm-80) REVERT: A 620 VAL cc_start: 0.5422 (m) cc_final: 0.5180 (m) REVERT: A 658 ASN cc_start: 0.7518 (t0) cc_final: 0.7316 (t0) REVERT: A 873 TYR cc_start: 0.7977 (m-80) cc_final: 0.7137 (m-80) REVERT: A 960 ASN cc_start: 0.8275 (m110) cc_final: 0.7966 (m110) REVERT: A 1000 ARG cc_start: 0.8447 (mmm160) cc_final: 0.7992 (tpt90) REVERT: A 1002 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8095 (tm-30) REVERT: A 1005 GLN cc_start: 0.8737 (mt0) cc_final: 0.8533 (mt0) REVERT: A 1110 TYR cc_start: 0.7272 (t80) cc_final: 0.6855 (t80) REVERT: B 49 HIS cc_start: 0.7505 (t-90) cc_final: 0.7284 (t-90) REVERT: B 309 GLU cc_start: 0.8552 (tp30) cc_final: 0.8231 (tp30) REVERT: B 721 SER cc_start: 0.8632 (m) cc_final: 0.8412 (m) REVERT: B 800 PHE cc_start: 0.6179 (m-80) cc_final: 0.5924 (m-80) REVERT: B 869 MET cc_start: 0.9155 (mtp) cc_final: 0.8887 (mtm) REVERT: B 872 GLN cc_start: 0.9282 (mt0) cc_final: 0.8930 (mt0) REVERT: B 935 GLN cc_start: 0.8927 (tt0) cc_final: 0.8720 (tm-30) REVERT: B 936 ASP cc_start: 0.8779 (t0) cc_final: 0.8429 (t0) REVERT: B 953 ASN cc_start: 0.8918 (m110) cc_final: 0.8664 (m-40) REVERT: B 957 GLN cc_start: 0.9122 (pm20) cc_final: 0.8777 (pm20) REVERT: B 962 LEU cc_start: 0.8564 (tt) cc_final: 0.8010 (tt) REVERT: B 1000 ARG cc_start: 0.7355 (mtt180) cc_final: 0.6578 (ttm110) REVERT: B 1002 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8691 (tm-30) REVERT: B 1050 MET cc_start: 0.7526 (tpp) cc_final: 0.6942 (tpp) REVERT: C 733 LYS cc_start: 0.8999 (pttm) cc_final: 0.8719 (pttm) REVERT: C 737 ASP cc_start: 0.7640 (t70) cc_final: 0.7396 (t70) REVERT: C 869 MET cc_start: 0.9165 (mtp) cc_final: 0.8878 (mtp) REVERT: C 970 PHE cc_start: 0.6877 (m-80) cc_final: 0.6471 (m-80) REVERT: C 995 ARG cc_start: 0.8475 (mmp80) cc_final: 0.8200 (mmp80) REVERT: C 1028 LYS cc_start: 0.8089 (ttmt) cc_final: 0.7735 (tppt) REVERT: D 39 MET cc_start: 0.5351 (tpt) cc_final: 0.5045 (tpt) REVERT: D 66 TYR cc_start: 0.7352 (m-10) cc_final: 0.6320 (m-10) REVERT: D 81 ASP cc_start: 0.5031 (t0) cc_final: 0.4813 (t0) REVERT: D 87 LEU cc_start: 0.8718 (mp) cc_final: 0.8316 (tp) REVERT: E 105 GLN cc_start: 0.6722 (tm-30) cc_final: 0.6138 (tp-100) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.1506 time to fit residues: 98.5520 Evaluate side-chains 349 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 150 optimal weight: 0.3980 chunk 79 optimal weight: 0.0770 chunk 292 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 257 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 245 optimal weight: 9.9990 chunk 266 optimal weight: 5.9990 overall best weight: 3.2944 ------------------------------------------------------------------------------- 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 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A 925 ASN ** A 928 ASN ** 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 762 GLN B 913 GLN B 954 HIS B1023 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.208037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.160152 restraints weight = 60827.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.163509 restraints weight = 41100.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.165993 restraints weight = 31633.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.167737 restraints weight = 25897.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.168588 restraints weight = 22555.293| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25587 Z= 0.189 Angle : 0.673 11.395 34824 Z= 0.345 Chirality : 0.047 0.344 3991 Planarity : 0.005 0.071 4439 Dihedral : 5.807 59.547 3761 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.09 % Favored : 93.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.14), residues: 3089 helix: 0.08 (0.19), residues: 691 sheet: -0.82 (0.23), residues: 482 loop : -1.20 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1039 TYR 0.034 0.002 TYR A 873 PHE 0.026 0.002 PHE C 906 TRP 0.036 0.002 TRP E 41 HIS 0.021 0.002 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00396 (25533) covalent geometry : angle 0.66111 (34698) SS BOND : bond 0.00422 ( 36) SS BOND : angle 1.31934 ( 72) hydrogen bonds : bond 0.04826 ( 797) hydrogen bonds : angle 6.48716 ( 2199) link_BETA1-4 : bond 0.00468 ( 6) link_BETA1-4 : angle 1.21642 ( 18) link_NAG-ASN : bond 0.00412 ( 12) link_NAG-ASN : angle 3.47071 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4657.50 seconds wall clock time: 81 minutes 24.38 seconds (4884.38 seconds total)