Starting phenix.real_space_refine on Wed Jul 24 06:44:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yz6_39686/07_2024/8yz6_39686.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yz6_39686/07_2024/8yz6_39686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yz6_39686/07_2024/8yz6_39686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yz6_39686/07_2024/8yz6_39686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yz6_39686/07_2024/8yz6_39686.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yz6_39686/07_2024/8yz6_39686.cif" } resolution = 4.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 15977 2.51 5 N 4139 2.21 5 O 4750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24972 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7521 Classifications: {'peptide': 959} Link IDs: {'PTRANS': 48, 'TRANS': 910} Chain breaks: 11 Chain: "B" Number of atoms: 7704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7704 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 48, 'TRANS': 935} Chain breaks: 10 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 7773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7773 Classifications: {'peptide': 990} Link IDs: {'PTRANS': 50, 'TRANS': 939} Chain breaks: 10 Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 888 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "E" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 837 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 100} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.39, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 10.32 Conformation dependent library (CDL) restraints added in 4.8 seconds 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5912 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 50 sheets defined 24.4% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.533A pdb=" N LEU A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.870A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.948A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.741A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 891 removed outlier: 4.282A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.093A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.592A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.882A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.091A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.986A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 890 removed outlier: 4.085A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 941 removed outlier: 5.335A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.720A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.982A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.125A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.868A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.651A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 4.584A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 423 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.790A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.514A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 891 removed outlier: 4.053A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 941 removed outlier: 5.186A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.233A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'E' and resid 95 through 99 removed outlier: 3.943A pdb=" N PHE E 99 " --> pdb=" O PRO E 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 removed outlier: 4.583A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.699A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.794A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.598A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.560A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.637A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.634A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.720A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.782A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.753A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 727 removed outlier: 3.595A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A1066 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.952A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1088 through 1089 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AB8, first strand: chain 'B' and resid 52 through 55 removed outlier: 4.037A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 190 through 195 removed outlier: 4.371A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 105 through 106 removed outlier: 3.763A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 201 through 205 removed outlier: 3.579A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.498A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.571A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.887A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.487A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.644A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.604A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.888A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.959A pdb=" N THR B 716 " --> pdb=" O GLN B1071 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1047 through 1050 removed outlier: 5.969A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1086 through 1088 removed outlier: 4.179A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.829A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 52 through 55 Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.602A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.684A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 94 through 95 removed outlier: 3.704A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.445A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 327 through 328 removed outlier: 3.740A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.798A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 552 through 554 removed outlier: 3.515A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 610 through 611 Processing sheet with id=AE5, first strand: chain 'C' and resid 655 through 656 removed outlier: 7.709A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 721 removed outlier: 4.021A pdb=" N THR C 716 " --> pdb=" O GLN C1071 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 724 through 728 removed outlier: 3.574A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1081 through 1083 removed outlier: 4.358A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.591A pdb=" N SER D 79 " --> pdb=" O TYR D 88 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 11 through 13 removed outlier: 3.612A pdb=" N THR D 122 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR D 38 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER D 54 " --> pdb=" O TRP D 41 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG D 43 " --> pdb=" O TRP D 52 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TRP D 52 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 11 through 13 removed outlier: 3.612A pdb=" N THR D 122 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE D 117 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 4 through 7 removed outlier: 11.893A pdb=" N CYS E 23 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N THR E 90 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 11.585A pdb=" N ALA E 25 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 11.163A pdb=" N THR E 88 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N GLN E 27 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASP E 86 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY E 84 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AF5, first strand: chain 'E' and resid 66 through 67 removed outlier: 6.499A pdb=" N TRP E 41 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR E 55 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU E 39 " --> pdb=" O TYR E 55 " (cutoff:3.500A) 803 hydrogen bonds defined for protein. 2199 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.24 Time building geometry restraints manager: 11.30 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: 96.35 - 104.62: 427 104.62 - 112.88: 13711 112.88 - 121.15: 13250 121.15 - 129.41: 7217 129.41 - 137.68: 93 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 2.440 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 2.440 nonbonded pdb=" OD1 ASN C 960 " pdb=" NZ LYS C 964 " model vdw 2.077 2.520 nonbonded pdb=" O ASP E 98 " pdb=" OH TYR E 102 " model vdw 2.092 2.440 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 61 or resid 63 through 176 or resid 185 through \ 356 or (resid 357 and (name N or name CA or name C or name O or name CB )) or r \ esid 358 through 377 or (resid 378 and (name N or name CA or name C or name O or \ name CB )) or resid 379 through 390 or (resid 391 and (name N or name CA or nam \ e C or name O or name CB )) or resid 392 through 518 or resid 521 through 527 or \ (resid 528 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 1 through 703 or resid 705 through 1135 or resid 1301)) selection = (chain 'B' and (resid 27 through 61 or resid 63 through 108 or resid 115 through \ 131 or resid 167 through 469 or resid 491 through 528 or resid 531 through 1135 \ or resid 1301)) selection = (chain 'C' and (resid 27 through 108 or resid 115 through 131 or resid 167 throu \ gh 356 or (resid 357 and (name N or name CA or name C or name O or name CB )) or \ resid 358 through 377 or (resid 378 and (name N or name CA or name C or name O \ or name CB )) or resid 379 through 390 or (resid 391 and (name N or name CA or n \ ame C or name O or name CB )) or resid 392 through 518 or resid 521 through 527 \ or (resid 528 and (name N or name CA or name C or name O or name CB )) or resid \ 531 through 703 or resid 705 through 1135 or resid 1301)) } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'N' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 70.210 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.990 ------------------------------------------------------------------------------- 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 25533 Z= 0.245 Angle : 0.672 12.677 34698 Z= 0.368 Chirality : 0.046 0.269 3991 Planarity : 0.005 0.100 4439 Dihedral : 13.464 107.115 9416 Min Nonbonded Distance : 1.194 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.76 % Favored : 96.02 % Rotamer: Outliers : 0.36 % Allowed : 0.29 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 3089 helix: 0.41 (0.20), residues: 677 sheet: -0.32 (0.24), residues: 480 loop : -1.15 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 64 HIS 0.007 0.001 HIS C 49 PHE 0.029 0.002 PHE C 906 TYR 0.021 0.002 TYR B 655 ARG 0.018 0.001 ARG B1014 *********************** 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 fitting. rotamer outliers: 10 poor density : 438 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7627 (m-10) cc_final: 0.7406 (m-10) REVERT: A 334 ASN cc_start: 0.7263 (OUTLIER) cc_final: 0.7019 (p0) REVERT: A 770 ILE cc_start: 0.9186 (mt) cc_final: 0.8902 (mt) REVERT: A 861 LEU cc_start: 0.9131 (mm) cc_final: 0.8864 (mm) REVERT: A 950 ASP cc_start: 0.8755 (t0) cc_final: 0.8437 (t0) REVERT: A 960 ASN cc_start: 0.7661 (m110) cc_final: 0.7391 (m110) REVERT: A 1019 ARG cc_start: 0.8305 (tpt-90) cc_final: 0.8104 (tpp80) REVERT: B 387 LEU cc_start: 0.6399 (tt) cc_final: 0.6169 (tt) REVERT: B 740 MET cc_start: 0.7283 (tpt) cc_final: 0.6732 (tpp) REVERT: B 935 GLN cc_start: 0.8793 (tt0) cc_final: 0.8459 (tm-30) REVERT: B 953 ASN cc_start: 0.8693 (m-40) cc_final: 0.8305 (m110) REVERT: B 957 GLN cc_start: 0.8886 (pm20) cc_final: 0.8632 (pm20) REVERT: B 1023 ASN cc_start: 0.9003 (m110) cc_final: 0.8153 (m110) REVERT: C 45 SER cc_start: 0.8367 (p) cc_final: 0.8107 (p) REVERT: C 46 SER cc_start: 0.8435 (m) cc_final: 0.8177 (p) REVERT: C 727 LEU cc_start: 0.8814 (mt) cc_final: 0.8578 (mt) REVERT: C 970 PHE cc_start: 0.6744 (m-80) cc_final: 0.6462 (m-80) REVERT: D 66 TYR cc_start: 0.6273 (m-10) cc_final: 0.5472 (m-10) REVERT: E 105 GLN cc_start: 0.5766 (tm-30) cc_final: 0.5289 (tp-100) outliers start: 10 outliers final: 2 residues processed: 446 average time/residue: 0.3615 time to fit residues: 252.6086 Evaluate side-chains 369 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 366 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 2.9990 chunk 237 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 285 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 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 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25533 Z= 0.319 Angle : 0.699 15.965 34698 Z= 0.362 Chirality : 0.047 0.182 3991 Planarity : 0.006 0.073 4439 Dihedral : 7.060 61.344 3761 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.22 % Favored : 93.65 % Rotamer: Outliers : 0.15 % Allowed : 5.50 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3089 helix: 0.18 (0.19), residues: 678 sheet: -0.65 (0.23), residues: 506 loop : -1.25 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 886 HIS 0.011 0.001 HIS C 49 PHE 0.024 0.002 PHE C 906 TYR 0.031 0.002 TYR C 756 ARG 0.013 0.001 ARG C 44 *********************** 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 425 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 421 time to evaluate : 2.726 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: 0.8153 (mm) cc_final: 0.7863 (mp) REVERT: A 825 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8382 (mmmt) REVERT: A 950 ASP cc_start: 0.8506 (t0) cc_final: 0.7787 (t0) REVERT: A 960 ASN cc_start: 0.7821 (m110) cc_final: 0.7565 (m110) REVERT: A 1001 LEU cc_start: 0.9022 (tp) cc_final: 0.8662 (tp) REVERT: A 1002 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7505 (tm-30) REVERT: A 1047 TYR cc_start: 0.8236 (m-80) cc_final: 0.8031 (m-80) REVERT: A 1110 TYR cc_start: 0.7057 (t80) cc_final: 0.6659 (t80) REVERT: B 740 MET cc_start: 0.7358 (tpt) cc_final: 0.6879 (tpp) REVERT: B 775 ASP cc_start: 0.7760 (m-30) cc_final: 0.7515 (m-30) REVERT: B 776 LYS cc_start: 0.8879 (ptpp) cc_final: 0.8370 (ptpp) REVERT: B 796 TYR cc_start: 0.5718 (t80) cc_final: 0.5196 (m-80) REVERT: B 935 GLN cc_start: 0.8837 (tt0) cc_final: 0.8578 (tm-30) REVERT: B 957 GLN cc_start: 0.8969 (pm20) cc_final: 0.8603 (pm20) REVERT: B 1017 GLU cc_start: 0.7205 (tt0) cc_final: 0.6975 (tt0) REVERT: B 1050 MET cc_start: 0.7673 (tpp) cc_final: 0.7247 (tpp) REVERT: C 46 SER cc_start: 0.8550 (m) cc_final: 0.8334 (p) REVERT: C 733 LYS cc_start: 0.9195 (pttm) cc_final: 0.8792 (pttm) REVERT: C 970 PHE cc_start: 0.6993 (m-80) cc_final: 0.6610 (m-80) REVERT: C 1030 SER cc_start: 0.8378 (m) cc_final: 0.7845 (p) REVERT: C 1050 MET cc_start: 0.7133 (tmm) cc_final: 0.6766 (tmm) REVERT: D 66 TYR cc_start: 0.6855 (m-10) cc_final: 0.6037 (m-10) REVERT: E 105 GLN cc_start: 0.5835 (tm-30) cc_final: 0.5435 (tp-100) outliers start: 4 outliers final: 1 residues processed: 424 average time/residue: 0.3648 time to fit residues: 245.1033 Evaluate side-chains 352 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 351 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 285 optimal weight: 6.9990 chunk 308 optimal weight: 4.9990 chunk 254 optimal weight: 0.9980 chunk 283 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 229 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A1010 GLN A1054 GLN A1106 GLN B 394 ASN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 87 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25533 Z= 0.167 Angle : 0.571 11.853 34698 Z= 0.293 Chirality : 0.045 0.623 3991 Planarity : 0.005 0.070 4439 Dihedral : 6.325 55.110 3761 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.86 % Rotamer: Outliers : 0.07 % Allowed : 3.17 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 3089 helix: 0.56 (0.20), residues: 679 sheet: -0.64 (0.23), residues: 512 loop : -1.13 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 64 HIS 0.012 0.001 HIS B 954 PHE 0.041 0.001 PHE A 275 TYR 0.019 0.001 TYR A 756 ARG 0.004 0.000 ARG C 44 *********************** 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 fitting. rotamer outliers: 2 poor density : 431 time to evaluate : 2.627 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 773 GLU cc_start: 0.8811 (pp20) cc_final: 0.8598 (pp20) REVERT: A 962 LEU cc_start: 0.8100 (tt) cc_final: 0.7651 (tt) REVERT: A 1001 LEU cc_start: 0.8959 (tp) cc_final: 0.8736 (tp) REVERT: A 1052 PHE cc_start: 0.8130 (m-10) cc_final: 0.7896 (m-10) REVERT: B 285 ILE cc_start: 0.6954 (mt) cc_final: 0.6692 (mt) REVERT: B 740 MET cc_start: 0.7349 (tpt) cc_final: 0.6796 (tpp) REVERT: B 796 TYR cc_start: 0.5391 (t80) cc_final: 0.5048 (m-80) REVERT: B 869 MET cc_start: 0.9161 (mtm) cc_final: 0.8765 (mtm) REVERT: B 935 GLN cc_start: 0.8689 (tt0) cc_final: 0.8411 (tm-30) REVERT: B 957 GLN cc_start: 0.8764 (pm20) cc_final: 0.8530 (pm20) REVERT: B 1023 ASN cc_start: 0.8987 (m110) cc_final: 0.8677 (m110) REVERT: B 1050 MET cc_start: 0.7461 (tpp) cc_final: 0.7126 (tpp) REVERT: B 1092 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7457 (tm-30) REVERT: C 46 SER cc_start: 0.8412 (m) cc_final: 0.8070 (p) REVERT: C 64 TRP cc_start: 0.4585 (t60) cc_final: 0.4267 (t60) REVERT: C 727 LEU cc_start: 0.8846 (mt) cc_final: 0.8396 (mt) REVERT: C 733 LYS cc_start: 0.9089 (pttm) cc_final: 0.8679 (pttm) REVERT: C 740 MET cc_start: 0.7643 (tpp) cc_final: 0.6845 (tpp) REVERT: C 869 MET cc_start: 0.9124 (mtp) cc_final: 0.8868 (mtp) REVERT: C 1050 MET cc_start: 0.7176 (tmm) cc_final: 0.6746 (tmm) REVERT: D 66 TYR cc_start: 0.6626 (m-10) cc_final: 0.5653 (m-10) outliers start: 2 outliers final: 1 residues processed: 432 average time/residue: 0.3436 time to fit residues: 233.4871 Evaluate side-chains 358 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 357 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 9.9990 chunk 214 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 136 optimal weight: 30.0000 chunk 191 optimal weight: 6.9990 chunk 286 optimal weight: 4.9990 chunk 303 optimal weight: 20.0000 chunk 149 optimal weight: 0.0470 chunk 271 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN B 564 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 804 GLN B 914 ASN B 954 HIS B 965 GLN 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 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25533 Z= 0.201 Angle : 0.586 12.217 34698 Z= 0.300 Chirality : 0.046 0.765 3991 Planarity : 0.005 0.064 4439 Dihedral : 6.073 55.122 3761 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.57 % Favored : 94.33 % Rotamer: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3089 helix: 0.53 (0.19), residues: 677 sheet: -0.66 (0.23), residues: 508 loop : -1.15 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 64 HIS 0.011 0.001 HIS B 954 PHE 0.017 0.001 PHE A 275 TYR 0.014 0.001 TYR C1067 ARG 0.004 0.000 ARG C 44 *********************** 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 421 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 420 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 LYS cc_start: 0.8663 (tptp) cc_final: 0.8397 (tptm) REVERT: A 957 GLN cc_start: 0.8293 (pt0) cc_final: 0.8020 (pt0) REVERT: A 1001 LEU cc_start: 0.9003 (tp) cc_final: 0.8732 (tp) REVERT: B 285 ILE cc_start: 0.7041 (mt) cc_final: 0.6772 (mt) REVERT: B 740 MET cc_start: 0.7306 (tpt) cc_final: 0.6835 (tpp) REVERT: B 796 TYR cc_start: 0.5396 (t80) cc_final: 0.4988 (m-80) REVERT: B 869 MET cc_start: 0.9202 (mtm) cc_final: 0.8831 (mtm) REVERT: B 935 GLN cc_start: 0.8754 (tt0) cc_final: 0.8479 (tm-30) REVERT: B 953 ASN cc_start: 0.8699 (m110) cc_final: 0.8492 (m110) REVERT: B 957 GLN cc_start: 0.8886 (pm20) cc_final: 0.8496 (pm20) REVERT: B 1000 ARG cc_start: 0.7556 (mtt180) cc_final: 0.7116 (mtp180) REVERT: B 1002 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8283 (tm-30) REVERT: B 1050 MET cc_start: 0.7524 (tpp) cc_final: 0.7073 (tpp) REVERT: C 733 LYS cc_start: 0.9155 (pttm) cc_final: 0.8720 (pttm) REVERT: C 740 MET cc_start: 0.7744 (tpp) cc_final: 0.6982 (tpp) REVERT: C 790 LYS cc_start: 0.5813 (mmtt) cc_final: 0.5567 (mmtm) REVERT: C 869 MET cc_start: 0.9084 (mtp) cc_final: 0.8770 (mtp) REVERT: D 39 MET cc_start: 0.5964 (tpt) cc_final: 0.5754 (tpt) REVERT: D 66 TYR cc_start: 0.6866 (m-10) cc_final: 0.5886 (m-10) outliers start: 1 outliers final: 1 residues processed: 420 average time/residue: 0.3466 time to fit residues: 231.5286 Evaluate side-chains 355 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 354 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 225 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 154 optimal weight: 8.9990 chunk 272 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN A 928 ASN A1010 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN B 414 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B1005 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 87 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 25533 Z= 0.492 Angle : 0.920 18.895 34698 Z= 0.476 Chirality : 0.053 0.578 3991 Planarity : 0.007 0.078 4439 Dihedral : 7.419 59.617 3761 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 30.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.81 % Favored : 91.03 % Rotamer: Outliers : 0.07 % Allowed : 4.73 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.14), residues: 3089 helix: -1.06 (0.17), residues: 671 sheet: -1.04 (0.24), residues: 466 loop : -1.65 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP C 64 HIS 0.017 0.003 HIS A1064 PHE 0.032 0.003 PHE C 906 TYR 0.030 0.003 TYR A 873 ARG 0.008 0.001 ARG C 44 *********************** 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 426 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 424 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.3317 (m-10) cc_final: 0.2628 (m-10) REVERT: A 237 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7805 (mmt180) REVERT: A 318 PHE cc_start: 0.6520 (t80) cc_final: 0.6248 (t80) REVERT: A 620 VAL cc_start: 0.5343 (m) cc_final: 0.5094 (m) REVERT: A 776 LYS cc_start: 0.8734 (tptp) cc_final: 0.8442 (tptp) REVERT: A 957 GLN cc_start: 0.8362 (pt0) cc_final: 0.8102 (pt0) REVERT: A 960 ASN cc_start: 0.7949 (m110) cc_final: 0.7718 (m110) REVERT: A 1001 LEU cc_start: 0.9030 (tp) cc_final: 0.8738 (tp) REVERT: A 1039 ARG cc_start: 0.8341 (ptm160) cc_final: 0.8083 (ptm160) REVERT: B 318 PHE cc_start: 0.7570 (t80) cc_final: 0.7366 (t80) REVERT: B 740 MET cc_start: 0.7298 (tpt) cc_final: 0.6737 (tpp) REVERT: B 775 ASP cc_start: 0.8030 (m-30) cc_final: 0.7803 (m-30) REVERT: B 869 MET cc_start: 0.9383 (mtm) cc_final: 0.8996 (mtt) REVERT: B 872 GLN cc_start: 0.9368 (mt0) cc_final: 0.9149 (mt0) REVERT: B 957 GLN cc_start: 0.9216 (pm20) cc_final: 0.8776 (pm20) REVERT: B 1002 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8541 (tm-30) REVERT: B 1017 GLU cc_start: 0.7534 (tt0) cc_final: 0.7198 (tt0) REVERT: B 1050 MET cc_start: 0.8069 (tpp) cc_final: 0.7419 (tpp) REVERT: C 223 LEU cc_start: 0.9169 (mt) cc_final: 0.8924 (mt) REVERT: C 733 LYS cc_start: 0.9221 (pttm) cc_final: 0.9016 (pttm) REVERT: C 869 MET cc_start: 0.9282 (mtp) cc_final: 0.9014 (mtp) REVERT: C 970 PHE cc_start: 0.7502 (m-80) cc_final: 0.7190 (m-80) REVERT: C 1002 GLN cc_start: 0.9091 (tp40) cc_final: 0.8847 (tp40) REVERT: C 1008 VAL cc_start: 0.9051 (t) cc_final: 0.8819 (t) REVERT: D 39 MET cc_start: 0.5722 (tpt) cc_final: 0.5458 (tpt) REVERT: D 66 TYR cc_start: 0.7313 (m-10) cc_final: 0.6647 (m-10) outliers start: 2 outliers final: 1 residues processed: 425 average time/residue: 0.3465 time to fit residues: 232.9919 Evaluate side-chains 346 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 345 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 5.9990 chunk 273 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 303 optimal weight: 9.9990 chunk 252 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 872 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN B 321 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25533 Z= 0.192 Angle : 0.638 12.870 34698 Z= 0.327 Chirality : 0.047 0.605 3991 Planarity : 0.005 0.063 4439 Dihedral : 6.415 57.280 3761 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 0.07 % Allowed : 1.89 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.14), residues: 3089 helix: -0.14 (0.19), residues: 676 sheet: -0.93 (0.23), residues: 496 loop : -1.38 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 64 HIS 0.018 0.001 HIS B 954 PHE 0.034 0.002 PHE A 275 TYR 0.021 0.001 TYR C 365 ARG 0.012 0.001 ARG C1039 *********************** 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 444 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 442 time to evaluate : 2.717 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 104 TRP cc_start: 0.3300 (m-10) cc_final: 0.2560 (m-10) REVERT: A 237 ARG cc_start: 0.8071 (mtp180) cc_final: 0.7752 (mmt180) REVERT: A 776 LYS cc_start: 0.8646 (tptp) cc_final: 0.8295 (tptm) REVERT: A 861 LEU cc_start: 0.9131 (mm) cc_final: 0.8906 (mm) REVERT: A 960 ASN cc_start: 0.7649 (m110) cc_final: 0.7419 (m110) REVERT: A 1001 LEU cc_start: 0.9071 (tp) cc_final: 0.8746 (tp) REVERT: A 1110 TYR cc_start: 0.7314 (t80) cc_final: 0.7066 (t80) REVERT: B 285 ILE cc_start: 0.7069 (mt) cc_final: 0.6817 (mt) REVERT: B 740 MET cc_start: 0.7343 (tpt) cc_final: 0.6723 (tpp) REVERT: B 775 ASP cc_start: 0.7730 (m-30) cc_final: 0.7467 (m-30) REVERT: B 869 MET cc_start: 0.9262 (mtm) cc_final: 0.8726 (mtm) REVERT: B 872 GLN cc_start: 0.9160 (mt0) cc_final: 0.8940 (mt0) REVERT: B 936 ASP cc_start: 0.8656 (t0) cc_final: 0.8209 (p0) REVERT: B 953 ASN cc_start: 0.8463 (m110) cc_final: 0.8238 (m-40) REVERT: B 1002 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8359 (tm-30) REVERT: B 1017 GLU cc_start: 0.6811 (tt0) cc_final: 0.6518 (tt0) REVERT: B 1050 MET cc_start: 0.7749 (tpp) cc_final: 0.7306 (tpp) REVERT: C 733 LYS cc_start: 0.9004 (pttm) cc_final: 0.8683 (pttm) REVERT: C 869 MET cc_start: 0.9072 (mtp) cc_final: 0.8700 (mtp) REVERT: C 970 PHE cc_start: 0.6903 (m-80) cc_final: 0.6493 (m-80) REVERT: D 66 TYR cc_start: 0.7045 (m-10) cc_final: 0.6289 (m-10) REVERT: D 87 LEU cc_start: 0.8772 (mp) cc_final: 0.8369 (tp) outliers start: 2 outliers final: 2 residues processed: 443 average time/residue: 0.3883 time to fit residues: 272.4788 Evaluate side-chains 375 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 373 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 255 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 302 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 184 optimal weight: 0.3980 chunk 139 optimal weight: 2.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 954 HIS B 955 ASN B1023 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25533 Z= 0.186 Angle : 0.607 11.160 34698 Z= 0.308 Chirality : 0.046 0.658 3991 Planarity : 0.005 0.062 4439 Dihedral : 6.044 56.450 3761 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.70 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.15), residues: 3089 helix: 0.15 (0.19), residues: 680 sheet: -0.88 (0.23), residues: 505 loop : -1.28 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 64 HIS 0.014 0.001 HIS B 954 PHE 0.036 0.001 PHE A 275 TYR 0.021 0.001 TYR A 655 ARG 0.017 0.001 ARG C1039 *********************** 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 437 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 2.671 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 104 TRP cc_start: 0.3361 (m-10) cc_final: 0.3101 (m100) REVERT: A 237 ARG cc_start: 0.8161 (mtp180) cc_final: 0.7821 (mmt180) REVERT: A 861 LEU cc_start: 0.9135 (mm) cc_final: 0.8906 (mm) REVERT: A 1000 ARG cc_start: 0.8156 (mmm160) cc_final: 0.7720 (tpt90) REVERT: A 1001 LEU cc_start: 0.9002 (tp) cc_final: 0.8772 (tp) REVERT: A 1110 TYR cc_start: 0.7279 (t80) cc_final: 0.7072 (t80) REVERT: B 285 ILE cc_start: 0.7020 (mt) cc_final: 0.6740 (mt) REVERT: B 740 MET cc_start: 0.7456 (tpt) cc_final: 0.6911 (tpp) REVERT: B 869 MET cc_start: 0.9196 (mtm) cc_final: 0.8924 (mtp) REVERT: B 872 GLN cc_start: 0.9115 (mt0) cc_final: 0.8894 (mt0) REVERT: B 936 ASP cc_start: 0.8617 (t0) cc_final: 0.8316 (t0) REVERT: B 950 ASP cc_start: 0.8812 (p0) cc_final: 0.8538 (p0) REVERT: B 953 ASN cc_start: 0.8704 (m110) cc_final: 0.8500 (m-40) REVERT: B 957 GLN cc_start: 0.8916 (pm20) cc_final: 0.8554 (pm20) REVERT: B 1002 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8234 (tm-30) REVERT: B 1050 MET cc_start: 0.7618 (tpp) cc_final: 0.7165 (tpp) REVERT: C 191 GLU cc_start: 0.7908 (tt0) cc_final: 0.7024 (mm-30) REVERT: C 733 LYS cc_start: 0.9022 (pttm) cc_final: 0.8722 (pttm) REVERT: C 869 MET cc_start: 0.9088 (mtp) cc_final: 0.8722 (mtp) REVERT: C 970 PHE cc_start: 0.6915 (m-80) cc_final: 0.6592 (m-80) REVERT: D 66 TYR cc_start: 0.7112 (m-10) cc_final: 0.6299 (m-10) REVERT: D 87 LEU cc_start: 0.8783 (mp) cc_final: 0.8399 (tp) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.3569 time to fit residues: 249.2899 Evaluate side-chains 379 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 206 optimal weight: 0.0170 chunk 149 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 237 optimal weight: 6.9990 overall best weight: 2.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25533 Z= 0.204 Angle : 0.616 11.022 34698 Z= 0.314 Chirality : 0.046 0.504 3991 Planarity : 0.005 0.085 4439 Dihedral : 5.984 57.190 3761 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.76 % Favored : 94.14 % Rotamer: Outliers : 0.07 % Allowed : 0.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 3089 helix: 0.08 (0.19), residues: 684 sheet: -0.82 (0.23), residues: 502 loop : -1.30 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 64 HIS 0.006 0.001 HIS A1064 PHE 0.034 0.001 PHE A 275 TYR 0.023 0.002 TYR A 756 ARG 0.018 0.001 ARG C1039 *********************** 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 435 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 433 time to evaluate : 2.759 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 104 TRP cc_start: 0.3369 (m-10) cc_final: 0.3098 (m100) REVERT: A 237 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7794 (mmt180) REVERT: A 776 LYS cc_start: 0.8768 (tptp) cc_final: 0.8465 (tptm) REVERT: A 861 LEU cc_start: 0.9160 (mm) cc_final: 0.8935 (mm) REVERT: A 872 GLN cc_start: 0.9040 (pt0) cc_final: 0.7971 (tm-30) REVERT: A 1000 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7746 (tpt90) REVERT: A 1001 LEU cc_start: 0.9025 (tp) cc_final: 0.8750 (tp) REVERT: B 285 ILE cc_start: 0.7026 (mt) cc_final: 0.6758 (mt) REVERT: B 740 MET cc_start: 0.7543 (tpt) cc_final: 0.7020 (tpp) REVERT: B 869 MET cc_start: 0.9269 (mtm) cc_final: 0.9001 (mtp) REVERT: B 900 MET cc_start: 0.7026 (mpp) cc_final: 0.6243 (mpp) REVERT: B 936 ASP cc_start: 0.8617 (t0) cc_final: 0.8134 (p0) REVERT: B 950 ASP cc_start: 0.8902 (p0) cc_final: 0.8534 (p0) REVERT: B 957 GLN cc_start: 0.8911 (pm20) cc_final: 0.8451 (pm20) REVERT: B 1002 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8248 (tm-30) REVERT: B 1017 GLU cc_start: 0.6987 (tt0) cc_final: 0.6778 (tt0) REVERT: B 1024 LEU cc_start: 0.8477 (tp) cc_final: 0.8274 (tp) REVERT: B 1050 MET cc_start: 0.7655 (tpp) cc_final: 0.7274 (tpp) REVERT: C 733 LYS cc_start: 0.9055 (pttm) cc_final: 0.8710 (pttm) REVERT: C 869 MET cc_start: 0.9122 (mtp) cc_final: 0.8832 (mtp) REVERT: C 872 GLN cc_start: 0.9107 (pm20) cc_final: 0.8727 (pm20) REVERT: D 66 TYR cc_start: 0.7153 (m-10) cc_final: 0.6356 (m-10) REVERT: D 87 LEU cc_start: 0.8772 (mp) cc_final: 0.8391 (tp) outliers start: 2 outliers final: 1 residues processed: 434 average time/residue: 0.3793 time to fit residues: 261.4659 Evaluate side-chains 352 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 351 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 264 optimal weight: 0.8980 chunk 282 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 221 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 281 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 949 GLN B 953 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25533 Z= 0.158 Angle : 0.583 9.235 34698 Z= 0.298 Chirality : 0.045 0.547 3991 Planarity : 0.005 0.118 4439 Dihedral : 5.661 56.667 3761 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 0.04 % Allowed : 0.44 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 3089 helix: 0.34 (0.20), residues: 681 sheet: -0.70 (0.23), residues: 508 loop : -1.22 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 64 HIS 0.004 0.001 HIS A1064 PHE 0.047 0.001 PHE C 981 TYR 0.027 0.001 TYR A 756 ARG 0.016 0.001 ARG C1039 *********************** 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 450 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 449 time to evaluate : 2.750 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 104 TRP cc_start: 0.3486 (m-10) cc_final: 0.3185 (m100) REVERT: A 237 ARG cc_start: 0.8155 (mtp180) cc_final: 0.7788 (mmt180) REVERT: A 776 LYS cc_start: 0.8781 (tptp) cc_final: 0.8289 (tptp) REVERT: A 861 LEU cc_start: 0.9073 (mm) cc_final: 0.8872 (mm) REVERT: A 869 MET cc_start: 0.8863 (mpp) cc_final: 0.8444 (mtm) REVERT: A 872 GLN cc_start: 0.9031 (pt0) cc_final: 0.7942 (tm-30) REVERT: A 1000 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7704 (mmm160) REVERT: A 1002 GLN cc_start: 0.7728 (tm-30) cc_final: 0.7518 (tm-30) REVERT: B 869 MET cc_start: 0.9152 (mtm) cc_final: 0.8789 (mtp) REVERT: B 900 MET cc_start: 0.6956 (mpp) cc_final: 0.6322 (mpp) REVERT: B 936 ASP cc_start: 0.8586 (t0) cc_final: 0.8072 (p0) REVERT: B 950 ASP cc_start: 0.8729 (p0) cc_final: 0.8468 (p0) REVERT: B 957 GLN cc_start: 0.8829 (pm20) cc_final: 0.8421 (pm20) REVERT: B 1002 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8217 (tm-30) REVERT: B 1050 MET cc_start: 0.7491 (tpp) cc_final: 0.7080 (tpp) REVERT: C 191 GLU cc_start: 0.8008 (tt0) cc_final: 0.7133 (mm-30) REVERT: C 733 LYS cc_start: 0.8993 (pttm) cc_final: 0.8650 (pttm) REVERT: C 869 MET cc_start: 0.9122 (mtp) cc_final: 0.8831 (mtp) REVERT: C 872 GLN cc_start: 0.9061 (pm20) cc_final: 0.8533 (pm20) REVERT: D 66 TYR cc_start: 0.7072 (m-10) cc_final: 0.6216 (m-10) REVERT: D 87 LEU cc_start: 0.8758 (mp) cc_final: 0.8417 (tp) REVERT: E 105 GLN cc_start: 0.6189 (tm-30) cc_final: 0.5286 (tp-100) outliers start: 1 outliers final: 0 residues processed: 449 average time/residue: 0.3443 time to fit residues: 244.0115 Evaluate side-chains 357 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 chunk 182 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 312 optimal weight: 5.9990 chunk 287 optimal weight: 6.9990 chunk 249 optimal weight: 0.0040 chunk 25 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- 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 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 804 GLN B 913 GLN B 949 GLN B 955 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25533 Z= 0.227 Angle : 0.626 9.895 34698 Z= 0.320 Chirality : 0.046 0.531 3991 Planarity : 0.005 0.069 4439 Dihedral : 5.777 57.887 3761 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.15 % Favored : 93.75 % Rotamer: Outliers : 0.04 % Allowed : 0.40 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3089 helix: 0.11 (0.19), residues: 681 sheet: -0.81 (0.23), residues: 487 loop : -1.21 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 64 HIS 0.007 0.001 HIS A1064 PHE 0.034 0.002 PHE C 981 TYR 0.029 0.002 TYR A 756 ARG 0.015 0.001 ARG B1039 ********************** 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 432 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 431 time to evaluate : 2.801 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 104 TRP cc_start: 0.3319 (m-10) cc_final: 0.3025 (m100) REVERT: A 237 ARG cc_start: 0.8186 (mtp180) cc_final: 0.7848 (mmt180) REVERT: A 394 ASN cc_start: 0.7501 (t0) cc_final: 0.7182 (t0) REVERT: A 658 ASN cc_start: 0.7580 (t0) cc_final: 0.7152 (t0) REVERT: A 1000 ARG cc_start: 0.8213 (mmm160) cc_final: 0.7834 (tpt90) REVERT: A 1001 LEU cc_start: 0.9089 (tp) cc_final: 0.8823 (tp) REVERT: A 1002 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7568 (tm-30) REVERT: A 1110 TYR cc_start: 0.7175 (t80) cc_final: 0.6935 (t80) REVERT: B 740 MET cc_start: 0.8012 (tpp) cc_final: 0.6897 (tpp) REVERT: B 900 MET cc_start: 0.6968 (mpp) cc_final: 0.6322 (mpp) REVERT: B 925 ASN cc_start: 0.8913 (m110) cc_final: 0.8683 (m110) REVERT: B 936 ASP cc_start: 0.8580 (t0) cc_final: 0.8093 (p0) REVERT: B 950 ASP cc_start: 0.8796 (p0) cc_final: 0.8593 (p0) REVERT: B 953 ASN cc_start: 0.8733 (m110) cc_final: 0.8441 (m110) REVERT: B 962 LEU cc_start: 0.8464 (tt) cc_final: 0.8068 (tt) REVERT: B 1002 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8308 (tm-30) REVERT: B 1050 MET cc_start: 0.7721 (tpp) cc_final: 0.7351 (tpp) REVERT: C 191 GLU cc_start: 0.7934 (tt0) cc_final: 0.7253 (mm-30) REVERT: C 733 LYS cc_start: 0.9106 (pttm) cc_final: 0.8784 (pttm) REVERT: C 869 MET cc_start: 0.9140 (mtp) cc_final: 0.8828 (mtp) REVERT: C 970 PHE cc_start: 0.7232 (m-80) cc_final: 0.6884 (m-80) REVERT: C 1038 LYS cc_start: 0.8108 (mptt) cc_final: 0.7728 (mptt) REVERT: D 66 TYR cc_start: 0.7205 (m-10) cc_final: 0.6412 (m-10) REVERT: D 87 LEU cc_start: 0.8769 (mp) cc_final: 0.8456 (tp) REVERT: E 105 GLN cc_start: 0.6072 (tm-30) cc_final: 0.5148 (tp-100) outliers start: 1 outliers final: 0 residues processed: 431 average time/residue: 0.3593 time to fit residues: 246.0014 Evaluate side-chains 360 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 9.9990 chunk 265 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 249 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 256 optimal weight: 0.4980 chunk 31 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 overall best weight: 2.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B1054 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.208425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.159835 restraints weight = 60918.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.163546 restraints weight = 43840.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.165337 restraints weight = 31691.348| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25533 Z= 0.201 Angle : 0.610 10.172 34698 Z= 0.311 Chirality : 0.046 0.525 3991 Planarity : 0.005 0.066 4439 Dihedral : 5.749 57.392 3761 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.86 % Favored : 94.04 % Rotamer: Outliers : 0.04 % Allowed : 0.29 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.15), residues: 3089 helix: 0.13 (0.20), residues: 686 sheet: -0.75 (0.23), residues: 508 loop : -1.25 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 64 HIS 0.005 0.001 HIS A1064 PHE 0.029 0.001 PHE C 981 TYR 0.029 0.001 TYR A 756 ARG 0.012 0.001 ARG A 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5557.88 seconds wall clock time: 100 minutes 31.57 seconds (6031.57 seconds total)